diff --git a/.gitignore b/.gitignore index e2fa6fec7..cf139a8b6 100644 --- a/.gitignore +++ b/.gitignore @@ -685,3 +685,21 @@ __pycache__ /docs/assets/Brittin2021* /docs/*_Brittin2021_data*.md /clean.sh +/docs/assets/Test_Nonpharyngeal_Chemical_Exc.json +/docs/assets/Test_Nonpharyngeal_Chemical_Exc.png +/docs/assets/Test_Nonpharyngeal_Chemical_Exc_graph.json +/docs/assets/Test_Nonpharyngeal_Chemical_Exc_graph.png +/docs/assets/Test_Nonpharyngeal_Chemical_Exc_hiveplot.json +/docs/assets/Test_Nonpharyngeal_Chemical_Exc_hiveplot.png +/docs/assets/Test_Nonpharyngeal_Chemical_Inh.json +/docs/assets/Test_Nonpharyngeal_Chemical_Inh.png +/docs/assets/Test_Nonpharyngeal_Chemical_Inh_graph.json +/docs/assets/Test_Nonpharyngeal_Chemical_Inh_graph.png +/docs/assets/Test_Nonpharyngeal_Chemical_Inh_hiveplot.json +/docs/assets/Test_Nonpharyngeal_Chemical_Inh_hiveplot.png +/docs/assets/Test_Nonpharyngeal_Electrical.json +/docs/assets/Test_Nonpharyngeal_Electrical.png +/docs/assets/Test_Nonpharyngeal_Electrical_graph.json +/docs/assets/Test_Nonpharyngeal_Electrical_graph.png +/docs/assets/Test_Nonpharyngeal_Electrical_hiveplot.json +/docs/assets/Test_Nonpharyngeal_Electrical_hiveplot.png diff --git a/cect/Analysis.py b/cect/Analysis.py new file mode 100644 index 000000000..4e6fd8045 --- /dev/null +++ b/cect/Analysis.py @@ -0,0 +1,143 @@ +import sys +import numpy as np + +from cect.Cells import get_contralateral_neuron + + +def test_bilaterals(): + from cect.White_whole import get_instance + + """ + from cect.Cook2019MaleReader import get_instance + from cect.Cook2019HermReader import get_instance + from cect.WitvlietDataReader1 import get_instance + from cect.WitvlietDataReader8 import get_instance + from cect.TestDataReader import get_instance + from cect.SpreadsheetDataReader import get_instance + from cect.Cook2020DataReader import get_instance + from cect.BrittinDataReader import get_instance + from cect.WormNeuroAtlasMAReader import get_instance + from cect.WormNeuroAtlasFuncReader import get_instance + from cect.RipollSanchezDataReader import get_instance + from cect.ConnectomeView import PHARYNX_VIEW as view + from cect.ConnectomeView import SOCIAL_VIEW as view + from cect.ConnectomeView import NEURONS_VIEW as view + from cect.ConnectomeView import RAW_VIEW as view""" + from cect.ConnectomeView import NONPHARYNGEAL_NEURONS_VIEW as view + + print( + "NOTE: For the sake of this paper, we excluded the pharyngeal neurons from the connectome data for both genders due to their distinction from the somatic nervous system." + ) + + cds = get_instance() + + cds2 = cds.get_connectome_view(view) + + synclass = "Chemical Inh" + synclass = "Chemical Exc" if "Raw" not in view.name else "Chemical" + + # synclass = "Acetylcholine" + # synclass = "Chemical" + # synclass = "Electrical" + + print(cds2.summary()) + + print("Keys: %s, plotting: %s" % (view.synclass_sets.keys(), synclass)) + + def array_info(conn_array): + nonzero = np.count_nonzero(conn_array) + print( + "- Connection - shape: %s, %i non-zero entries, %i total\n%s\n" + % ( + conn_array.shape, + nonzero, + np.sum(conn_array), + conn_array, + ) + ) + + dim = cds2.connections[synclass].shape[0] + + new_conn_array = np.zeros([dim, dim], dtype=np.float64) + array_info(new_conn_array) + + for synclass in [ + "Chemical", + "Chemical Exc", + "Chemical Inh", + "Electrical", + "Contact", + "Functional", + "Extrasynaptic", + ]: + print(" Adding conns of type: %s" % synclass) + if synclass in cds2.connections: + conns_cs = cds2.connections[synclass] + + array_info(conns_cs) + for i in range(len(conns_cs)): + for j in range(len(conns_cs[i])): + if ( + i != j + ): # Kim et al 2024: Self-connections are treated as nonexistent (∀𝐴𝑖𝑖 = 0). + new_conn_array[i, j] = ( + new_conn_array[i, j] or conns_cs[i, j] > 0 + ) + + amal = "CS+GJ" + print("Amalgamated array:") + array_info(new_conn_array) + + # fig = cds2.to_plotly_hive_plot_fig(list(view.synclass_sets.keys())[0], view) + # fig = cds2.to_plotly_graph_fig(synclass, view) + # fig = cds2.to_plotly_matrix_fig(list(view.synclass_sets.keys())[0], view) + + conn_count = 0 + symm_conn_count = 0 + + POS_ZERO_NEG_COLORMAP2 = ["red", "pink", "white", "lightblue", "blue"] + POS_ZERO_COLORMAP2 = ["white", "lightblue", "blue"] + + colormap = POS_ZERO_COLORMAP2 + + scaled_conn_array = np.array(new_conn_array) + + for i in range(len(new_conn_array)): + pre = cds2.nodes[i] + pre_ = get_contralateral_neuron(pre) + for j in range(len(new_conn_array[i])): + post = cds2.nodes[j] + post_ = get_contralateral_neuron(post) + w = new_conn_array[i][j] + if w != 0: + print(f"Connection {conn_count}:\t{pre}->{post} ({w})") + assert pre is not post + w_ = new_conn_array[cds2.nodes.index(pre_), cds2.nodes.index(post_)] + print(f" - Mirror:\t{pre_}->{post_} ({w_})\n") + symm_conn_count += w_ + if w_ == 0: + scaled_conn_array[i][j] = 0.5 + scaled_conn_array[ + cds2.nodes.index(pre_), cds2.nodes.index(post_) + ] = -1 + colormap = POS_ZERO_NEG_COLORMAP2 + conn_count += 1 + + print( + f"Of {(len(new_conn_array)**2)} possible edges, {conn_count} are connected, {symm_conn_count} are mirrored {'%.2f'%(100*symm_conn_count/conn_count)}% " + ) + + cds2.connections[amal] = scaled_conn_array + + # import plotly.io as pio + # pio.renderers.default = "browser" + if "-nogui" not in sys.argv: + # cds2.connection_number_plot + + fig = cds2.to_plotly_matrix_fig(amal, view, colormap, bold_bilaterals=True) + + fig.show() + + +if __name__ == "__main__": + test_bilaterals() diff --git a/cect/BrittinDataReader.py b/cect/BrittinDataReader.py index c7823571f..cce8b3c94 100644 --- a/cect/BrittinDataReader.py +++ b/cect/BrittinDataReader.py @@ -12,6 +12,8 @@ from cect.ConnectomeDataset import ConnectomeDataset from cect.ConnectomeDataset import get_dataset_source_on_github +from cect.Cells import is_one_of_bilateral_pair +from cect.Cells import get_contralateral_neuron import os from openpyxl import load_workbook @@ -40,7 +42,7 @@ def __init__(self, reference_graph): cells, neuron_conns = self.read_data() for conn in neuron_conns: - self.add_connection_info(conn) + self.add_connection_info(conn, check_overwritten_connections=True) def read_data(self): cells = [] @@ -50,11 +52,14 @@ def read_data(self): sheet = wb.get_sheet_by_name(self.reference_graph) + bilaterals = [] + single_cells = [] + print_("Opened sheet %s in Excel file: %s" % (sheet, filename)) - print(dir(sheet)) + # print(dir(sheet)) for row in sheet.rows: - print(row[0].value) + # print(row[0].value) if "cell_1" not in row[0].value: delta = int(row[3].value) if delta == 4: @@ -64,8 +69,10 @@ def read_data(self): syntype = "Contact" synclass = "%s%s" % (self.reference_graph, row[3].value) synclass = "Contact" + ci = ConnectionInfo(pre, post, num, syntype, synclass) - print("Adding %s" % ci) + conns.append(ci) + ci = ConnectionInfo(post, pre, num, syntype, synclass) conns.append(ci) if pre not in cells: @@ -73,6 +80,29 @@ def read_data(self): if post not in cells: cells.append(post) + pre_ = get_contralateral_neuron(pre) + post_ = get_contralateral_neuron(post) + ci_ = ConnectionInfo(pre_, post_, num, syntype, synclass) + conns.append(ci_) + ci_ = ConnectionInfo(post_, pre_, num, syntype, synclass) + conns.append(ci_) + + if pre_ not in cells: + cells.append(pre_) + if post_ not in cells: + cells.append(post_) + + for cell in cells: + if is_one_of_bilateral_pair(cell): + bilaterals.append(cell) + else: + single_cells.append(cell) + + print_( + "Finished processing %i cells, %i bilateral and %i single cells: %s" + % (len(cells), len(bilaterals), len(single_cells), sorted(single_cells)) + ) + return cells, conns diff --git a/cect/CellInfo.py b/cect/CellInfo.py index cc4dea182..9d0e6f242 100644 --- a/cect/CellInfo.py +++ b/cect/CellInfo.py @@ -247,6 +247,7 @@ def generate_cell_info_pages(connectomes): ) reference_cs = "Cook2019Male" if is_male_specific_cell(cell) else "Cook2019Herm" + # reference_cs = "White_whole" reference_gj = reference_cs reference_mono = "Bentley2016_MA" @@ -262,8 +263,7 @@ def generate_cell_info_pages(connectomes): conns_to_pep = "???" conns_from_func = "???" conns_to_func = "???" - conns_from_cont = "???" - conns_to_cont = "???" + conns_cont = "???" conns_gj = "???" tables_md = "" @@ -303,7 +303,7 @@ def generate_cell_info_pages(connectomes): if cds_name == reference_func: conns_to_func = _get_top_list(conns, max_conn_cells) if cds_name == reference_cont: - conns_to_cont = _get_top_list(conns, max_conn_cells) + conns_cont = _get_top_list(conns, max_conn_cells) for c in conns: cc = get_cell_internal_link( @@ -352,7 +352,7 @@ def generate_cell_info_pages(connectomes): if cds_name == reference_func: conns_from_func = _get_top_list(conns, max_conn_cells) if cds_name == reference_cont: - conns_from_cont = _get_top_list(conns, max_conn_cells) + pass # same as to... for c in conns: cc = get_cell_internal_link( @@ -382,24 +382,26 @@ def generate_cell_info_pages(connectomes): - + + + + + - - - + - + - + - +
ChemicalElectrical {conns_gj}
  \u2195
Chemical {conns_to_cs} \u2198 {cell_link} \u2197 {conns_from_cs}
Monoaminergic{conns_to_mono}{conns_from_mono}
Peptidergic {conns_to_pep}{conns_from_pep}Monoaminergic{conns_to_mono}{conns_from_mono}
Functional {conns_to_func}{conns_from_func}Peptidergic {conns_to_pep}{conns_from_pep}
Contactome {conns_to_cont}\u2197\u2198{conns_from_cont}Functional {conns_to_func}{conns_from_func}
  \u2195
Electrical {conns_gj}Contactomic {conns_cont}
diff --git a/cect/Cells.py b/cect/Cells.py index 8b09100b8..5016a6bf4 100644 --- a/cect/Cells.py +++ b/cect/Cells.py @@ -13,6 +13,8 @@ from cect.WormAtlasInfo import WA_COLORS from cect import print_ +from typing import List + ALL_KNOWN_CHEMICAL_NEUROTRANSMITTERS = [ "Acetylcholine", @@ -41,7 +43,7 @@ connectomes = None -def get_cell_notes(cell): +def get_cell_notes(cell: str): """Get a short description of the cell, mainly cell type Args: @@ -499,7 +501,7 @@ def get_cell_notes(cell): for cell in MALE_HEAD_SENSORY_NEURONS: cell_notes[cell] = "male head sensory neuron" -MALE_SENSORY_NEURONS = [ +MALE_NON_HEAD_SENSORY_NEURONS = [ "R1AL", "R1AR", "R1BL", @@ -554,10 +556,10 @@ def get_cell_notes(cell): "SPVR", ] -for cell in MALE_SENSORY_NEURONS: +for cell in MALE_NON_HEAD_SENSORY_NEURONS: cell_notes[cell] = "male sensory neuron" -MALE_INTERNEURONS = [ +MALE_NON_HEAD_INTERNEURONS = [ "PVV", "PVX", "PVY", @@ -593,15 +595,15 @@ def get_cell_notes(cell): ] -for cell in MALE_INTERNEURONS: +for cell in MALE_NON_HEAD_INTERNEURONS: cell_notes[cell] = "male interneuron" MALE_SPECIFIC_NEURONS = ( MALE_HEAD_INTERNEURONS + + MALE_NON_HEAD_INTERNEURONS + MALE_HEAD_SENSORY_NEURONS - + MALE_INTERNEURONS - + MALE_SENSORY_NEURONS + + MALE_NON_HEAD_SENSORY_NEURONS ) UNKNOWN_FUNCTION_NEURONS = ["CANL", "CANR"] @@ -1522,7 +1524,9 @@ def get_primary_classification(): classification[cell] = cell_type elif cell_type == "interneuron": for cell in ( - INTERNEURONS_COOK + MALE_HEAD_INTERNEURONS + MALE_INTERNEURONS + INTERNEURONS_COOK + + MALE_HEAD_INTERNEURONS + + MALE_NON_HEAD_INTERNEURONS ): classification[cell] = cell_type elif cell_type == "motor neuron": @@ -1532,7 +1536,7 @@ def get_primary_classification(): for cell in ( SENSORY_NEURONS_COOK + MALE_HEAD_SENSORY_NEURONS - + MALE_SENSORY_NEURONS + + MALE_NON_HEAD_SENSORY_NEURONS ): classification[cell] = cell_type elif cell_type == "odd numbered pharyngeal muscle": @@ -1669,7 +1673,7 @@ def get_primary_classification(): return classification -def is_known_cell(cell): +def is_known_cell(cell: str): """Is this string the name of one of the known cells? Args: @@ -1681,7 +1685,7 @@ def is_known_cell(cell): return cell in ALL_PREFERRED_CELL_NAMES -def get_SIM_class(cell): +def get_SIM_class(cell: str): """ PROVISIONAL method to return whether a cell is Sensory/Interneuron/Motorneuron (or Other) @@ -1717,11 +1721,33 @@ def get_SIM_class(cell): return "Other" -def is_one_of_bilateral_pair(cell): +def is_one_of_bilateral_pair(cell: str): return is_bilateral_left(cell) or is_bilateral_right(cell) -def is_bilateral_left(cell): +def get_contralateral_neuron(cell: str): + """Gets the contralateral neuron for a given neuron, based on Kim et al. 2024: https://doi.org/10.1101/2024.10.03.616419 + + Args: + cell (_type_): _description_ + + Raises: + Exception: _description_ + + Returns: + _type_: _description_ + """ + if not is_any_neuron(cell): + raise Exception("Not yet implemented/tested for non neuronal cells") + if is_bilateral_left(cell): + return cell[:-1] + "R" + if is_bilateral_right(cell): + return cell[:-1] + "L" + else: + return cell + + +def is_bilateral_left(cell: str): if ( cell in ALL_PREFERRED_CELL_NAMES and cell.endswith("L") @@ -1732,7 +1758,7 @@ def is_bilateral_left(cell): return False -def is_bilateral_right(cell): +def is_bilateral_right(cell: str): if ( cell in ALL_PREFERRED_CELL_NAMES and cell.endswith("R") @@ -1743,7 +1769,7 @@ def is_bilateral_right(cell): return False -def convert_to_preferred_muscle_name(muscle): +def convert_to_preferred_muscle_name(muscle: str): if muscle.startswith("BWM-VL"): return "MVL%s" % muscle[6:] elif muscle.startswith("BWM-VR"): @@ -1813,7 +1839,7 @@ def convert_to_preferred_muscle_name(muscle): return muscle + "???" -def convert_to_preferred_phar_cell_name(cell): +def convert_to_preferred_phar_cell_name(cell: str): if cell == "mc1v": return "mc1V" elif cell == "mc1dr": @@ -1843,7 +1869,7 @@ def get_marginal_cell_prefixes(): return ["mc"] -def is_marginal_cell(cell): +def is_marginal_cell(cell: str): known_mc_prefix = get_marginal_cell_prefixes() return cell.startswith(tuple(known_mc_prefix)) @@ -1856,48 +1882,48 @@ def get_body_wall_muscle_prefixes(): return ["BWM-D", "BWM-V", "LegacyBodyWallMuscles", "vBWM", "dBWM"] -def is_potential_muscle(cell): +def is_potential_muscle(cell: str): if cell in PREFERRED_MUSCLE_NAMES: return True known_muscle_prefixes = get_all_muscle_prefixes() return cell.startswith(tuple(known_muscle_prefixes)) -def is_known_muscle(cell): +def is_known_muscle(cell: str): if cell in PREFERRED_MUSCLE_NAMES: return True return False -def is_potential_body_wall_muscle(cell): +def is_potential_body_wall_muscle(cell: str): known_muscle_prefixes = get_body_wall_muscle_prefixes() return cell.startswith(tuple(known_muscle_prefixes)) -def is_known_body_wall_muscle(cell): +def is_known_body_wall_muscle(cell: str): return cell in BODY_WALL_MUSCLE_NAMES -def is_pharyngeal_cell(cell): +def is_pharyngeal_cell(cell: str): return cell in ALL_PHARYNGEAL_CELLS -def is_herm_neuron(cell): +def is_herm_neuron(cell: str): return cell in PREFERRED_HERM_NEURON_NAMES -def is_male_specific_cell(cell): +def is_male_specific_cell(cell: str): return ( cell in MALE_SPECIFIC_NEURONS + MALE_SPECIFIC_MUSCLES + MALE_SPECIFIC_OTHER_CELLS ) -def is_any_neuron(cell): +def is_any_neuron(cell: str): return cell in PREFERRED_HERM_NEURON_NAMES + MALE_SPECIFIC_NEURONS -def remove_leading_index_zero(cell): +def remove_leading_index_zero(cell: str): """ Returns neuron name with an index without leading zero. E.g. VB01 -> VB1. """ @@ -1908,7 +1934,7 @@ def remove_leading_index_zero(cell): return cell -def are_bilateral_pair(cell_a, cell_b): +def are_bilateral_pair(cell_a: str, cell_b: str): if cell_a[:-1] == cell_b[:-1] and ( (cell_a[-1] == "L" and cell_b[-1] == "R") or (cell_b[-1] == "L" and cell_a[-1] == "R") @@ -1918,7 +1944,7 @@ def are_bilateral_pair(cell_a, cell_b): return False -def get_standard_color(cell): +def get_standard_color(cell: str): from cect.WormAtlasInfo import WA_COLORS if cell in BODY_WALL_MUSCLE_NAMES + UNSPECIFIED_BODY_WALL_MUSCLES: @@ -1931,10 +1957,15 @@ def get_standard_color(cell): return WA_COLORS["Hermaphrodite"]["Muscle"]["odd numbered pharyngeal muscle"] elif cell in EVEN_PHARYNGEAL_MUSCLE_NAMES: return WA_COLORS["Hermaphrodite"]["Muscle"]["even numbered pharyngeal muscle"] - elif cell in INTERNEURONS_COOK + MALE_HEAD_INTERNEURONS + MALE_INTERNEURONS: + elif ( + cell in INTERNEURONS_COOK + MALE_HEAD_INTERNEURONS + MALE_NON_HEAD_INTERNEURONS + ): return WA_COLORS["Hermaphrodite"]["Nervous Tissue"]["interneuron"] elif ( - cell in SENSORY_NEURONS_COOK + MALE_HEAD_SENSORY_NEURONS + MALE_SENSORY_NEURONS + cell + in SENSORY_NEURONS_COOK + + MALE_HEAD_SENSORY_NEURONS + + MALE_NON_HEAD_SENSORY_NEURONS ): return WA_COLORS["Hermaphrodite"]["Nervous Tissue"]["sensory neuron"] elif cell in MOTORNEURONS_COOK: @@ -2021,7 +2052,7 @@ def get_standard_color(cell): raise Exception("Unknown cell: %s!" % cell) -def get_short_description(cell): +def get_short_description(cell: str): if cell in cell_notes: desc = cell_notes[cell] if cell in SENSORY_NEURONS_COOK: @@ -2061,7 +2092,11 @@ def get_short_description(cell): def get_cell_internal_link( - cell_name, html=False, text=None, use_color=False, individual_cell_page=False + cell_name: str, + html: bool = False, + text: str = None, + use_color: bool = False, + individual_cell_page: bool = False, ): url = "../Cells/index.html#%s" % cell_name @@ -2087,7 +2122,7 @@ def get_cell_internal_link( ) -def get_cell_osbv1_link(cell, text="OSB 3D", button=False): +def get_cell_osbv1_link(cell: str, text: str = "OSB 3D", button: bool = False): osbv1_link = f"https://v1.opensourcebrain.org/projects/c302/repository/revisions/development/show/examples/cells?explorer=https%253A%252F%252Fraw.githubusercontent.com%252Fopenworm%252Fc302%252Fdevelopment%252Fexamples%252Fcells%252F{cell}.cell.nml" if button: @@ -2095,7 +2130,9 @@ def get_cell_osbv1_link(cell, text="OSB 3D", button=False): return f'{text}' if is_herm_neuron(cell) else "" -def get_cell_wormatlas_link(cell_name, html=False, text=None, button=False): +def get_cell_wormatlas_link( + cell_name: str, html: bool = False, text: str = None, button: bool = False +): url = None known_other = { @@ -2229,7 +2266,7 @@ def get_cell_wormatlas_link(cell_name, html=False, text=None, button=False): return cell_name -def _get_dataset_link(reader_name, html=False, text=None): +def _get_dataset_link(reader_name: str, html: bool = False, text: str = None): url = "%s_data_graph.md" % reader_name if html: @@ -2238,7 +2275,7 @@ def _get_dataset_link(reader_name, html=False, text=None): return "[%s](%s)" % (reader_name if text is None else text, url) -def _generate_cell_table(cell_type, cells): +def _generate_cell_table(cell_type: str, cells: List[str]): import plotly.graph_objects as go from cect.Comparison import _format_json @@ -2400,7 +2437,7 @@ def _generate_cell_table(cell_type, cells): cell_type, INTERNEURONS_COOK + MALE_HEAD_INTERNEURONS - + MALE_INTERNEURONS, + + MALE_NON_HEAD_INTERNEURONS, ) ) elif cell_type == "motor neuron": @@ -2411,7 +2448,7 @@ def _generate_cell_table(cell_type, cells): cell_type, SENSORY_NEURONS_COOK + MALE_HEAD_SENSORY_NEURONS - + MALE_SENSORY_NEURONS, + + MALE_NON_HEAD_SENSORY_NEURONS, ) ) elif cell_type == "odd numbered pharyngeal muscle": diff --git a/cect/Comparison.py b/cect/Comparison.py index 4c16ca31a..e26d619f6 100644 --- a/cect/Comparison.py +++ b/cect/Comparison.py @@ -146,7 +146,7 @@ def get_hive_plot_markdown(reader_name, view, connectome, synclass, indent=" return f'\n{indent}
\n{indent}```plotly\n{indent}{{ "file_path": "./{asset_filename}" }}\n{indent}```\n' -def generate_comparison_page(quick: bool, color_table=True): +def generate_comparison_page(quick: bool, color_table=True, dataset_pages=True): connectomes = {} all_connectomes = {} @@ -238,243 +238,247 @@ def generate_comparison_page(quick: bool, color_table=True): if reader_name in reader_pages: connectomes[reader_name] = connectome - if connectome is not None: - from cect.ConnectomeView import ALL_VIEWS - - indent = " " - - for view in ALL_VIEWS: - print_("Generating view: %s (%s)" % (view.name, view.id)) - - view_prefix = "" if view.id == "Raw" else "%s_" % view.id - - matrix_filename = "docs/%s%s.md" % ( - view_prefix, - reader_pages[reader_name], - ) - graph_filename = "docs/%s%s_graph.md" % ( - view_prefix, - reader_pages[reader_name], - ) - hiveplot_filename = "docs/%s%s_hiveplot.md" % ( - view_prefix, - reader_pages[reader_name], - ) - - for filename in [ - graph_filename, - matrix_filename, - hiveplot_filename, - ]: - with open(filename, "w") as f: - graph = "graph" in filename - hiveplot = "hiveplot" in filename - matrix = not graph and not hiveplot - - f.write( - '---\ntitle: "Dataset: %s"\nsearch:\n exclude: true\n---\n\n' - % reader_name - ) - - desc_full = "" - - f.write(""" -!!! example inline "Choose Dataset" + if dataset_pages: + if connectome is not None: + from cect.ConnectomeView import ALL_VIEWS - """) - for rr in reader_pages: - view_prefix = ( - "" if view.id == "Raw" else "%s_" % view.id - ) + indent = " " + + for view in ALL_VIEWS: + print_("Generating view: %s (%s)" % (view.name, view.id)) + + view_prefix = "" if view.id == "Raw" else "%s_" % view.id + + matrix_filename = "docs/%s%s.md" % ( + view_prefix, + reader_pages[reader_name], + ) + graph_filename = "docs/%s%s_graph.md" % ( + view_prefix, + reader_pages[reader_name], + ) + hiveplot_filename = "docs/%s%s_hiveplot.md" % ( + view_prefix, + reader_pages[reader_name], + ) + + for filename in [ + graph_filename, + matrix_filename, + hiveplot_filename, + ]: + with open(filename, "w") as f: + graph = "graph" in filename + hiveplot = "hiveplot" in filename + matrix = not graph and not hiveplot f.write( - '%s%s%s ' + '---\ntitle: "Dataset: %s"\nsearch:\n exclude: true\n---\n\n' + % reader_name + ) + + desc_full = "" + + f.write(""" +!!! example "Choose Dataset" + + """) + for rr in reader_pages: + view_prefix = ( + "" if view.id == "Raw" else "%s_" % view.id + ) + + f.write( + '%s%s%s ' + % ( + "" if rr == reader_name else "", + view_prefix, + reader_pages[rr], + "_graph" + if graph + else ("_hiveplot" if hiveplot else ""), + rr, + "" if rr == reader_name else "", + ) + ) + + dp = ( + 'Dataset taken from %s. ' % ( - "" if rr == reader_name else "", - view_prefix, - reader_pages[rr], - "_graph" - if graph - else ("_hiveplot" if hiveplot else ""), - rr, - "" if rr == reader_name else "", + description_page, + description_page.replace( + "_20", " et al. 20" + ).replace("_19", " et al. 19"), ) + if description_page is not None + else "" ) - - dp = ( - 'Dataset taken from %s' - % ( - description_page, - description_page.replace( - "_20", " et al. 20" - ).replace("_19", " et al. 19"), + reader_page = ( + "../api/%s" + % reader_module.__name__.replace(".", "/") ) - if description_page is not None - else "" - ) - reader_page = "../api/%s" % reader_module.__name__.replace( - ".", "/" - ) - reader_class = reader_module.__name__.split(".")[1] - reader_info = ( - f'Reader: {reader_class}' - ) - desc_full = f'{dp}\n

{reader_module.READER_DESCRIPTION}.   {reader_info}

\n' - - f.write( - """ - -!!! tip "Choose View" + reader_class = reader_module.__name__.split(".")[1] + reader_info = f'Python Reader: {reader_class}' + desc_full = f"{dp}{reader_module.READER_DESCRIPTION}.   {reader_info}\n" + + f.write( + """ + + %s """ - ) + % desc_full + ) - for viewb in ALL_VIEWS: - viewb_prefix = ( - "" if viewb.id == "Raw" else "%s_" % viewb.id + f.write( + """ + +!!! abstract inline "Choose Graph type" + + """ ) f.write( - '%s %s%s%s' + '%s Graph%s - ' % ( - "" if view.id == viewb.id else "", - viewb_prefix, + "" if graph else "", + view_prefix, reader_pages[reader_name], - "_graph" - if graph - else ("_hiveplot" if hiveplot else ""), - viewb.name, - "" if view.id == viewb.id else "", - "" if "Fig 3" in view.name else " - ", + "" if graph else "", + ) + ) + f.write( + '%s Matrix%s - ' + % ( + "" if matrix else "", + view_prefix, + reader_pages[reader_name], + "" if matrix else "", + ) + ) + f.write( + '%s Hive plot%s \n\n' + % ( + "" if hiveplot else "", + view_prefix, + reader_pages[reader_name], + "" if hiveplot else "", ) ) - f.write( - """ - %s + cv = connectome.get_connectome_view(view) -!!! abstract "Choose Graph type" + f.write( + """ +!!! tip "Choose View" """ - % view.description - ) - - f.write( - '%s Graph%s - ' - % ( - "" if graph else "", - view_prefix, - reader_pages[reader_name], - "" if graph else "", - ) - ) - f.write( - '%s Matrix%s - ' - % ( - "" if matrix else "", - view_prefix, - reader_pages[reader_name], - "" if matrix else "", ) - ) - f.write( - '%s Hive plot%s \n\n' - % ( - "" if hiveplot else "", - view_prefix, - reader_pages[reader_name], - "" if hiveplot else "", - ) - ) - - cv = connectome.get_connectome_view(view) - # f.write('=== "%s"\n' % view.name) - f.write( - """ -

-%s -""" - % desc_full - ) - - no_conns = True - - for sc in view.synclass_sets: - if matrix: - mkdown_fig = get_matrix_markdown( - reader_name, - view, - cv, - sc, - indent=indent, + for viewb in ALL_VIEWS: + viewb_prefix = ( + "" if viewb.id == "Raw" else "%s_" % viewb.id ) - elif graph: - mkdown_fig = get_2d_graph_markdown( - reader_name, - view, - cv, - sc, - indent=indent, + f.write( + '%s %s%s%s' + % ( + "" if view.id == viewb.id else "", + viewb_prefix, + reader_pages[reader_name], + "_graph" + if graph + else ("_hiveplot" if hiveplot else ""), + viewb.name, + "" if view.id == viewb.id else "", + "" if "Fig 3" in view.name else " - ", + ) ) + f.write( + """ - elif hiveplot: - mkdown_fig = get_hive_plot_markdown( - reader_name, - view, - cv, - sc, - indent=indent, - ) + %s +""" + % view.description + ) - if mkdown_fig is not None: - no_conns = False - f.write('=== "%s"\n%s\n' % (sc, mkdown_fig)) + no_conns = True - if no_conns: - f.write("No connections present in this view\n") + for sc in view.synclass_sets: + if matrix: + mkdown_fig = get_matrix_markdown( + reader_name, + view, + cv, + sc, + indent=indent, + ) - cell_types = { - "Neurons (herm)": preferred, - "Missing neurons": missing_preferred, - "Muscles": muscles, - "Other cells": not_in_preferred, - } + elif graph: + mkdown_fig = get_2d_graph_markdown( + reader_name, + view, + cv, + sc, + indent=indent, + ) - for t in cell_types: - f.write("\n### %s (%i)\n" % (t, len(cell_types[t]))) - if len(cell_types[t]) > 0: - f.write( - "
Full list of %s%s\n" - % ( - t.replace("herm", "hermaphrodite only"), - ( - " (known hermaphrodite neurons not present)" - if "Missing" in t - else " in this dataset" - ), + elif hiveplot: + mkdown_fig = get_hive_plot_markdown( + reader_name, + view, + cv, + sc, + indent=indent, ) - ) - ss = sorted(cell_types[t]) - for n in ss: + + if mkdown_fig is not None: + no_conns = False + f.write('=== "%s"\n%s\n' % (sc, mkdown_fig)) + + if no_conns: + f.write("No connections present in this view\n") + + cell_types = { + "Neurons (herm)": preferred, + "Missing neurons": missing_preferred, + "Muscles": muscles, + "Other cells": not_in_preferred, + } + + for t in cell_types: + f.write("\n### %s (%i)\n" % (t, len(cell_types[t]))) + if len(cell_types[t]) > 0: f.write( - "%s\n" + "
Full list of %s%s\n" % ( - get_cell_internal_link( - n, - html=True, - use_color=True, - individual_cell_page=True, - ) + t.replace("herm", "hermaphrodite only"), + ( + " (known hermaphrodite neurons not present)" + if "Missing" in t + else " in this dataset" + ), ) ) - if n is not ss[-1]: - f.write(" | ") + ss = sorted(cell_types[t]) + for n in ss: + f.write( + "%s\n" + % ( + get_cell_internal_link( + n, + html=True, + use_color=True, + individual_cell_page=True, + ) + ) + ) + if n is not ss[-1]: + f.write(" | ") - f.write("\n
\n") + f.write("\n
\n") - print_("Written page: %s" % filename) + print_("Written page: %s" % filename) neurons, neuron_conns = connectome.get_neuron_to_neuron_conns() neurons2muscles, muscles, muscle_conns = connectome.get_neuron_to_muscle_conns() @@ -549,32 +553,63 @@ def generate_comparison_page(quick: bool, color_table=True): from cect.Cells import COOK_GROUPING_1 if color_table: - STYLE = '"width:80px"' - table_html += f'\n \n \n' + STYLE = '"width:80px;font-family:Arial"' + font_size = "190%" + table_html += f'
\n \n \n' readers_to_include = [] for reader_name, reader_info in readers.items(): - if "Test" not in reader_name and "SSData" not in reader_name: + if ( + "Test" not in reader_name + and "SSData" not in reader_name + and "Witvliet2" not in reader_name + and "Witvliet3" not in reader_name + and "Witvliet4" not in reader_name + and "Witvliet7" not in reader_name + and "WormNeuroAtlas" not in reader_name + and "RipollSanchezMidRange" not in reader_name + and "RipollSanchezLongRange" not in reader_name + ): readers_to_include.append(reader_name) + better_names = {} for reader_name in readers_to_include: better_name = ( reader_name.replace("_", " ") .replace("201", " 201") .replace("202", " 202") - .replace("chez", "chez ") + .replace("Sanchez", " Sanchez et al. 2023 ") + .replace("tley", "tley et al.") + .replace("Cook", "Cook et al.") + .replace("ttin", "ttin et al.") .replace("19", "19 ") .replace("liet", "liet ") .replace("MA", "Monoamin.") .replace("PEP", "Peptid.") + .replace("ite A", "ite et al. 1986 N2U/Adult") + .replace("ite L4", "ite et al. 1986 JSU/L4") + .replace("ite whole", "ite et al. 1986 Whole worm") + .replace("Randi", "Randi et al.") + .replace("Varshney", "Varshney et al. 2011") + .replace("Witvliet 1", "Witvliet et al. 2021 1 (L1)") + .replace("Witvliet 5", "Witvliet et al. 2021 5 (L2)") + .replace("Witvliet 6", "Witvliet et al. 2021 6 (L3)") + .replace("Witvliet 8", "Witvliet et al. 2021 8 (Adult)") ) - table_html += f' \n' + better_names[reader_name] = better_name + + # table_html += f' \n' for group in COOK_GROUPING_1: - table_html += f' \n\n' + + for reader_name in readers_to_include: + table_html += f' \n\n\n" table_html += " \n
{better_name}{better_name}
{group}\n' + table_html += f' {group}
{better_names[reader_name]}\n' + + for group in COOK_GROUPING_1: + # table_html += f'
{group}\n' - for reader_name in readers_to_include: connectome = all_connectomes[reader_name] cells_here = "" for cell in sorted(COOK_GROUPING_1[group]): @@ -589,16 +624,16 @@ def generate_comparison_page(quick: bool, color_table=True): else: pass # cells_here+='%s '%cell - if (cells_here.split("
")[-1]).count(" ") > 9: + if (cells_here.split("
")[-1]).count(" ") > 14: cells_here += "
\n" - table_html += f"
{cells_here}\n" + table_html += f' {cells_here}\n' table_html += "
\n" - main_mk += table_html.replace("150%", "100%") + main_mk += table_html.replace(font_size, "100%") main_mk += df_all.to_markdown() @@ -635,6 +670,6 @@ def generate_comparison_page(quick: bool, color_table=True): if __name__ == "__main__": quick = len(sys.argv) > 1 and eval(sys.argv[1]) - connectomes = generate_comparison_page(quick, color_table=True) + connectomes = generate_comparison_page(quick, color_table=True, dataset_pages=False) print("Finished. All loaded connectomes:\n%s" % connectomes) diff --git a/cect/ConnectomeDataset.py b/cect/ConnectomeDataset.py index 876229e67..d06ca0a8f 100644 --- a/cect/ConnectomeDataset.py +++ b/cect/ConnectomeDataset.py @@ -7,6 +7,7 @@ from cect.Cells import get_standard_color from cect.Cells import is_bilateral_left from cect.Cells import is_bilateral_right +from cect.Cells import is_one_of_bilateral_pair from cect.Cells import are_bilateral_pair from cect.Cells import SENSORY_NEURONS_NONPHARYNGEAL_COOK from cect.Cells import INTERNEURONS_NONPHARYNGEAL_COOK @@ -16,6 +17,7 @@ from cect.Cells import is_known_muscle from cect.Cells import is_pharyngeal_cell from cect.Cells import is_known_cell +from cect.Cells import get_SIM_class import numpy as np import math @@ -24,8 +26,6 @@ import pprint import random -from cect.Cells import get_SIM_class - random.seed(10) @@ -101,7 +101,9 @@ def to_networkx_graph(self, synclass, view=None): return Gn - def add_connection_info(self, conn: ConnectionInfo): + def add_connection_info( + self, conn: ConnectionInfo, check_overwritten_connections: bool = False + ): if self.verbose: print_("---- Adding: %s" % conn) @@ -131,6 +133,26 @@ def add_connection_info(self, conn: ConnectionInfo): pre_index = self.nodes.index(conn.pre_cell) post_index = self.nodes.index(conn.post_cell) + if conn_array[pre_index, post_index] != 0: + print_( + "Preexisting connection (%i conns already) at (%i,%i) - %s..." + % (len(self.connection_infos), pre_index, post_index, conn) + ) + if conn_array[pre_index, post_index] != conn.number: + info = ( + " *** Existing connection at (%i,%i), was: %s, setting to: %s" + % ( + pre_index, + post_index, + conn_array[pre_index, post_index], + conn.number, + ) + ) + if check_overwritten_connections: + raise Exception(info) + else: + print_(info) + conn_array[pre_index, post_index] = conn.number if self.verbose: @@ -303,24 +325,30 @@ def get_connectome_view(self, view): return cv def summary(self): - info = "Nodes present: %s\n" % self.nodes + info = "Nodes present (%i): %s\n" % (len(self.nodes), self.nodes) for c in self.connections: conn_array = self.connections[c] - info += ( - "- Connection type - %s: %s, %i non-zero entries, %i total\n%s\n" - % ( - c, - conn_array.shape, - np.count_nonzero(conn_array), - np.sum(conn_array), - conn_array, + nonzero = np.count_nonzero(conn_array) + if nonzero > 0: + info += ( + "- Connection type - %s: %s, %i non-zero entries, %i total\n%s\n" + % ( + c, + conn_array.shape, + nonzero, + np.sum(conn_array), + conn_array, + ) ) - ) return info - def to_plotly_matrix_fig(self, synclass, view, color_continuous_scale=None): - import plotly.express as px - + def to_plotly_matrix_fig( + self, + synclass: str, + view: str, + color_continuous_scale: bool = None, + bold_bilaterals: bool = False, + ): conn_array = self.connections[synclass] zmin = np.min(conn_array) @@ -343,12 +371,15 @@ def to_plotly_matrix_fig(self, synclass, view, color_continuous_scale=None): ) def get_color_html(color, node): - return f'{node}' + font_weight = "" + if bold_bilaterals and is_one_of_bilateral_pair(node): + font_weight = "font-weight:bold;" + return f'{node}' node_colors = [ ( view.get_node_set(node).color - if view.has_color() + if view is not None and view.has_color() else get_standard_color(node) ) for node in self.nodes @@ -361,6 +392,8 @@ def get_color_html(color, node): get_color_html(color, node) for node, color in zip(self.nodes, node_colors) ] + import plotly.express as px + fig = px.imshow( conn_array, labels=dict(x="Postsynaptic", y="Presynaptic", color="Weight"), @@ -390,7 +423,7 @@ def get_color_html(color, node): other_line = False for i, node_value in enumerate(self.nodes): - if not view.get_node_set(node_value).is_one_cell(): + if view is not None and not view.get_node_set(node_value).is_one_cell(): break if not sens_line and node_value in SENSORY_NEURONS_NONPHARYNGEAL_COOK: diff --git a/cect/ConnectomeView.py b/cect/ConnectomeView.py index bacf28abd..4b10be749 100644 --- a/cect/ConnectomeView.py +++ b/cect/ConnectomeView.py @@ -7,6 +7,10 @@ from cect.Cells import INTERNEURONS_NONPHARYNGEAL_COOK from cect.Cells import UNKNOWN_FUNCTION_NEURONS from cect.Cells import MALE_SPECIFIC_NEURONS +from cect.Cells import MALE_HEAD_INTERNEURONS +from cect.Cells import MALE_NON_HEAD_INTERNEURONS +from cect.Cells import MALE_HEAD_SENSORY_NEURONS +from cect.Cells import MALE_NON_HEAD_SENSORY_NEURONS from cect.Cells import PREFERRED_MUSCLE_NAMES from cect.Cells import ALL_NON_NEURON_MUSCLE_CELLS @@ -156,15 +160,41 @@ def get_index_of_cell(self, cell): NEURONS_VIEW = View( "Neurons", "Neurons", - "All 302 hermaphrodite neurons (whether present or not in the connectome dataset)", + "All 302 **hermaphrodite** neurons (whether present or not in the connectome dataset)", [], EXC_INH_GJ_FUNC_CONT_SYN_CLASSES, ) +NONPHARYNGEAL_NEURONS_HERM_VIEW = View( + "Nonpharyngeal", + "Nonpharyngeal Neurons", + "All **hermaphrodite** neurons except those in the pharynx", + [], + EXC_INH_GJ_FUNC_CONT_SYN_CLASSES, + only_show_existing_nodes=False, +) + +NONPHARYNGEAL_NEURONS_HM_VIEW = View( + "Nonpharyngeal", + "Nonpharyngeal Neurons", + "All neurons (herm. & male) except those in the pharynx", + [], + EXC_INH_GJ_FUNC_CONT_SYN_CLASSES, + only_show_existing_nodes=False, +) + for cell in ( sorted(PHARYNGEAL_NEURONS) - + sorted(SENSORY_NEURONS_NONPHARYNGEAL_COOK) - + sorted(INTERNEURONS_NONPHARYNGEAL_COOK) + + sorted( + SENSORY_NEURONS_NONPHARYNGEAL_COOK + + MALE_HEAD_SENSORY_NEURONS + + MALE_NON_HEAD_SENSORY_NEURONS + ) + + sorted( + INTERNEURONS_NONPHARYNGEAL_COOK + + MALE_HEAD_INTERNEURONS + + MALE_NON_HEAD_INTERNEURONS + ) + sorted( HEAD_MOTORNEURONS_COOK + VENTRAL_CORD_MOTORNEURONS @@ -174,14 +204,21 @@ def get_index_of_cell(self, cell): ) + sorted(UNKNOWN_FUNCTION_NEURONS) ): - NEURONS_VIEW.node_sets.append(NodeSet(cell, [cell], get_standard_color(cell))) RAW_VIEW.node_sets.append(NodeSet(cell, [cell], get_standard_color(cell))) -for cell in ( - sorted(MALE_SPECIFIC_NEURONS) - + sorted(PREFERRED_MUSCLE_NAMES) - + sorted(ALL_NON_NEURON_MUSCLE_CELLS) -): + if cell not in MALE_SPECIFIC_NEURONS: + NEURONS_VIEW.node_sets.append(NodeSet(cell, [cell], get_standard_color(cell))) + + if cell not in PHARYNGEAL_NEURONS: + if cell not in MALE_SPECIFIC_NEURONS: + NONPHARYNGEAL_NEURONS_HERM_VIEW.node_sets.append( + NodeSet(cell, [cell], get_standard_color(cell)) + ) + NONPHARYNGEAL_NEURONS_HM_VIEW.node_sets.append( + NodeSet(cell, [cell], get_standard_color(cell)) + ) + +for cell in sorted(PREFERRED_MUSCLE_NAMES) + sorted(ALL_NON_NEURON_MUSCLE_CELLS): RAW_VIEW.node_sets.append(NodeSet(cell, [cell], get_standard_color(cell))) assert len(NEURONS_VIEW.node_sets) == 302 @@ -473,6 +510,7 @@ def get_index_of_cell(self, cell): RAW_VIEW, NEURONS_VIEW, PHARYNX_VIEW, + NONPHARYNGEAL_NEURONS_HERM_VIEW, SOCIAL_VIEW, ESCAPE_VIEW, COOK_FIG3_VIEW, @@ -498,7 +536,11 @@ def get_index_of_cell(self, cell): EXC_INH_GJ_SYN_CLASSES, ) - from cect.TestDataReader import tdr_instance + # from cect.TestDataReader import get_instance + # from cect.Cook2019HermReader import get_instance + from cect.White_whole import get_instance + + tdr_instance = get_instance() print(NodeSet(COOK_FIG3_VIEW, COOK_FIG3_VIEW)) @@ -524,6 +566,9 @@ def get_index_of_cell(self, cell): print("------- Escape ---------") print(tdr_instance.get_connectome_view(ESCAPE_VIEW).summary()) + print("------- Nonpharyngeal ---------") + print(tdr_instance.get_connectome_view(NONPHARYNGEAL_NEURONS_HM_VIEW).summary()) + """ from cect.Cells import ALL_PREFERRED_CELL_NAMES diff --git a/cect/data/all_cell_info.csv b/cect/data/all_cell_info.csv index 4b4309581..baf2897fd 100644 --- a/cect/data/all_cell_info.csv +++ b/cect/data/all_cell_info.csv @@ -303,10 +303,6 @@ VD8,Ventral cord motor neuron,Ventral D-type Motor Neuron 8,P7.app,"Ventralcord VD9,Ventral cord motor neuron,Ventral D-type Motor Neuron 9,P8.app,"Ventral cord motor neuron, innervates vent body muscles, reciprocal inhibitor" MCML,Male head interneuron,Mystery Cell of the Male Left,AmsoL,Male specific interneuron MCMR,Male head interneuron,Mystery Cell of the Male Right,AmsoR,Male specific interneuron -CEMDL,Male head sensory neuron,CEphalic Male Sensory Neuron Dorsal Left,AB plaaaaaap,"Male specific cephalic neurons (programmed cell death in hermaphrodite embryo) open to outside, possible function in male chemotaxis toward hermaphrodite" -CEMDR,Male head sensory neuron,CEphalic Male Sensory Neuron Dorsal Right,AB arpapaaap,"Male specific cephalic neurons (programmed cell death in hermaphrodite embryo) open to outside, possible function in male chemotaxis toward hermaphrodite" -CEMVL,Male head sensory neuron,CEphalic Male Sensory Neuron Ventral Left,AB plpaapapp,"Male specific cephalic neurons (programmed cell death in hermaphrodite embryo) open to outside, possible function in male chemotaxis toward hermaphrodite" -CEMVR,Male head sensory neuron,CEphalic Male Sensory Neuron Ventral Right,AB prpaapapp,"Male specific cephalic neurons (programmed cell death in hermaphrodite embryo) open to outside, possible function in male chemotaxis toward hermaphrodite" PVV,Male interneuron,Posterior Ventral Process V,P11.paaa,"Male specific motor neuron, pre-anal ganglion" PVX,Male interneuron,Posterior Ventral Process X,P12.aap,"Male specific interneuron, cell body in pre-anal ganglion, postsynaptic in ring and ventral cord" PVY,Male interneuron,Posterior Ventral Process Y,P11.paap,"Male specific interneuron, cell body in pre-anal ganglion" @@ -339,6 +335,10 @@ CP06,Male interneuron,"C-type Neuron, Posterior Daughter after Division 6",P8.aa CP07,Male interneuron,"C-type Neuron, Posterior Daughter after Division 7",P9.aapp,Male specific motor neuron in ventral cord CP08,Male interneuron,"C-type Neuron, Posterior Daughter after Division 8",P10.aapp,"Male specific interneuron, projects into preanal ganglion" CP09,Male interneuron,"C-type Neuron, Posterior Daughter after Division 9",P11.aapp,"Male specific interneuron, projects into preanal ganglion" +CEMDL,Male head sensory neuron,CEphalic Male Sensory Neuron Dorsal Left,AB plaaaaaap,"Male specific cephalic neurons (programmed cell death in hermaphrodite embryo) open to outside, possible function in male chemotaxis toward hermaphrodite" +CEMDR,Male head sensory neuron,CEphalic Male Sensory Neuron Dorsal Right,AB arpapaaap,"Male specific cephalic neurons (programmed cell death in hermaphrodite embryo) open to outside, possible function in male chemotaxis toward hermaphrodite" +CEMVL,Male head sensory neuron,CEphalic Male Sensory Neuron Ventral Left,AB plpaapapp,"Male specific cephalic neurons (programmed cell death in hermaphrodite embryo) open to outside, possible function in male chemotaxis toward hermaphrodite" +CEMVR,Male head sensory neuron,CEphalic Male Sensory Neuron Ventral Right,AB prpaapapp,"Male specific cephalic neurons (programmed cell death in hermaphrodite embryo) open to outside, possible function in male chemotaxis toward hermaphrodite" R1AL,Male sensory neuron,Ray 1 Neuron A Left,"V5L.pppppaaa, (R1.aaaL)","Male sensory rays, neuron, striated rootlet, cell body in left lumbar ganglion" R1AR,Male sensory neuron,Ray 1 Neuron A Right,"V5R.pppppaaa, (R1.aaaR)","Male sensory rays, neuron, striated rootlet, cell body in right lumbar ganglion" R1BL,Male sensory neuron,Ray 1 Neuron B Left,"V5L.pppppapa, (R1.apaL)","Male sensory rays, neuron, darkly staining tip, open to outside, cell body in left lumbar ganglion" diff --git a/docs/AddDataset.md b/docs/AddDataset.md index 02dd3122e..bc668fb1b 100644 --- a/docs/AddDataset.md +++ b/docs/AddDataset.md @@ -4,9 +4,9 @@ We are very keen to incorporate other published datasets on worm neuronal connec ## A) Add it yourself -1) [Fork](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/working-with-forks/fork-a-repo) the repository https://github.com/openworm/ConnectomeToolbox. +1) [Fork](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/working-with-forks/fork-a-repo) the [main repository](https://github.com/openworm/ConnectomeToolbox). -2) Add the source file of your dataset (usually the adjacency matrices of connection weights) into the [data folder](https://github.com/openworm/ConnectomeToolbox/tree/main/cect/data). +2) Add the source file of your dataset (usually the adjacency matrices of connection weights in, for example csv, Excel or Matlab format) into the [data folder](https://github.com/openworm/ConnectomeToolbox/tree/main/cect/data). 3) Create a Reader for the dataset, which converts it to our internal format. See examples for loading structured datasets in [CSV format](https://github.com/pgleeson/ConnectomeToolbox/blob/main/cect/Cook2020DataReader.py), [XLSX format](https://github.com/openworm/ConnectomeToolbox/blob/main/cect/Cook2019DataReader.py) or [XLS format](https://github.com/openworm/ConnectomeToolbox/blob/6847151db6a5dc9bc3fea1c5a40d01d1a6b024fa/cect/SpreadsheetDataReader.py). @@ -14,7 +14,7 @@ We are very keen to incorporate other published datasets on worm neuronal connec 5) Run [./test.sh](https://github.com/openworm/ConnectomeToolbox/blob/main/test.sh) in your local directory (or `./test.sh -q` for a quicker test) to install the latest version of the code and attempt to regenerate the website locally with your changes. -6) Commit the code and [open a pull request](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-pull-requests) to https://github.com/openworm/ConnectomeToolbox with your changes. Note, enabling [GitHub Actions](https://github.com/features/actions) on the repository containing your fork will cause a number of [tests](https://github.com/openworm/ConnectomeToolbox/tree/main/.github/workflows) to be run automatically when you commit, which should pass before you open the pull request. +6) Commit the code and [open a pull request](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-pull-requests) to [https://github.com/openworm/ConnectomeToolbox](https://github.com/openworm/ConnectomeToolbox) with your changes. Note, enabling [GitHub Actions](https://github.com/features/actions) on the repository containing your fork will cause a number of [tests](https://github.com/openworm/ConnectomeToolbox/tree/main/.github/workflows) to be run automatically when you commit, which should pass before you open the pull request. ## B) Tell us about the dataset diff --git a/docs/Cells.md b/docs/Cells.md index 3ca6e677e..399d8729f 100644 --- a/docs/Cells.md +++ b/docs/Cells.md @@ -526,7 +526,7 @@ title: C. elegans cells | PVPL | Layer 3 interneuron | [White_A](White_A_data_graph.md), [White_L4](White_L4_data_graph.md), [White_whole](White_whole_data_graph.md), [Varshney](Varshney_data_graph.md), [Bentley2016_PEP](Bentley2016_PEP_data_graph.md), [Cook2019Herm](Cook2019Herm_data_graph.md), [Cook2019Male](Cook2019Male_data_graph.md), [Brittin2021](Brittin2021_data_graph.md), [Witvliet1](Witvliet1_data_graph.md), [Witvliet2](Witvliet2_data_graph.md), [Witvliet3](Witvliet3_data_graph.md), [Witvliet4](Witvliet4_data_graph.md), [Witvliet5](Witvliet5_data_graph.md), [Witvliet6](Witvliet6_data_graph.md), [Witvliet7](Witvliet7_data_graph.md), [Witvliet8](Witvliet8_data_graph.md), [WormNeuroAtlas](WormNeuroAtlas_data_graph.md), [RipollSanchezShortRange](RipollSanchezShortRange_data_graph.md), [RipollSanchezMidRange](RipollSanchezMidRange_data_graph.md), [RipollSanchezLongRange](RipollSanchezLongRange_data_graph.md), [SSData](SSData_data_graph.md), [UpdSSData](UpdSSData_data_graph.md), [UpdSSData2](UpdSSData2_data_graph.md) | [WormAtlas](https://www.wormatlas.org/neurons/Individual Neurons/PVPframeset.html)
OSB 3D | | PVPR | Layer 3 interneuron | [White_A](White_A_data_graph.md), [White_L4](White_L4_data_graph.md), [White_whole](White_whole_data_graph.md), [Varshney](Varshney_data_graph.md), [Bentley2016_PEP](Bentley2016_PEP_data_graph.md), [Cook2019Herm](Cook2019Herm_data_graph.md), [Cook2019Male](Cook2019Male_data_graph.md), [Brittin2021](Brittin2021_data_graph.md), [Witvliet1](Witvliet1_data_graph.md), [Witvliet2](Witvliet2_data_graph.md), [Witvliet3](Witvliet3_data_graph.md), [Witvliet4](Witvliet4_data_graph.md), [Witvliet5](Witvliet5_data_graph.md), [Witvliet6](Witvliet6_data_graph.md), [Witvliet7](Witvliet7_data_graph.md), [Witvliet8](Witvliet8_data_graph.md), [WormNeuroAtlas](WormNeuroAtlas_data_graph.md), [RipollSanchezShortRange](RipollSanchezShortRange_data_graph.md), [RipollSanchezMidRange](RipollSanchezMidRange_data_graph.md), [RipollSanchezLongRange](RipollSanchezLongRange_data_graph.md), [SSData](SSData_data_graph.md), [UpdSSData](UpdSSData_data_graph.md), [UpdSSData2](UpdSSData2_data_graph.md) | [WormAtlas](https://www.wormatlas.org/neurons/Individual Neurons/PVPframeset.html)
OSB 3D | | PVQL | Layer 3 interneuron | [White_A](White_A_data_graph.md), [White_L4](White_L4_data_graph.md), [White_whole](White_whole_data_graph.md), [Varshney](Varshney_data_graph.md), [Bentley2016_MA](Bentley2016_MA_data_graph.md), [Bentley2016_PEP](Bentley2016_PEP_data_graph.md), [Cook2019Herm](Cook2019Herm_data_graph.md), [Cook2019Male](Cook2019Male_data_graph.md), [Brittin2021](Brittin2021_data_graph.md), [Witvliet1](Witvliet1_data_graph.md), [Witvliet2](Witvliet2_data_graph.md), [Witvliet3](Witvliet3_data_graph.md), [Witvliet4](Witvliet4_data_graph.md), [Witvliet5](Witvliet5_data_graph.md), [Witvliet6](Witvliet6_data_graph.md), [Witvliet7](Witvliet7_data_graph.md), [Witvliet8](Witvliet8_data_graph.md), [WormNeuroAtlas](WormNeuroAtlas_data_graph.md), [RipollSanchezShortRange](RipollSanchezShortRange_data_graph.md), [RipollSanchezMidRange](RipollSanchezMidRange_data_graph.md), [RipollSanchezLongRange](RipollSanchezLongRange_data_graph.md), [SSData](SSData_data_graph.md), [UpdSSData](UpdSSData_data_graph.md), [UpdSSData2](UpdSSData2_data_graph.md) | [WormAtlas](https://www.wormatlas.org/neurons/Individual Neurons/PVQframeset.html)
OSB 3D | -| PVQR | Layer 3 interneuron | [White_A](White_A_data_graph.md), [White_L4](White_L4_data_graph.md), [White_whole](White_whole_data_graph.md), [Varshney](Varshney_data_graph.md), [Bentley2016_MA](Bentley2016_MA_data_graph.md), [Bentley2016_PEP](Bentley2016_PEP_data_graph.md), [Cook2019Herm](Cook2019Herm_data_graph.md), [Cook2019Male](Cook2019Male_data_graph.md), [Witvliet1](Witvliet1_data_graph.md), [Witvliet2](Witvliet2_data_graph.md), [Witvliet3](Witvliet3_data_graph.md), [Witvliet4](Witvliet4_data_graph.md), [Witvliet5](Witvliet5_data_graph.md), [Witvliet6](Witvliet6_data_graph.md), [Witvliet7](Witvliet7_data_graph.md), [Witvliet8](Witvliet8_data_graph.md), [WormNeuroAtlas](WormNeuroAtlas_data_graph.md), [RipollSanchezShortRange](RipollSanchezShortRange_data_graph.md), [RipollSanchezMidRange](RipollSanchezMidRange_data_graph.md), [RipollSanchezLongRange](RipollSanchezLongRange_data_graph.md), [SSData](SSData_data_graph.md), [UpdSSData](UpdSSData_data_graph.md), [UpdSSData2](UpdSSData2_data_graph.md) | [WormAtlas](https://www.wormatlas.org/neurons/Individual Neurons/PVQframeset.html)
OSB 3D | +| PVQR | Layer 3 interneuron | [White_A](White_A_data_graph.md), [White_L4](White_L4_data_graph.md), [White_whole](White_whole_data_graph.md), [Varshney](Varshney_data_graph.md), [Bentley2016_MA](Bentley2016_MA_data_graph.md), [Bentley2016_PEP](Bentley2016_PEP_data_graph.md), [Cook2019Herm](Cook2019Herm_data_graph.md), [Cook2019Male](Cook2019Male_data_graph.md), [Brittin2021](Brittin2021_data_graph.md), [Witvliet1](Witvliet1_data_graph.md), [Witvliet2](Witvliet2_data_graph.md), [Witvliet3](Witvliet3_data_graph.md), [Witvliet4](Witvliet4_data_graph.md), [Witvliet5](Witvliet5_data_graph.md), [Witvliet6](Witvliet6_data_graph.md), [Witvliet7](Witvliet7_data_graph.md), [Witvliet8](Witvliet8_data_graph.md), [WormNeuroAtlas](WormNeuroAtlas_data_graph.md), [RipollSanchezShortRange](RipollSanchezShortRange_data_graph.md), [RipollSanchezMidRange](RipollSanchezMidRange_data_graph.md), [RipollSanchezLongRange](RipollSanchezLongRange_data_graph.md), [SSData](SSData_data_graph.md), [UpdSSData](UpdSSData_data_graph.md), [UpdSSData2](UpdSSData2_data_graph.md) | [WormAtlas](https://www.wormatlas.org/neurons/Individual Neurons/PVQframeset.html)
OSB 3D | | PVR | Layer 3 interneuron | [White_A](White_A_data_graph.md), [White_L4](White_L4_data_graph.md), [White_whole](White_whole_data_graph.md), [Varshney](Varshney_data_graph.md), [Bentley2016_PEP](Bentley2016_PEP_data_graph.md), [Cook2019Herm](Cook2019Herm_data_graph.md), [Cook2019Male](Cook2019Male_data_graph.md), [Witvliet1](Witvliet1_data_graph.md), [Witvliet2](Witvliet2_data_graph.md), [Witvliet3](Witvliet3_data_graph.md), [Witvliet4](Witvliet4_data_graph.md), [Witvliet5](Witvliet5_data_graph.md), [Witvliet6](Witvliet6_data_graph.md), [Witvliet7](Witvliet7_data_graph.md), [Witvliet8](Witvliet8_data_graph.md), [WormNeuroAtlas](WormNeuroAtlas_data_graph.md), [RipollSanchezShortRange](RipollSanchezShortRange_data_graph.md), [RipollSanchezMidRange](RipollSanchezMidRange_data_graph.md), [RipollSanchezLongRange](RipollSanchezLongRange_data_graph.md), [SSData](SSData_data_graph.md), [UpdSSData](UpdSSData_data_graph.md), [UpdSSData2](UpdSSData2_data_graph.md) | [WormAtlas](https://www.wormatlas.org/neurons/Individual Neurons/PVRframeset.html)
OSB 3D | | PVT | Layer 2 interneuron | [White_A](White_A_data_graph.md), [White_L4](White_L4_data_graph.md), [White_whole](White_whole_data_graph.md), [Varshney](Varshney_data_graph.md), [Bentley2016_MA](Bentley2016_MA_data_graph.md), [Bentley2016_PEP](Bentley2016_PEP_data_graph.md), [Cook2019Herm](Cook2019Herm_data_graph.md), [Cook2019Male](Cook2019Male_data_graph.md), [Brittin2021](Brittin2021_data_graph.md), [Witvliet1](Witvliet1_data_graph.md), [Witvliet2](Witvliet2_data_graph.md), [Witvliet3](Witvliet3_data_graph.md), [Witvliet4](Witvliet4_data_graph.md), [Witvliet5](Witvliet5_data_graph.md), [Witvliet6](Witvliet6_data_graph.md), [Witvliet7](Witvliet7_data_graph.md), [Witvliet8](Witvliet8_data_graph.md), [WormNeuroAtlas](WormNeuroAtlas_data_graph.md), [RipollSanchezShortRange](RipollSanchezShortRange_data_graph.md), [RipollSanchezMidRange](RipollSanchezMidRange_data_graph.md), [RipollSanchezLongRange](RipollSanchezLongRange_data_graph.md), [SSData](SSData_data_graph.md), [UpdSSData](UpdSSData_data_graph.md), [UpdSSData2](UpdSSData2_data_graph.md) | [WormAtlas](https://www.wormatlas.org/neurons/Individual Neurons/PVTframeset.html)
OSB 3D | | PVV | Male interneuron | [Cook2019Male](Cook2019Male_data_graph.md) | [WormAtlas](https://www.wormatlas.org/neurons/Individual Neurons/PVVframeset.html)
| @@ -550,7 +550,7 @@ title: C. elegans cells | RIML | Layer 1 interneuron; motorneuron in White et al., 1986 | [White_A](White_A_data_graph.md), [White_L4](White_L4_data_graph.md), [White_whole](White_whole_data_graph.md), [Varshney](Varshney_data_graph.md), [Bentley2016_MA](Bentley2016_MA_data_graph.md), [Bentley2016_PEP](Bentley2016_PEP_data_graph.md), [Cook2019Herm](Cook2019Herm_data_graph.md), [Cook2019Male](Cook2019Male_data_graph.md), [Brittin2021](Brittin2021_data_graph.md), [Witvliet1](Witvliet1_data_graph.md), [Witvliet2](Witvliet2_data_graph.md), [Witvliet3](Witvliet3_data_graph.md), [Witvliet4](Witvliet4_data_graph.md), [Witvliet5](Witvliet5_data_graph.md), [Witvliet6](Witvliet6_data_graph.md), [Witvliet7](Witvliet7_data_graph.md), [Witvliet8](Witvliet8_data_graph.md), [WormNeuroAtlas](WormNeuroAtlas_data_graph.md), [Randi2023](Randi2023_data_graph.md), [RipollSanchezShortRange](RipollSanchezShortRange_data_graph.md), [RipollSanchezMidRange](RipollSanchezMidRange_data_graph.md), [RipollSanchezLongRange](RipollSanchezLongRange_data_graph.md), [SSData](SSData_data_graph.md), [UpdSSData](UpdSSData_data_graph.md), [UpdSSData2](UpdSSData2_data_graph.md) | [WormAtlas](https://www.wormatlas.org/neurons/Individual Neurons/RIMframeset.html)
OSB 3D | | RIMR | Layer 1 interneuron; motorneuron in White et al., 1986 | [White_A](White_A_data_graph.md), [White_L4](White_L4_data_graph.md), [White_whole](White_whole_data_graph.md), [Varshney](Varshney_data_graph.md), [Bentley2016_MA](Bentley2016_MA_data_graph.md), [Bentley2016_PEP](Bentley2016_PEP_data_graph.md), [Cook2019Herm](Cook2019Herm_data_graph.md), [Cook2019Male](Cook2019Male_data_graph.md), [Brittin2021](Brittin2021_data_graph.md), [Witvliet1](Witvliet1_data_graph.md), [Witvliet2](Witvliet2_data_graph.md), [Witvliet3](Witvliet3_data_graph.md), [Witvliet4](Witvliet4_data_graph.md), [Witvliet5](Witvliet5_data_graph.md), [Witvliet6](Witvliet6_data_graph.md), [Witvliet7](Witvliet7_data_graph.md), [Witvliet8](Witvliet8_data_graph.md), [WormNeuroAtlas](WormNeuroAtlas_data_graph.md), [Randi2023](Randi2023_data_graph.md), [RipollSanchezShortRange](RipollSanchezShortRange_data_graph.md), [RipollSanchezMidRange](RipollSanchezMidRange_data_graph.md), [RipollSanchezLongRange](RipollSanchezLongRange_data_graph.md), [SSData](SSData_data_graph.md), [UpdSSData](UpdSSData_data_graph.md), [UpdSSData2](UpdSSData2_data_graph.md) | [WormAtlas](https://www.wormatlas.org/neurons/Individual Neurons/RIMframeset.html)
OSB 3D | | RIPL | Linker to pharynx | [White_A](White_A_data_graph.md), [White_L4](White_L4_data_graph.md), [White_whole](White_whole_data_graph.md), [Varshney](Varshney_data_graph.md), [Bentley2016_PEP](Bentley2016_PEP_data_graph.md), [Cook2019Herm](Cook2019Herm_data_graph.md), [Cook2019Male](Cook2019Male_data_graph.md), [Cook2020](Cook2020_data_graph.md), [Brittin2021](Brittin2021_data_graph.md), [Witvliet1](Witvliet1_data_graph.md), [Witvliet2](Witvliet2_data_graph.md), [Witvliet3](Witvliet3_data_graph.md), [Witvliet4](Witvliet4_data_graph.md), [Witvliet5](Witvliet5_data_graph.md), [Witvliet6](Witvliet6_data_graph.md), [Witvliet7](Witvliet7_data_graph.md), [Witvliet8](Witvliet8_data_graph.md), [WormNeuroAtlas](WormNeuroAtlas_data_graph.md), [Randi2023](Randi2023_data_graph.md), [RipollSanchezShortRange](RipollSanchezShortRange_data_graph.md), [RipollSanchezMidRange](RipollSanchezMidRange_data_graph.md), [RipollSanchezLongRange](RipollSanchezLongRange_data_graph.md), [SSData](SSData_data_graph.md), [UpdSSData](UpdSSData_data_graph.md), [UpdSSData2](UpdSSData2_data_graph.md) | [WormAtlas](https://www.wormatlas.org/neurons/Individual Neurons/RIPframeset.html)
OSB 3D | -| RIPR | Linker to pharynx | [White_A](White_A_data_graph.md), [White_L4](White_L4_data_graph.md), [White_whole](White_whole_data_graph.md), [Varshney](Varshney_data_graph.md), [Bentley2016_PEP](Bentley2016_PEP_data_graph.md), [Cook2019Herm](Cook2019Herm_data_graph.md), [Cook2019Male](Cook2019Male_data_graph.md), [Cook2020](Cook2020_data_graph.md), [Witvliet1](Witvliet1_data_graph.md), [Witvliet2](Witvliet2_data_graph.md), [Witvliet3](Witvliet3_data_graph.md), [Witvliet4](Witvliet4_data_graph.md), [Witvliet5](Witvliet5_data_graph.md), [Witvliet6](Witvliet6_data_graph.md), [Witvliet7](Witvliet7_data_graph.md), [Witvliet8](Witvliet8_data_graph.md), [WormNeuroAtlas](WormNeuroAtlas_data_graph.md), [Randi2023](Randi2023_data_graph.md), [RipollSanchezShortRange](RipollSanchezShortRange_data_graph.md), [RipollSanchezMidRange](RipollSanchezMidRange_data_graph.md), [RipollSanchezLongRange](RipollSanchezLongRange_data_graph.md), [SSData](SSData_data_graph.md), [UpdSSData](UpdSSData_data_graph.md), [UpdSSData2](UpdSSData2_data_graph.md) | [WormAtlas](https://www.wormatlas.org/neurons/Individual Neurons/RIPframeset.html)
OSB 3D | +| RIPR | Linker to pharynx | [White_A](White_A_data_graph.md), [White_L4](White_L4_data_graph.md), [White_whole](White_whole_data_graph.md), [Varshney](Varshney_data_graph.md), [Bentley2016_PEP](Bentley2016_PEP_data_graph.md), [Cook2019Herm](Cook2019Herm_data_graph.md), [Cook2019Male](Cook2019Male_data_graph.md), [Cook2020](Cook2020_data_graph.md), [Brittin2021](Brittin2021_data_graph.md), [Witvliet1](Witvliet1_data_graph.md), [Witvliet2](Witvliet2_data_graph.md), [Witvliet3](Witvliet3_data_graph.md), [Witvliet4](Witvliet4_data_graph.md), [Witvliet5](Witvliet5_data_graph.md), [Witvliet6](Witvliet6_data_graph.md), [Witvliet7](Witvliet7_data_graph.md), [Witvliet8](Witvliet8_data_graph.md), [WormNeuroAtlas](WormNeuroAtlas_data_graph.md), [Randi2023](Randi2023_data_graph.md), [RipollSanchezShortRange](RipollSanchezShortRange_data_graph.md), [RipollSanchezMidRange](RipollSanchezMidRange_data_graph.md), [RipollSanchezLongRange](RipollSanchezLongRange_data_graph.md), [SSData](SSData_data_graph.md), [UpdSSData](UpdSSData_data_graph.md), [UpdSSData2](UpdSSData2_data_graph.md) | [WormAtlas](https://www.wormatlas.org/neurons/Individual Neurons/RIPframeset.html)
OSB 3D | | RIR | Category 4 interneuron | [White_A](White_A_data_graph.md), [White_L4](White_L4_data_graph.md), [White_whole](White_whole_data_graph.md), [Varshney](Varshney_data_graph.md), [Bentley2016_PEP](Bentley2016_PEP_data_graph.md), [Cook2019Herm](Cook2019Herm_data_graph.md), [Cook2019Male](Cook2019Male_data_graph.md), [Brittin2021](Brittin2021_data_graph.md), [Witvliet1](Witvliet1_data_graph.md), [Witvliet2](Witvliet2_data_graph.md), [Witvliet3](Witvliet3_data_graph.md), [Witvliet4](Witvliet4_data_graph.md), [Witvliet5](Witvliet5_data_graph.md), [Witvliet6](Witvliet6_data_graph.md), [Witvliet7](Witvliet7_data_graph.md), [Witvliet8](Witvliet8_data_graph.md), [WormNeuroAtlas](WormNeuroAtlas_data_graph.md), [Randi2023](Randi2023_data_graph.md), [RipollSanchezShortRange](RipollSanchezShortRange_data_graph.md), [RipollSanchezMidRange](RipollSanchezMidRange_data_graph.md), [RipollSanchezLongRange](RipollSanchezLongRange_data_graph.md), [SSData](SSData_data_graph.md), [UpdSSData](UpdSSData_data_graph.md), [UpdSSData2](UpdSSData2_data_graph.md) | [WormAtlas](https://www.wormatlas.org/neurons/Individual Neurons/RIRframeset.html)
OSB 3D | | RIS | Layer 3 interneuron | [White_A](White_A_data_graph.md), [White_L4](White_L4_data_graph.md), [White_whole](White_whole_data_graph.md), [Varshney](Varshney_data_graph.md), [Bentley2016_MA](Bentley2016_MA_data_graph.md), [Bentley2016_PEP](Bentley2016_PEP_data_graph.md), [Cook2019Herm](Cook2019Herm_data_graph.md), [Cook2019Male](Cook2019Male_data_graph.md), [Brittin2021](Brittin2021_data_graph.md), [Witvliet1](Witvliet1_data_graph.md), [Witvliet2](Witvliet2_data_graph.md), [Witvliet3](Witvliet3_data_graph.md), [Witvliet4](Witvliet4_data_graph.md), [Witvliet5](Witvliet5_data_graph.md), [Witvliet6](Witvliet6_data_graph.md), [Witvliet7](Witvliet7_data_graph.md), [Witvliet8](Witvliet8_data_graph.md), [WormNeuroAtlas](WormNeuroAtlas_data_graph.md), [Randi2023](Randi2023_data_graph.md), [RipollSanchezShortRange](RipollSanchezShortRange_data_graph.md), [RipollSanchezMidRange](RipollSanchezMidRange_data_graph.md), [RipollSanchezLongRange](RipollSanchezLongRange_data_graph.md), [SSData](SSData_data_graph.md), [UpdSSData](UpdSSData_data_graph.md), [UpdSSData2](UpdSSData2_data_graph.md) | [WormAtlas](https://www.wormatlas.org/neurons/Individual Neurons/RISframeset.html)
OSB 3D | | RMFL | Layer 2 interneuron | [White_A](White_A_data_graph.md), [White_L4](White_L4_data_graph.md), [White_whole](White_whole_data_graph.md), [Varshney](Varshney_data_graph.md), [Bentley2016_MA](Bentley2016_MA_data_graph.md), [Bentley2016_PEP](Bentley2016_PEP_data_graph.md), [Cook2019Herm](Cook2019Herm_data_graph.md), [Cook2019Male](Cook2019Male_data_graph.md), [Brittin2021](Brittin2021_data_graph.md), [Witvliet5](Witvliet5_data_graph.md), [Witvliet6](Witvliet6_data_graph.md), [Witvliet7](Witvliet7_data_graph.md), [Witvliet8](Witvliet8_data_graph.md), [WormNeuroAtlas](WormNeuroAtlas_data_graph.md), [Randi2023](Randi2023_data_graph.md), [RipollSanchezShortRange](RipollSanchezShortRange_data_graph.md), [RipollSanchezMidRange](RipollSanchezMidRange_data_graph.md), [RipollSanchezLongRange](RipollSanchezLongRange_data_graph.md), [SSData](SSData_data_graph.md), [UpdSSData](UpdSSData_data_graph.md), [UpdSSData2](UpdSSData2_data_graph.md) | [WormAtlas](https://www.wormatlas.org/neurons/Individual Neurons/RMFframeset.html)
OSB 3D | @@ -672,7 +672,7 @@ title: C. elegans cells | SMDVL | Sublateral motor neuron | [White_A](White_A_data_graph.md), [White_L4](White_L4_data_graph.md), [White_whole](White_whole_data_graph.md), [Varshney](Varshney_data_graph.md), [Bentley2016_MA](Bentley2016_MA_data_graph.md), [Bentley2016_PEP](Bentley2016_PEP_data_graph.md), [Cook2019Herm](Cook2019Herm_data_graph.md), [Cook2019Male](Cook2019Male_data_graph.md), [Brittin2021](Brittin2021_data_graph.md), [Witvliet1](Witvliet1_data_graph.md), [Witvliet2](Witvliet2_data_graph.md), [Witvliet3](Witvliet3_data_graph.md), [Witvliet4](Witvliet4_data_graph.md), [Witvliet5](Witvliet5_data_graph.md), [Witvliet6](Witvliet6_data_graph.md), [Witvliet7](Witvliet7_data_graph.md), [Witvliet8](Witvliet8_data_graph.md), [WormNeuroAtlas](WormNeuroAtlas_data_graph.md), [Randi2023](Randi2023_data_graph.md), [RipollSanchezShortRange](RipollSanchezShortRange_data_graph.md), [RipollSanchezMidRange](RipollSanchezMidRange_data_graph.md), [RipollSanchezLongRange](RipollSanchezLongRange_data_graph.md), [SSData](SSData_data_graph.md), [UpdSSData](UpdSSData_data_graph.md), [UpdSSData2](UpdSSData2_data_graph.md) | [WormAtlas](https://www.wormatlas.org/neurons/Individual Neurons/SMDframeset.html)
OSB 3D | | SMDVR | Sublateral motor neuron | [White_A](White_A_data_graph.md), [White_L4](White_L4_data_graph.md), [White_whole](White_whole_data_graph.md), [Varshney](Varshney_data_graph.md), [Bentley2016_MA](Bentley2016_MA_data_graph.md), [Bentley2016_PEP](Bentley2016_PEP_data_graph.md), [Cook2019Herm](Cook2019Herm_data_graph.md), [Cook2019Male](Cook2019Male_data_graph.md), [Brittin2021](Brittin2021_data_graph.md), [Witvliet1](Witvliet1_data_graph.md), [Witvliet2](Witvliet2_data_graph.md), [Witvliet3](Witvliet3_data_graph.md), [Witvliet4](Witvliet4_data_graph.md), [Witvliet5](Witvliet5_data_graph.md), [Witvliet6](Witvliet6_data_graph.md), [Witvliet7](Witvliet7_data_graph.md), [Witvliet8](Witvliet8_data_graph.md), [WormNeuroAtlas](WormNeuroAtlas_data_graph.md), [Randi2023](Randi2023_data_graph.md), [RipollSanchezShortRange](RipollSanchezShortRange_data_graph.md), [RipollSanchezMidRange](RipollSanchezMidRange_data_graph.md), [RipollSanchezLongRange](RipollSanchezLongRange_data_graph.md), [SSData](SSData_data_graph.md), [UpdSSData](UpdSSData_data_graph.md), [UpdSSData2](UpdSSData2_data_graph.md) | [WormAtlas](https://www.wormatlas.org/neurons/Individual Neurons/SMDframeset.html)
OSB 3D | | URADL | Head motor neuron | [White_A](White_A_data_graph.md), [White_L4](White_L4_data_graph.md), [White_whole](White_whole_data_graph.md), [Varshney](Varshney_data_graph.md), [Bentley2016_PEP](Bentley2016_PEP_data_graph.md), [Cook2019Herm](Cook2019Herm_data_graph.md), [Cook2019Male](Cook2019Male_data_graph.md), [Brittin2021](Brittin2021_data_graph.md), [Witvliet1](Witvliet1_data_graph.md), [Witvliet2](Witvliet2_data_graph.md), [Witvliet3](Witvliet3_data_graph.md), [Witvliet4](Witvliet4_data_graph.md), [Witvliet5](Witvliet5_data_graph.md), [Witvliet6](Witvliet6_data_graph.md), [Witvliet7](Witvliet7_data_graph.md), [Witvliet8](Witvliet8_data_graph.md), [WormNeuroAtlas](WormNeuroAtlas_data_graph.md), [Randi2023](Randi2023_data_graph.md), [RipollSanchezShortRange](RipollSanchezShortRange_data_graph.md), [RipollSanchezMidRange](RipollSanchezMidRange_data_graph.md), [RipollSanchezLongRange](RipollSanchezLongRange_data_graph.md), [SSData](SSData_data_graph.md), [UpdSSData](UpdSSData_data_graph.md), [UpdSSData2](UpdSSData2_data_graph.md) | [WormAtlas](https://www.wormatlas.org/neurons/Individual Neurons/URAframeset.html)
OSB 3D | -| URADR | Head motor neuron | [White_A](White_A_data_graph.md), [White_L4](White_L4_data_graph.md), [White_whole](White_whole_data_graph.md), [Varshney](Varshney_data_graph.md), [Bentley2016_PEP](Bentley2016_PEP_data_graph.md), [Cook2019Herm](Cook2019Herm_data_graph.md), [Cook2019Male](Cook2019Male_data_graph.md), [Witvliet1](Witvliet1_data_graph.md), [Witvliet2](Witvliet2_data_graph.md), [Witvliet3](Witvliet3_data_graph.md), [Witvliet4](Witvliet4_data_graph.md), [Witvliet5](Witvliet5_data_graph.md), [Witvliet6](Witvliet6_data_graph.md), [Witvliet7](Witvliet7_data_graph.md), [Witvliet8](Witvliet8_data_graph.md), [WormNeuroAtlas](WormNeuroAtlas_data_graph.md), [Randi2023](Randi2023_data_graph.md), [RipollSanchezShortRange](RipollSanchezShortRange_data_graph.md), [RipollSanchezMidRange](RipollSanchezMidRange_data_graph.md), [RipollSanchezLongRange](RipollSanchezLongRange_data_graph.md), [SSData](SSData_data_graph.md), [UpdSSData](UpdSSData_data_graph.md), [UpdSSData2](UpdSSData2_data_graph.md) | [WormAtlas](https://www.wormatlas.org/neurons/Individual Neurons/URAframeset.html)
OSB 3D | +| URADR | Head motor neuron | [White_A](White_A_data_graph.md), [White_L4](White_L4_data_graph.md), [White_whole](White_whole_data_graph.md), [Varshney](Varshney_data_graph.md), [Bentley2016_PEP](Bentley2016_PEP_data_graph.md), [Cook2019Herm](Cook2019Herm_data_graph.md), [Cook2019Male](Cook2019Male_data_graph.md), [Brittin2021](Brittin2021_data_graph.md), [Witvliet1](Witvliet1_data_graph.md), [Witvliet2](Witvliet2_data_graph.md), [Witvliet3](Witvliet3_data_graph.md), [Witvliet4](Witvliet4_data_graph.md), [Witvliet5](Witvliet5_data_graph.md), [Witvliet6](Witvliet6_data_graph.md), [Witvliet7](Witvliet7_data_graph.md), [Witvliet8](Witvliet8_data_graph.md), [WormNeuroAtlas](WormNeuroAtlas_data_graph.md), [Randi2023](Randi2023_data_graph.md), [RipollSanchezShortRange](RipollSanchezShortRange_data_graph.md), [RipollSanchezMidRange](RipollSanchezMidRange_data_graph.md), [RipollSanchezLongRange](RipollSanchezLongRange_data_graph.md), [SSData](SSData_data_graph.md), [UpdSSData](UpdSSData_data_graph.md), [UpdSSData2](UpdSSData2_data_graph.md) | [WormAtlas](https://www.wormatlas.org/neurons/Individual Neurons/URAframeset.html)
OSB 3D | | URAVL | Head motor neuron | [White_A](White_A_data_graph.md), [White_L4](White_L4_data_graph.md), [White_whole](White_whole_data_graph.md), [Varshney](Varshney_data_graph.md), [Bentley2016_PEP](Bentley2016_PEP_data_graph.md), [Cook2019Herm](Cook2019Herm_data_graph.md), [Cook2019Male](Cook2019Male_data_graph.md), [Brittin2021](Brittin2021_data_graph.md), [Witvliet1](Witvliet1_data_graph.md), [Witvliet2](Witvliet2_data_graph.md), [Witvliet3](Witvliet3_data_graph.md), [Witvliet4](Witvliet4_data_graph.md), [Witvliet5](Witvliet5_data_graph.md), [Witvliet6](Witvliet6_data_graph.md), [Witvliet7](Witvliet7_data_graph.md), [Witvliet8](Witvliet8_data_graph.md), [WormNeuroAtlas](WormNeuroAtlas_data_graph.md), [Randi2023](Randi2023_data_graph.md), [RipollSanchezShortRange](RipollSanchezShortRange_data_graph.md), [RipollSanchezMidRange](RipollSanchezMidRange_data_graph.md), [RipollSanchezLongRange](RipollSanchezLongRange_data_graph.md), [SSData](SSData_data_graph.md), [UpdSSData](UpdSSData_data_graph.md), [UpdSSData2](UpdSSData2_data_graph.md) | [WormAtlas](https://www.wormatlas.org/neurons/Individual Neurons/URAframeset.html)
OSB 3D | | URAVR | Head motor neuron | [White_A](White_A_data_graph.md), [White_L4](White_L4_data_graph.md), [White_whole](White_whole_data_graph.md), [Varshney](Varshney_data_graph.md), [Bentley2016_PEP](Bentley2016_PEP_data_graph.md), [Cook2019Herm](Cook2019Herm_data_graph.md), [Cook2019Male](Cook2019Male_data_graph.md), [Brittin2021](Brittin2021_data_graph.md), [Witvliet1](Witvliet1_data_graph.md), [Witvliet2](Witvliet2_data_graph.md), [Witvliet3](Witvliet3_data_graph.md), [Witvliet4](Witvliet4_data_graph.md), [Witvliet5](Witvliet5_data_graph.md), [Witvliet6](Witvliet6_data_graph.md), [Witvliet7](Witvliet7_data_graph.md), [Witvliet8](Witvliet8_data_graph.md), [WormNeuroAtlas](WormNeuroAtlas_data_graph.md), [Randi2023](Randi2023_data_graph.md), [RipollSanchezShortRange](RipollSanchezShortRange_data_graph.md), [RipollSanchezMidRange](RipollSanchezMidRange_data_graph.md), [RipollSanchezLongRange](RipollSanchezLongRange_data_graph.md), [SSData](SSData_data_graph.md), [UpdSSData](UpdSSData_data_graph.md), [UpdSSData2](UpdSSData2_data_graph.md) | [WormAtlas](https://www.wormatlas.org/neurons/Individual Neurons/URAframeset.html)
OSB 3D | | VA1 | Ventral cord motor neuron | [White_whole](White_whole_data_graph.md), [Varshney](Varshney_data_graph.md), [Bentley2016_MA](Bentley2016_MA_data_graph.md), [Bentley2016_PEP](Bentley2016_PEP_data_graph.md), [Cook2019Herm](Cook2019Herm_data_graph.md), [Cook2019Male](Cook2019Male_data_graph.md), [WormNeuroAtlas](WormNeuroAtlas_data_graph.md), [Randi2023](Randi2023_data_graph.md), [RipollSanchezShortRange](RipollSanchezShortRange_data_graph.md), [RipollSanchezMidRange](RipollSanchezMidRange_data_graph.md), [RipollSanchezLongRange](RipollSanchezLongRange_data_graph.md), [SSData](SSData_data_graph.md), [UpdSSData](UpdSSData_data_graph.md), [UpdSSData2](UpdSSData2_data_graph.md) | [WormAtlas](https://www.wormatlas.org/neurons/Individual Neurons/VAframeset.html)
OSB 3D | @@ -764,7 +764,7 @@ title: C. elegans cells | ASEL | Amphid | [White_A](White_A_data_graph.md), [White_L4](White_L4_data_graph.md), [White_whole](White_whole_data_graph.md), [Varshney](Varshney_data_graph.md), [Bentley2016_MA](Bentley2016_MA_data_graph.md), [Bentley2016_PEP](Bentley2016_PEP_data_graph.md), [Cook2019Herm](Cook2019Herm_data_graph.md), [Cook2019Male](Cook2019Male_data_graph.md), [Brittin2021](Brittin2021_data_graph.md), [Witvliet1](Witvliet1_data_graph.md), [Witvliet2](Witvliet2_data_graph.md), [Witvliet3](Witvliet3_data_graph.md), [Witvliet4](Witvliet4_data_graph.md), [Witvliet5](Witvliet5_data_graph.md), [Witvliet6](Witvliet6_data_graph.md), [Witvliet7](Witvliet7_data_graph.md), [Witvliet8](Witvliet8_data_graph.md), [WormNeuroAtlas](WormNeuroAtlas_data_graph.md), [Randi2023](Randi2023_data_graph.md), [RipollSanchezShortRange](RipollSanchezShortRange_data_graph.md), [RipollSanchezMidRange](RipollSanchezMidRange_data_graph.md), [RipollSanchezLongRange](RipollSanchezLongRange_data_graph.md), [SSData](SSData_data_graph.md), [UpdSSData](UpdSSData_data_graph.md), [UpdSSData2](UpdSSData2_data_graph.md) | [WormAtlas](https://www.wormatlas.org/neurons/Individual Neurons/ASEframeset.html)
OSB 3D | | ASER | Amphid | [White_A](White_A_data_graph.md), [White_L4](White_L4_data_graph.md), [White_whole](White_whole_data_graph.md), [Varshney](Varshney_data_graph.md), [Bentley2016_MA](Bentley2016_MA_data_graph.md), [Bentley2016_PEP](Bentley2016_PEP_data_graph.md), [Cook2019Herm](Cook2019Herm_data_graph.md), [Cook2019Male](Cook2019Male_data_graph.md), [Brittin2021](Brittin2021_data_graph.md), [Witvliet1](Witvliet1_data_graph.md), [Witvliet2](Witvliet2_data_graph.md), [Witvliet3](Witvliet3_data_graph.md), [Witvliet4](Witvliet4_data_graph.md), [Witvliet5](Witvliet5_data_graph.md), [Witvliet6](Witvliet6_data_graph.md), [Witvliet7](Witvliet7_data_graph.md), [Witvliet8](Witvliet8_data_graph.md), [WormNeuroAtlas](WormNeuroAtlas_data_graph.md), [Randi2023](Randi2023_data_graph.md), [RipollSanchezShortRange](RipollSanchezShortRange_data_graph.md), [RipollSanchezMidRange](RipollSanchezMidRange_data_graph.md), [RipollSanchezLongRange](RipollSanchezLongRange_data_graph.md), [SSData](SSData_data_graph.md), [UpdSSData](UpdSSData_data_graph.md), [UpdSSData2](UpdSSData2_data_graph.md) | [WormAtlas](https://www.wormatlas.org/neurons/Individual Neurons/ASEframeset.html)
OSB 3D | | ASGL | Amphid | [White_A](White_A_data_graph.md), [White_L4](White_L4_data_graph.md), [White_whole](White_whole_data_graph.md), [Varshney](Varshney_data_graph.md), [Bentley2016_MA](Bentley2016_MA_data_graph.md), [Bentley2016_PEP](Bentley2016_PEP_data_graph.md), [Cook2019Herm](Cook2019Herm_data_graph.md), [Cook2019Male](Cook2019Male_data_graph.md), [Brittin2021](Brittin2021_data_graph.md), [Witvliet1](Witvliet1_data_graph.md), [Witvliet2](Witvliet2_data_graph.md), [Witvliet3](Witvliet3_data_graph.md), [Witvliet4](Witvliet4_data_graph.md), [Witvliet5](Witvliet5_data_graph.md), [Witvliet6](Witvliet6_data_graph.md), [Witvliet7](Witvliet7_data_graph.md), [Witvliet8](Witvliet8_data_graph.md), [WormNeuroAtlas](WormNeuroAtlas_data_graph.md), [Randi2023](Randi2023_data_graph.md), [RipollSanchezShortRange](RipollSanchezShortRange_data_graph.md), [RipollSanchezMidRange](RipollSanchezMidRange_data_graph.md), [RipollSanchezLongRange](RipollSanchezLongRange_data_graph.md), [SSData](SSData_data_graph.md), [UpdSSData](UpdSSData_data_graph.md), [UpdSSData2](UpdSSData2_data_graph.md) | [WormAtlas](https://www.wormatlas.org/neurons/Individual Neurons/ASGframeset.html)
OSB 3D | -| ASGR | Amphid | [White_A](White_A_data_graph.md), [White_L4](White_L4_data_graph.md), [White_whole](White_whole_data_graph.md), [Varshney](Varshney_data_graph.md), [Bentley2016_MA](Bentley2016_MA_data_graph.md), [Bentley2016_PEP](Bentley2016_PEP_data_graph.md), [Cook2019Herm](Cook2019Herm_data_graph.md), [Cook2019Male](Cook2019Male_data_graph.md), [Witvliet1](Witvliet1_data_graph.md), [Witvliet2](Witvliet2_data_graph.md), [Witvliet3](Witvliet3_data_graph.md), [Witvliet4](Witvliet4_data_graph.md), [Witvliet5](Witvliet5_data_graph.md), [Witvliet6](Witvliet6_data_graph.md), [Witvliet7](Witvliet7_data_graph.md), [Witvliet8](Witvliet8_data_graph.md), [WormNeuroAtlas](WormNeuroAtlas_data_graph.md), [Randi2023](Randi2023_data_graph.md), [RipollSanchezShortRange](RipollSanchezShortRange_data_graph.md), [RipollSanchezMidRange](RipollSanchezMidRange_data_graph.md), [RipollSanchezLongRange](RipollSanchezLongRange_data_graph.md), [SSData](SSData_data_graph.md), [UpdSSData](UpdSSData_data_graph.md), [UpdSSData2](UpdSSData2_data_graph.md) | [WormAtlas](https://www.wormatlas.org/neurons/Individual Neurons/ASGframeset.html)
OSB 3D | +| ASGR | Amphid | [White_A](White_A_data_graph.md), [White_L4](White_L4_data_graph.md), [White_whole](White_whole_data_graph.md), [Varshney](Varshney_data_graph.md), [Bentley2016_MA](Bentley2016_MA_data_graph.md), [Bentley2016_PEP](Bentley2016_PEP_data_graph.md), [Cook2019Herm](Cook2019Herm_data_graph.md), [Cook2019Male](Cook2019Male_data_graph.md), [Brittin2021](Brittin2021_data_graph.md), [Witvliet1](Witvliet1_data_graph.md), [Witvliet2](Witvliet2_data_graph.md), [Witvliet3](Witvliet3_data_graph.md), [Witvliet4](Witvliet4_data_graph.md), [Witvliet5](Witvliet5_data_graph.md), [Witvliet6](Witvliet6_data_graph.md), [Witvliet7](Witvliet7_data_graph.md), [Witvliet8](Witvliet8_data_graph.md), [WormNeuroAtlas](WormNeuroAtlas_data_graph.md), [Randi2023](Randi2023_data_graph.md), [RipollSanchezShortRange](RipollSanchezShortRange_data_graph.md), [RipollSanchezMidRange](RipollSanchezMidRange_data_graph.md), [RipollSanchezLongRange](RipollSanchezLongRange_data_graph.md), [SSData](SSData_data_graph.md), [UpdSSData](UpdSSData_data_graph.md), [UpdSSData2](UpdSSData2_data_graph.md) | [WormAtlas](https://www.wormatlas.org/neurons/Individual Neurons/ASGframeset.html)
OSB 3D | | ASHL | Amphid, nociceptive | [White_A](White_A_data_graph.md), [White_L4](White_L4_data_graph.md), [White_whole](White_whole_data_graph.md), [Varshney](Varshney_data_graph.md), [Bentley2016_MA](Bentley2016_MA_data_graph.md), [Bentley2016_PEP](Bentley2016_PEP_data_graph.md), [Cook2019Herm](Cook2019Herm_data_graph.md), [Cook2019Male](Cook2019Male_data_graph.md), [Brittin2021](Brittin2021_data_graph.md), [Witvliet1](Witvliet1_data_graph.md), [Witvliet2](Witvliet2_data_graph.md), [Witvliet3](Witvliet3_data_graph.md), [Witvliet4](Witvliet4_data_graph.md), [Witvliet5](Witvliet5_data_graph.md), [Witvliet6](Witvliet6_data_graph.md), [Witvliet7](Witvliet7_data_graph.md), [Witvliet8](Witvliet8_data_graph.md), [WormNeuroAtlas](WormNeuroAtlas_data_graph.md), [Randi2023](Randi2023_data_graph.md), [RipollSanchezShortRange](RipollSanchezShortRange_data_graph.md), [RipollSanchezMidRange](RipollSanchezMidRange_data_graph.md), [RipollSanchezLongRange](RipollSanchezLongRange_data_graph.md), [SSData](SSData_data_graph.md), [UpdSSData](UpdSSData_data_graph.md), [UpdSSData2](UpdSSData2_data_graph.md) | [WormAtlas](https://www.wormatlas.org/neurons/Individual Neurons/ASHframeset.html)
OSB 3D | | ASHR | Amphid, nociceptive | [White_A](White_A_data_graph.md), [White_L4](White_L4_data_graph.md), [White_whole](White_whole_data_graph.md), [Varshney](Varshney_data_graph.md), [Bentley2016_MA](Bentley2016_MA_data_graph.md), [Bentley2016_PEP](Bentley2016_PEP_data_graph.md), [Cook2019Herm](Cook2019Herm_data_graph.md), [Cook2019Male](Cook2019Male_data_graph.md), [Brittin2021](Brittin2021_data_graph.md), [Witvliet1](Witvliet1_data_graph.md), [Witvliet2](Witvliet2_data_graph.md), [Witvliet3](Witvliet3_data_graph.md), [Witvliet4](Witvliet4_data_graph.md), [Witvliet5](Witvliet5_data_graph.md), [Witvliet6](Witvliet6_data_graph.md), [Witvliet7](Witvliet7_data_graph.md), [Witvliet8](Witvliet8_data_graph.md), [WormNeuroAtlas](WormNeuroAtlas_data_graph.md), [Randi2023](Randi2023_data_graph.md), [RipollSanchezShortRange](RipollSanchezShortRange_data_graph.md), [RipollSanchezMidRange](RipollSanchezMidRange_data_graph.md), [RipollSanchezLongRange](RipollSanchezLongRange_data_graph.md), [SSData](SSData_data_graph.md), [UpdSSData](UpdSSData_data_graph.md), [UpdSSData2](UpdSSData2_data_graph.md), [Test](Test_data_graph.md) | [WormAtlas](https://www.wormatlas.org/neurons/Individual Neurons/ASHframeset.html)
OSB 3D | | ASIL | Amphid | [White_A](White_A_data_graph.md), [White_L4](White_L4_data_graph.md), [White_whole](White_whole_data_graph.md), [Varshney](Varshney_data_graph.md), [Bentley2016_MA](Bentley2016_MA_data_graph.md), [Bentley2016_PEP](Bentley2016_PEP_data_graph.md), [Cook2019Herm](Cook2019Herm_data_graph.md), [Cook2019Male](Cook2019Male_data_graph.md), [Brittin2021](Brittin2021_data_graph.md), [Witvliet1](Witvliet1_data_graph.md), [Witvliet2](Witvliet2_data_graph.md), [Witvliet3](Witvliet3_data_graph.md), [Witvliet4](Witvliet4_data_graph.md), [Witvliet5](Witvliet5_data_graph.md), [Witvliet6](Witvliet6_data_graph.md), [Witvliet7](Witvliet7_data_graph.md), [Witvliet8](Witvliet8_data_graph.md), [WormNeuroAtlas](WormNeuroAtlas_data_graph.md), [Randi2023](Randi2023_data_graph.md), [RipollSanchezShortRange](RipollSanchezShortRange_data_graph.md), [RipollSanchezMidRange](RipollSanchezMidRange_data_graph.md), [RipollSanchezLongRange](RipollSanchezLongRange_data_graph.md), [SSData](SSData_data_graph.md), [UpdSSData](UpdSSData_data_graph.md), [UpdSSData2](UpdSSData2_data_graph.md) | [WormAtlas](https://www.wormatlas.org/neurons/Individual Neurons/ASIframeset.html)
OSB 3D | @@ -775,7 +775,7 @@ title: C. elegans cells | ASKR | Amphid | [White_A](White_A_data_graph.md), [White_L4](White_L4_data_graph.md), [White_whole](White_whole_data_graph.md), [Varshney](Varshney_data_graph.md), [Bentley2016_MA](Bentley2016_MA_data_graph.md), [Bentley2016_PEP](Bentley2016_PEP_data_graph.md), [Cook2019Herm](Cook2019Herm_data_graph.md), [Cook2019Male](Cook2019Male_data_graph.md), [Brittin2021](Brittin2021_data_graph.md), [Witvliet1](Witvliet1_data_graph.md), [Witvliet2](Witvliet2_data_graph.md), [Witvliet3](Witvliet3_data_graph.md), [Witvliet4](Witvliet4_data_graph.md), [Witvliet5](Witvliet5_data_graph.md), [Witvliet6](Witvliet6_data_graph.md), [Witvliet7](Witvliet7_data_graph.md), [Witvliet8](Witvliet8_data_graph.md), [WormNeuroAtlas](WormNeuroAtlas_data_graph.md), [Randi2023](Randi2023_data_graph.md), [RipollSanchezShortRange](RipollSanchezShortRange_data_graph.md), [RipollSanchezMidRange](RipollSanchezMidRange_data_graph.md), [RipollSanchezLongRange](RipollSanchezLongRange_data_graph.md), [SSData](SSData_data_graph.md), [UpdSSData](UpdSSData_data_graph.md), [UpdSSData2](UpdSSData2_data_graph.md), [Test](Test_data_graph.md) | [WormAtlas](https://www.wormatlas.org/neurons/Individual Neurons/ASKframeset.html)
OSB 3D | | AVM | Mechanosensory | [White_A](White_A_data_graph.md), [White_L4](White_L4_data_graph.md), [White_whole](White_whole_data_graph.md), [Varshney](Varshney_data_graph.md), [Bentley2016_MA](Bentley2016_MA_data_graph.md), [Bentley2016_PEP](Bentley2016_PEP_data_graph.md), [Cook2019Herm](Cook2019Herm_data_graph.md), [Cook2019Male](Cook2019Male_data_graph.md), [Brittin2021](Brittin2021_data_graph.md), [Witvliet5](Witvliet5_data_graph.md), [Witvliet6](Witvliet6_data_graph.md), [Witvliet7](Witvliet7_data_graph.md), [Witvliet8](Witvliet8_data_graph.md), [WormNeuroAtlas](WormNeuroAtlas_data_graph.md), [RipollSanchezShortRange](RipollSanchezShortRange_data_graph.md), [RipollSanchezMidRange](RipollSanchezMidRange_data_graph.md), [RipollSanchezLongRange](RipollSanchezLongRange_data_graph.md), [SSData](SSData_data_graph.md), [UpdSSData](UpdSSData_data_graph.md), [UpdSSData2](UpdSSData2_data_graph.md) | [WormAtlas](https://www.wormatlas.org/neurons/Individual Neurons/AVMframeset.html)
OSB 3D | | AWAL | Amphid | [White_A](White_A_data_graph.md), [White_L4](White_L4_data_graph.md), [White_whole](White_whole_data_graph.md), [Varshney](Varshney_data_graph.md), [Bentley2016_PEP](Bentley2016_PEP_data_graph.md), [Cook2019Herm](Cook2019Herm_data_graph.md), [Cook2019Male](Cook2019Male_data_graph.md), [Brittin2021](Brittin2021_data_graph.md), [Witvliet1](Witvliet1_data_graph.md), [Witvliet2](Witvliet2_data_graph.md), [Witvliet3](Witvliet3_data_graph.md), [Witvliet4](Witvliet4_data_graph.md), [Witvliet5](Witvliet5_data_graph.md), [Witvliet6](Witvliet6_data_graph.md), [Witvliet7](Witvliet7_data_graph.md), [Witvliet8](Witvliet8_data_graph.md), [WormNeuroAtlas](WormNeuroAtlas_data_graph.md), [Randi2023](Randi2023_data_graph.md), [RipollSanchezShortRange](RipollSanchezShortRange_data_graph.md), [RipollSanchezMidRange](RipollSanchezMidRange_data_graph.md), [RipollSanchezLongRange](RipollSanchezLongRange_data_graph.md), [SSData](SSData_data_graph.md), [UpdSSData](UpdSSData_data_graph.md), [UpdSSData2](UpdSSData2_data_graph.md) | [WormAtlas](https://www.wormatlas.org/neurons/Individual Neurons/AWAframeset.html)
OSB 3D | -| AWAR | Amphid | [White_A](White_A_data_graph.md), [White_L4](White_L4_data_graph.md), [White_whole](White_whole_data_graph.md), [Varshney](Varshney_data_graph.md), [Bentley2016_PEP](Bentley2016_PEP_data_graph.md), [Cook2019Herm](Cook2019Herm_data_graph.md), [Cook2019Male](Cook2019Male_data_graph.md), [Witvliet1](Witvliet1_data_graph.md), [Witvliet2](Witvliet2_data_graph.md), [Witvliet3](Witvliet3_data_graph.md), [Witvliet4](Witvliet4_data_graph.md), [Witvliet5](Witvliet5_data_graph.md), [Witvliet6](Witvliet6_data_graph.md), [Witvliet7](Witvliet7_data_graph.md), [Witvliet8](Witvliet8_data_graph.md), [WormNeuroAtlas](WormNeuroAtlas_data_graph.md), [Randi2023](Randi2023_data_graph.md), [RipollSanchezShortRange](RipollSanchezShortRange_data_graph.md), [RipollSanchezMidRange](RipollSanchezMidRange_data_graph.md), [RipollSanchezLongRange](RipollSanchezLongRange_data_graph.md), [SSData](SSData_data_graph.md), [UpdSSData](UpdSSData_data_graph.md), [UpdSSData2](UpdSSData2_data_graph.md) | [WormAtlas](https://www.wormatlas.org/neurons/Individual Neurons/AWAframeset.html)
OSB 3D | +| AWAR | Amphid | [White_A](White_A_data_graph.md), [White_L4](White_L4_data_graph.md), [White_whole](White_whole_data_graph.md), [Varshney](Varshney_data_graph.md), [Bentley2016_PEP](Bentley2016_PEP_data_graph.md), [Cook2019Herm](Cook2019Herm_data_graph.md), [Cook2019Male](Cook2019Male_data_graph.md), [Brittin2021](Brittin2021_data_graph.md), [Witvliet1](Witvliet1_data_graph.md), [Witvliet2](Witvliet2_data_graph.md), [Witvliet3](Witvliet3_data_graph.md), [Witvliet4](Witvliet4_data_graph.md), [Witvliet5](Witvliet5_data_graph.md), [Witvliet6](Witvliet6_data_graph.md), [Witvliet7](Witvliet7_data_graph.md), [Witvliet8](Witvliet8_data_graph.md), [WormNeuroAtlas](WormNeuroAtlas_data_graph.md), [Randi2023](Randi2023_data_graph.md), [RipollSanchezShortRange](RipollSanchezShortRange_data_graph.md), [RipollSanchezMidRange](RipollSanchezMidRange_data_graph.md), [RipollSanchezLongRange](RipollSanchezLongRange_data_graph.md), [SSData](SSData_data_graph.md), [UpdSSData](UpdSSData_data_graph.md), [UpdSSData2](UpdSSData2_data_graph.md) | [WormAtlas](https://www.wormatlas.org/neurons/Individual Neurons/AWAframeset.html)
OSB 3D | | AWBL | Amphid | [White_A](White_A_data_graph.md), [White_L4](White_L4_data_graph.md), [White_whole](White_whole_data_graph.md), [Varshney](Varshney_data_graph.md), [Bentley2016_MA](Bentley2016_MA_data_graph.md), [Bentley2016_PEP](Bentley2016_PEP_data_graph.md), [Cook2019Herm](Cook2019Herm_data_graph.md), [Cook2019Male](Cook2019Male_data_graph.md), [Brittin2021](Brittin2021_data_graph.md), [Witvliet1](Witvliet1_data_graph.md), [Witvliet2](Witvliet2_data_graph.md), [Witvliet3](Witvliet3_data_graph.md), [Witvliet4](Witvliet4_data_graph.md), [Witvliet5](Witvliet5_data_graph.md), [Witvliet6](Witvliet6_data_graph.md), [Witvliet7](Witvliet7_data_graph.md), [Witvliet8](Witvliet8_data_graph.md), [WormNeuroAtlas](WormNeuroAtlas_data_graph.md), [Randi2023](Randi2023_data_graph.md), [RipollSanchezShortRange](RipollSanchezShortRange_data_graph.md), [RipollSanchezMidRange](RipollSanchezMidRange_data_graph.md), [RipollSanchezLongRange](RipollSanchezLongRange_data_graph.md), [SSData](SSData_data_graph.md), [UpdSSData](UpdSSData_data_graph.md), [UpdSSData2](UpdSSData2_data_graph.md) | [WormAtlas](https://www.wormatlas.org/neurons/Individual Neurons/AWBframeset.html)
OSB 3D | | AWBR | Amphid | [White_A](White_A_data_graph.md), [White_L4](White_L4_data_graph.md), [White_whole](White_whole_data_graph.md), [Varshney](Varshney_data_graph.md), [Bentley2016_MA](Bentley2016_MA_data_graph.md), [Bentley2016_PEP](Bentley2016_PEP_data_graph.md), [Cook2019Herm](Cook2019Herm_data_graph.md), [Cook2019Male](Cook2019Male_data_graph.md), [Brittin2021](Brittin2021_data_graph.md), [Witvliet1](Witvliet1_data_graph.md), [Witvliet2](Witvliet2_data_graph.md), [Witvliet3](Witvliet3_data_graph.md), [Witvliet4](Witvliet4_data_graph.md), [Witvliet5](Witvliet5_data_graph.md), [Witvliet6](Witvliet6_data_graph.md), [Witvliet7](Witvliet7_data_graph.md), [Witvliet8](Witvliet8_data_graph.md), [WormNeuroAtlas](WormNeuroAtlas_data_graph.md), [Randi2023](Randi2023_data_graph.md), [RipollSanchezShortRange](RipollSanchezShortRange_data_graph.md), [RipollSanchezMidRange](RipollSanchezMidRange_data_graph.md), [RipollSanchezLongRange](RipollSanchezLongRange_data_graph.md), [SSData](SSData_data_graph.md), [UpdSSData](UpdSSData_data_graph.md), [UpdSSData2](UpdSSData2_data_graph.md), [Test](Test_data_graph.md) | [WormAtlas](https://www.wormatlas.org/neurons/Individual Neurons/AWBframeset.html)
OSB 3D | | AWCL | Amphid | [White_A](White_A_data_graph.md), [White_L4](White_L4_data_graph.md), [White_whole](White_whole_data_graph.md), [Varshney](Varshney_data_graph.md), [Bentley2016_PEP](Bentley2016_PEP_data_graph.md), [Cook2019Herm](Cook2019Herm_data_graph.md), [Cook2019Male](Cook2019Male_data_graph.md), [Brittin2021](Brittin2021_data_graph.md), [Witvliet1](Witvliet1_data_graph.md), [Witvliet2](Witvliet2_data_graph.md), [Witvliet3](Witvliet3_data_graph.md), [Witvliet4](Witvliet4_data_graph.md), [Witvliet5](Witvliet5_data_graph.md), [Witvliet6](Witvliet6_data_graph.md), [Witvliet7](Witvliet7_data_graph.md), [Witvliet8](Witvliet8_data_graph.md), [Randi2023](Randi2023_data_graph.md), [RipollSanchezShortRange](RipollSanchezShortRange_data_graph.md), [RipollSanchezMidRange](RipollSanchezMidRange_data_graph.md), [RipollSanchezLongRange](RipollSanchezLongRange_data_graph.md), [SSData](SSData_data_graph.md), [UpdSSData](UpdSSData_data_graph.md), [UpdSSData2](UpdSSData2_data_graph.md) | [WormAtlas](https://www.wormatlas.org/neurons/Individual Neurons/AWCframeset.html)
OSB 3D | @@ -802,7 +802,7 @@ title: C. elegans cells | IL1VL | Cephalic | [White_A](White_A_data_graph.md), [White_L4](White_L4_data_graph.md), [White_whole](White_whole_data_graph.md), [Varshney](Varshney_data_graph.md), [Bentley2016_MA](Bentley2016_MA_data_graph.md), [Bentley2016_PEP](Bentley2016_PEP_data_graph.md), [Cook2019Herm](Cook2019Herm_data_graph.md), [Cook2019Male](Cook2019Male_data_graph.md), [Brittin2021](Brittin2021_data_graph.md), [Witvliet1](Witvliet1_data_graph.md), [Witvliet2](Witvliet2_data_graph.md), [Witvliet3](Witvliet3_data_graph.md), [Witvliet4](Witvliet4_data_graph.md), [Witvliet5](Witvliet5_data_graph.md), [Witvliet6](Witvliet6_data_graph.md), [Witvliet7](Witvliet7_data_graph.md), [Witvliet8](Witvliet8_data_graph.md), [WormNeuroAtlas](WormNeuroAtlas_data_graph.md), [Randi2023](Randi2023_data_graph.md), [RipollSanchezShortRange](RipollSanchezShortRange_data_graph.md), [RipollSanchezMidRange](RipollSanchezMidRange_data_graph.md), [RipollSanchezLongRange](RipollSanchezLongRange_data_graph.md), [SSData](SSData_data_graph.md), [UpdSSData](UpdSSData_data_graph.md), [UpdSSData2](UpdSSData2_data_graph.md) | [WormAtlas](https://www.wormatlas.org/neurons/Individual Neurons/IL1frameset.html)
OSB 3D | | IL1VR | Cephalic | [White_A](White_A_data_graph.md), [White_L4](White_L4_data_graph.md), [White_whole](White_whole_data_graph.md), [Varshney](Varshney_data_graph.md), [Bentley2016_MA](Bentley2016_MA_data_graph.md), [Bentley2016_PEP](Bentley2016_PEP_data_graph.md), [Cook2019Herm](Cook2019Herm_data_graph.md), [Cook2019Male](Cook2019Male_data_graph.md), [Brittin2021](Brittin2021_data_graph.md), [Witvliet1](Witvliet1_data_graph.md), [Witvliet2](Witvliet2_data_graph.md), [Witvliet3](Witvliet3_data_graph.md), [Witvliet4](Witvliet4_data_graph.md), [Witvliet5](Witvliet5_data_graph.md), [Witvliet6](Witvliet6_data_graph.md), [Witvliet7](Witvliet7_data_graph.md), [Witvliet8](Witvliet8_data_graph.md), [WormNeuroAtlas](WormNeuroAtlas_data_graph.md), [Randi2023](Randi2023_data_graph.md), [RipollSanchezShortRange](RipollSanchezShortRange_data_graph.md), [RipollSanchezMidRange](RipollSanchezMidRange_data_graph.md), [RipollSanchezLongRange](RipollSanchezLongRange_data_graph.md), [SSData](SSData_data_graph.md), [UpdSSData](UpdSSData_data_graph.md), [UpdSSData2](UpdSSData2_data_graph.md) | [WormAtlas](https://www.wormatlas.org/neurons/Individual Neurons/IL1frameset.html)
OSB 3D | | IL2DL | Cephalic | [White_A](White_A_data_graph.md), [White_L4](White_L4_data_graph.md), [White_whole](White_whole_data_graph.md), [Varshney](Varshney_data_graph.md), [Bentley2016_MA](Bentley2016_MA_data_graph.md), [Bentley2016_PEP](Bentley2016_PEP_data_graph.md), [Cook2019Herm](Cook2019Herm_data_graph.md), [Cook2019Male](Cook2019Male_data_graph.md), [Brittin2021](Brittin2021_data_graph.md), [Witvliet1](Witvliet1_data_graph.md), [Witvliet2](Witvliet2_data_graph.md), [Witvliet3](Witvliet3_data_graph.md), [Witvliet4](Witvliet4_data_graph.md), [Witvliet5](Witvliet5_data_graph.md), [Witvliet6](Witvliet6_data_graph.md), [Witvliet7](Witvliet7_data_graph.md), [Witvliet8](Witvliet8_data_graph.md), [WormNeuroAtlas](WormNeuroAtlas_data_graph.md), [Randi2023](Randi2023_data_graph.md), [RipollSanchezShortRange](RipollSanchezShortRange_data_graph.md), [RipollSanchezMidRange](RipollSanchezMidRange_data_graph.md), [RipollSanchezLongRange](RipollSanchezLongRange_data_graph.md), [SSData](SSData_data_graph.md), [UpdSSData](UpdSSData_data_graph.md), [UpdSSData2](UpdSSData2_data_graph.md) | [WormAtlas](https://www.wormatlas.org/neurons/Individual Neurons/IL2frameset.html)
OSB 3D | -| IL2DR | Cephalic | [White_A](White_A_data_graph.md), [White_L4](White_L4_data_graph.md), [White_whole](White_whole_data_graph.md), [Varshney](Varshney_data_graph.md), [Bentley2016_MA](Bentley2016_MA_data_graph.md), [Bentley2016_PEP](Bentley2016_PEP_data_graph.md), [Cook2019Herm](Cook2019Herm_data_graph.md), [Cook2019Male](Cook2019Male_data_graph.md), [Witvliet1](Witvliet1_data_graph.md), [Witvliet2](Witvliet2_data_graph.md), [Witvliet3](Witvliet3_data_graph.md), [Witvliet4](Witvliet4_data_graph.md), [Witvliet5](Witvliet5_data_graph.md), [Witvliet6](Witvliet6_data_graph.md), [Witvliet7](Witvliet7_data_graph.md), [Witvliet8](Witvliet8_data_graph.md), [WormNeuroAtlas](WormNeuroAtlas_data_graph.md), [Randi2023](Randi2023_data_graph.md), [RipollSanchezShortRange](RipollSanchezShortRange_data_graph.md), [RipollSanchezMidRange](RipollSanchezMidRange_data_graph.md), [RipollSanchezLongRange](RipollSanchezLongRange_data_graph.md), [SSData](SSData_data_graph.md), [UpdSSData](UpdSSData_data_graph.md), [UpdSSData2](UpdSSData2_data_graph.md) | [WormAtlas](https://www.wormatlas.org/neurons/Individual Neurons/IL2frameset.html)
OSB 3D | +| IL2DR | Cephalic | [White_A](White_A_data_graph.md), [White_L4](White_L4_data_graph.md), [White_whole](White_whole_data_graph.md), [Varshney](Varshney_data_graph.md), [Bentley2016_MA](Bentley2016_MA_data_graph.md), [Bentley2016_PEP](Bentley2016_PEP_data_graph.md), [Cook2019Herm](Cook2019Herm_data_graph.md), [Cook2019Male](Cook2019Male_data_graph.md), [Brittin2021](Brittin2021_data_graph.md), [Witvliet1](Witvliet1_data_graph.md), [Witvliet2](Witvliet2_data_graph.md), [Witvliet3](Witvliet3_data_graph.md), [Witvliet4](Witvliet4_data_graph.md), [Witvliet5](Witvliet5_data_graph.md), [Witvliet6](Witvliet6_data_graph.md), [Witvliet7](Witvliet7_data_graph.md), [Witvliet8](Witvliet8_data_graph.md), [WormNeuroAtlas](WormNeuroAtlas_data_graph.md), [Randi2023](Randi2023_data_graph.md), [RipollSanchezShortRange](RipollSanchezShortRange_data_graph.md), [RipollSanchezMidRange](RipollSanchezMidRange_data_graph.md), [RipollSanchezLongRange](RipollSanchezLongRange_data_graph.md), [SSData](SSData_data_graph.md), [UpdSSData](UpdSSData_data_graph.md), [UpdSSData2](UpdSSData2_data_graph.md) | [WormAtlas](https://www.wormatlas.org/neurons/Individual Neurons/IL2frameset.html)
OSB 3D | | IL2L | Cephalic | [White_A](White_A_data_graph.md), [White_L4](White_L4_data_graph.md), [White_whole](White_whole_data_graph.md), [Varshney](Varshney_data_graph.md), [Bentley2016_MA](Bentley2016_MA_data_graph.md), [Bentley2016_PEP](Bentley2016_PEP_data_graph.md), [Cook2019Herm](Cook2019Herm_data_graph.md), [Cook2019Male](Cook2019Male_data_graph.md), [Brittin2021](Brittin2021_data_graph.md), [Witvliet1](Witvliet1_data_graph.md), [Witvliet2](Witvliet2_data_graph.md), [Witvliet3](Witvliet3_data_graph.md), [Witvliet4](Witvliet4_data_graph.md), [Witvliet5](Witvliet5_data_graph.md), [Witvliet6](Witvliet6_data_graph.md), [Witvliet7](Witvliet7_data_graph.md), [Witvliet8](Witvliet8_data_graph.md), [WormNeuroAtlas](WormNeuroAtlas_data_graph.md), [Randi2023](Randi2023_data_graph.md), [RipollSanchezShortRange](RipollSanchezShortRange_data_graph.md), [RipollSanchezMidRange](RipollSanchezMidRange_data_graph.md), [RipollSanchezLongRange](RipollSanchezLongRange_data_graph.md), [SSData](SSData_data_graph.md), [UpdSSData](UpdSSData_data_graph.md), [UpdSSData2](UpdSSData2_data_graph.md) | [WormAtlas](https://www.wormatlas.org/neurons/Individual Neurons/IL2frameset.html)
OSB 3D | | IL2R | Cephalic | [White_A](White_A_data_graph.md), [White_L4](White_L4_data_graph.md), [White_whole](White_whole_data_graph.md), [Varshney](Varshney_data_graph.md), [Bentley2016_MA](Bentley2016_MA_data_graph.md), [Bentley2016_PEP](Bentley2016_PEP_data_graph.md), [Cook2019Herm](Cook2019Herm_data_graph.md), [Cook2019Male](Cook2019Male_data_graph.md), [Brittin2021](Brittin2021_data_graph.md), [Witvliet1](Witvliet1_data_graph.md), [Witvliet2](Witvliet2_data_graph.md), [Witvliet3](Witvliet3_data_graph.md), [Witvliet4](Witvliet4_data_graph.md), [Witvliet5](Witvliet5_data_graph.md), [Witvliet6](Witvliet6_data_graph.md), [Witvliet7](Witvliet7_data_graph.md), [Witvliet8](Witvliet8_data_graph.md), [WormNeuroAtlas](WormNeuroAtlas_data_graph.md), [Randi2023](Randi2023_data_graph.md), [RipollSanchezShortRange](RipollSanchezShortRange_data_graph.md), [RipollSanchezMidRange](RipollSanchezMidRange_data_graph.md), [RipollSanchezLongRange](RipollSanchezLongRange_data_graph.md), [SSData](SSData_data_graph.md), [UpdSSData](UpdSSData_data_graph.md), [UpdSSData2](UpdSSData2_data_graph.md) | [WormAtlas](https://www.wormatlas.org/neurons/Individual Neurons/IL2frameset.html)
OSB 3D | | IL2VL | Cephalic | [White_A](White_A_data_graph.md), [White_L4](White_L4_data_graph.md), [White_whole](White_whole_data_graph.md), [Varshney](Varshney_data_graph.md), [Bentley2016_MA](Bentley2016_MA_data_graph.md), [Bentley2016_PEP](Bentley2016_PEP_data_graph.md), [Cook2019Herm](Cook2019Herm_data_graph.md), [Cook2019Male](Cook2019Male_data_graph.md), [Brittin2021](Brittin2021_data_graph.md), [Witvliet1](Witvliet1_data_graph.md), [Witvliet2](Witvliet2_data_graph.md), [Witvliet3](Witvliet3_data_graph.md), [Witvliet4](Witvliet4_data_graph.md), [Witvliet5](Witvliet5_data_graph.md), [Witvliet6](Witvliet6_data_graph.md), [Witvliet7](Witvliet7_data_graph.md), [Witvliet8](Witvliet8_data_graph.md), [WormNeuroAtlas](WormNeuroAtlas_data_graph.md), [Randi2023](Randi2023_data_graph.md), [RipollSanchezShortRange](RipollSanchezShortRange_data_graph.md), [RipollSanchezMidRange](RipollSanchezMidRange_data_graph.md), [RipollSanchezLongRange](RipollSanchezLongRange_data_graph.md), [SSData](SSData_data_graph.md), [UpdSSData](UpdSSData_data_graph.md), [UpdSSData2](UpdSSData2_data_graph.md) | [WormAtlas](https://www.wormatlas.org/neurons/Individual Neurons/IL2frameset.html)
OSB 3D | diff --git a/docs/Comparison.md b/docs/Comparison.md index a971fb267..825805acb 100644 --- a/docs/Comparison.md +++ b/docs/Comparison.md @@ -1,855 +1,483 @@ # Comparison between data readers - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + - - - - + + - - - - + + + + - - + + + + -
White AWhite L4White wholeVarshneyBentley 2016 Monoamin.Bentley 2016 Peptid.Cook 2019 HermCook 2019 MaleCook 2020Brittin 2021Witvliet 1Witvliet 2Witvliet 3Witvliet 4Witvliet 5Witvliet 6Witvliet 7Witvliet 8WormNeuroAtlasRandi 2023RipollSanchez ShortRangeRipollSanchez MidRangeRipollSanchez LongRange Pharyngeal neuronsSensory neuronsInterneuronsMotorneuronsUnknown function neuronsBody wall musclesOther musclesOther cellsMale specific neuronsMale specific muscles Male other cells
Pharyngeal neurons - - -           
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White et al. 1986 N2U/Adult + +                
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Sensory neurons -           
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White et al. 1986 JSU/L4 + +                
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          -
          
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+   +
+       + + +
Interneurons -           
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-          
-          
-          
-          
-          -
          
-          
-          
-          
-          
-          
-          -
          
-          
-          
-          
-          
-          
-          -
          
-          
-          
-          
-          
-          
-          
-   -
          
-          
-          
-          
-          
-          
-          
-    -
          
-          
-          
-          
-          
-          
-          
-      -
          
-          
-          
-          
-          
-          
-          
-      -
          
-          
-          
-          
-          
-          
-          
-          
-  -
          
-          
-          
-          
-          
-          
-  -
          
-          
-          
-          
-          
-          
-          
-          
-  -
          
-          
-          
-          
-          
-          
-          
-          
-  -
          
-          
-          
-          
-          
-          
-          
-          
-  +
White et al. 1986 Whole worm +                
+      +
               
+               
+               
+               
+               
+         +
               
+               
+               
+               
+               
+       +
               
+               
+               
+               
+               
+               
+               
+            +
+ +     +        + + +
Motorneurons -           
-          
-          
-       -
          
-          
-          
-     -
          
-          
-          
-          
-          
-          
-          
-          
-          
-          
-          
-       -
          
-          
-          
-          
-          
-          
-          
-          
-          
-          
-          
-      -
          
-          
-          
-          
-          
-          
-          
-          
-          
+
Varshney et al. 2011 + +                
+               
+               
+               
+               
+         +
               
+               
+               
+               
+               
+       +
               
+               
+               
+               
+               
+               
+               
+           +
+ + + + + + +
Bentley et al. 2016 Monoamin. +                
+    +
               
+               
+               
+               
+              +
               
+               
+              +
               
+               
+               
+               
+               
+               
          -
          
-          
-          
-          
-          
-          
-          
-          
-          
-          
-          
-       -
          
-          
-          
-          
-          
-          
-          
-          
-          
-          
-          
-       -
          
-          
-          
-          
-          
-          
-          
-          
-          
-          
-         -
-           
-          
-          
-    -
          
-          
-          
-   -
          
-          
-          
-   -
          
-          
-          
-   -
          
-          
-          
-     -
          
-          
-          
-      -
          
-          
-          
-     -
          
-          
-          
-       -
          
-          
-          
-       -
          
-          
-          
-          
-          
-          
-          
-          
-          
-          
-          
-       -
          
-          
-          
-          
-   -
          
-          
-          
-          
-          
-          
-          
-          
-          
-          
-          
-       -
          
-          
-          
-          
-          
-          
-          
-          
-          
-          
-          
-       -
          
-          
-          
-          
-          
-          
-          
-          
-          
-          
-          
-       +
+ + + + + +
Unknown function neurons - - - - - - -    -    - - - - - - - -   -   - - - -    -    -    +Bentley et al. 2016 Peptid. +                
+      +
               
+               
+               
+               
+               
+         +
               
+               
+               
+               
+               
+       +
               
+               
+               
+               
+               
+               
+               
+            +
+ + + + + +
Body wall muscles -           
-          
-          
-   -
          
-          
-          
-   -
- - - -           
-          
-          
-          
-          
-          
-          
-          
-          
-      -
          
-          
-          
-          
-          
-          
-          
-          
-          
+
Cook et al. 2019 Herm +                
+      +
               
+               
+               
+               
+               
+         +
               
+               
+               
+               
+               
+       +
               
+               
+               
+               
+               
+               
+               
+            +
   +                
+               
+               
+               
+               
+               
      -
- -           
-        -
          
-          
-  -
          
-          
-        -
          
-          
-       -
          
-          
-         -
          
-          
-          
-   -
          
-          
-          
-   -
          
-          
-          
-   -
- - - - +                
+               
+         +
               
+               
+       +
+ +
Other muscles - - -     - - - -           
-          
-          
-         -
          
-          
-   -
          
-          
- -
- - - - - - - - - - - - - +Cook et al. 2019 Male +                
+      +
               
+               
+               
+               
+               
+        +
               
+               
+               
+               
+               
+      +
               
+               
+               
+               
+               
+               
+               
+    +
   +                
+               
+               
+               
+               
+               
+      +
               
+        +
               
+               
+   +
               
+               
+               
+               
+               
+               +
               
+               
+        +
              
Other cells -           -       -        - - - -           
-          
-          
+
Cook et al. 2020 +                
+      +
+    + + + +                
+      +
               
       -
          
-          
-          
-   -
          
-          
-  -
-           -           
-  -
          -           
- -
          -           -           -         - - - - - + + + +
Brittin et al. 2021 + +                
+               
+               
+               
+        +
               
+               
+               
+               
+             +
               
+               
+     +
+ + + + + + +
Witvliet et al. 2021 1 (L1) + +                
+               
+               
+               
+  +
               
+               
+               
+               
+         +
               
+               
+   +
+                
+   +
+           + + +
Male specific neurons - - - - - - - -           
-          
-          
-          
-          
-          
-          
-          
-          -
- - - - - - - - - - - - - - +Witvliet et al. 2021 5 (L2) + +                
+               
+               
+               
+        +
               
+               
+               
+               
+             +
               
+               
+      +
+                
+              +
+           + + +
Male specific muscles - - - - - - - -           
-          
-          
-        -
- - - - - - - - - - - - - - +Witvliet et al. 2021 6 (L3) + +                
+               
+               
+               
+        +
               
+               
+               
+               
+              +
               
+               
+     +
  +                
+               
+   +
+           + + + +
Witvliet et al. 2021 8 (Adult) + +                
+               
+               
+               
+          +
               
+               
+               
+               
+               
+ +
               
+               
+       +
+                
+               
+   +
+         + + + +
Randi et al. 2023 +                
+     +
               
+               
+               
+               +
               
+               
+               
+               
+  +
               
+               
+             +
+ + + + + +
Male other cells - - - - - - - -           
-     -
- - - - - - - - - - - - - - +Ripoll Sanchez et al. 2023 ShortRange +                
+      +
               
+               
+               
+               
+               
+         +
               
+               
+               
+               
+               
+       +
               
+               
+               
+               
+               
+               
+               
+            +
   + + + + + +
@@ -865,7 +493,7 @@ | [Cook2019Herm](Cook2019Herm_data.md) | 302 | 0 | 36 | 119 | 5908 | 183 | 1084 | Gen_CS (3709)
Gen_GJ (2199)
| Gen_CS (1051)
Gen_GJ (33)
| | [Cook2019Male](Cook2019Male_data.md) | 292 | 10 | 135 | 147 | 5923 | 209 | 1174 | Gen_CS (4048)
Gen_GJ (1875)
| Gen_CS (1134)
Gen_GJ (40)
| | [Cook2020](Cook2020_data.md) | 22 | 280 | 21 | 19 | 456 | 20 | 218 | Gen_CS (336)
Gen_GJ (120)
| Gen_CS (176)
Gen_GJ (42)
| -| [Brittin2021](Brittin2021_data.md) | 167 | 135 | 0 | 0 | 1258 | 0 | 0 | Contact (1258)
| | +| [Brittin2021](Brittin2021_data.md) | 173 | 129 | 0 | 0 | 5032 | 0 | 0 | Contact (5032)
| | | [Witvliet1](Witvliet1_data.md) | 161 | 141 | 9 | 17 | 841 | 33 | 78 | Gen_CS (675)
Gen_GJ (166)
| Gen_CS (78)
| | [Witvliet2](Witvliet2_data.md) | 162 | 140 | 11 | 21 | 1107 | 32 | 91 | Gen_CS (865)
Gen_GJ (242)
| Gen_CS (91)
| | [Witvliet3](Witvliet3_data.md) | 162 | 140 | 9 | 27 | 1075 | 35 | 100 | Gen_CS (887)
Gen_GJ (188)
| Gen_CS (100)
| diff --git a/docs/Comparison_table.html b/docs/Comparison_table.html index 861735866..925e6cf72 100644 --- a/docs/Comparison_table.html +++ b/docs/Comparison_table.html @@ -10,855 +10,483 @@ - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + - - - - + + - - - - + + + + - - + + + + -
White AWhite L4White wholeVarshneyBentley 2016 Monoamin.Bentley 2016 Peptid.Cook 2019 HermCook 2019 MaleCook 2020Brittin 2021Witvliet 1Witvliet 2Witvliet 3Witvliet 4Witvliet 5Witvliet 6Witvliet 7Witvliet 8WormNeuroAtlasRandi 2023RipollSanchez ShortRangeRipollSanchez MidRangeRipollSanchez LongRange Pharyngeal neuronsSensory neuronsInterneuronsMotorneuronsUnknown function neuronsBody wall musclesOther musclesOther cellsMale specific neuronsMale specific muscles Male other cells
Pharyngeal neurons - - -           
-          
- -
-           
-         -
          
-          
- -
          
-          
- -
          
-          
- -
          
-          
- -
- - - - - - - - -           
-          
- -
          
-          -
          
-          
- -
          
-          
- -
          
-          
+
White et al. 1986 N2U/Adult + +                
+               
+               
+               
+          +
               
+               
+               
+               
+               
+
               
+               
+       +
+                
+               
+   +
+           + + +
Sensory neurons -           
-          
-          
-          
-          
-          
-          -
          
-          
-          
-          
-          
-          
+
White et al. 1986 JSU/L4 + +                
+               
+               
+               
          -
          
-          
-          
-          
-          
-          
-          
-          
-    -
          
-          
-          
-          
-          
-          
-          
-          
-    -
          
-          
-          
-          
-          
-          
-          
-    -
          
-          
-          
-          
-          
-          
-          
-          
-    -
          
-          
-          
-          
-          
-          
-          
-          
-    -
          
-          
-          
-          
-          
-          
-          
-          
-   -
-           
-          
-          
-          
-          
-          
-     -
          
-          
-          
-          
-          
-          
-  -
          
-          
-          
-          
-          
-          
-  -
          
-          
-          
-          
-          
-          
-  -
          
-          
-          
-          
-          
-          
-      -
          
-          
-          
-          
-          
-          
-        -
          
-          
-          
-          
-          
-          
-        -
          
-          
-          
-          
-          
-          
-          -
          
-          
-          
-          
-          
-          
-          -
          
-          
-          
-          
-          
-          
-          
-          
-  -
          
-          
-          
-          
-          
-          -
          
-          
-          
-          
-          
-          
-          
-          
-    -
          
-          
-          
-          
-          
-          
-          
-          
-    -
          
-          
-          
-          
-          
-          
-          
-          
-    +
               
+               
+               
+               
+               
+ +
               
+               
+     +
+                
+               
+   +
+       + + +
Interneurons -           
-          
-          
-          
-          
-          
-          
-      -
          
-          
-          
-          
-          
-          
-          
-      -
          
-          
-          
-          
-          
-          
-          
-          
-  -
          
-          
-          
-          
-          
-          
-          
-          
-  -
          
-          
-          
-          
-    -
          
-          
-          
-          
-          
-          
-          
-          
-  -
          
-          
-          
-          
-          
-          
-          
-          
-  -
          
-          
-          
-          
-          
-          
-          
-          
- -
   -           
-          
-          
-          
-          
-          
-          
- -
          
-          
-          
-          
-          
-          
-         -
          
-          
-          
-          
-          
-          
-          -
          
-          
-          
-          
-          
-          
-          -
          
-          
-          
-          
-          
-          
-          -
          
-          
-          
-          
-          
-          
-          
-   -
          
-          
-          
-          
-          
-          
-          
-    -
          
-          
-          
-          
-          
-          
-          
-      -
          
-          
-          
-          
-          
-          
-          
-      -
          
-          
-          
-          
-          
-          
-          
-          
-  -
          
-          
-          
-          
-          
-          
-  -
          
-          
-          
-          
-          
-          
-          
-          
-  -
          
-          
-          
-          
-          
-          
-          
-          
-  -
          
-          
-          
-          
-          
-          
-          
-          
-  +
White et al. 1986 Whole worm +                
+      +
               
+               
+               
+               
+               
+         +
               
+               
+               
+               
+               
+       +
               
+               
+               
+               
+               
+               
+               
+            +
+ +     +        + + +
Motorneurons -           
-          
-          
-       -
          
-          
-          
-     -
          
-          
-          
-          
-          
-          
-          
-          
-          
-          
-          
-       -
          
-          
-          
-          
-          
-          
-          
-          
-          
-          
-          
-      -
          
-          
-          
-          
-          
-          
-          
-          
-          
+
Varshney et al. 2011 + +                
+               
+               
+               
+               
+         +
               
+               
+               
+               
+               
+       +
               
+               
+               
+               
+               
+               
+               
+           +
+ + + + + + +
Bentley et al. 2016 Monoamin. +                
+    +
               
+               
+               
+               
+              +
               
+               
+              +
               
+               
+               
+               
+               
+               
          -
          
-          
-          
-          
-          
-          
-          
-          
-          
-          
-          
-       -
          
-          
-          
-          
-          
-          
-          
-          
-          
-          
-          
-       -
          
-          
-          
-          
-          
-          
-          
-          
-          
-          
-         -
-           
-          
-          
-    -
          
-          
-          
-   -
          
-          
-          
-   -
          
-          
-          
-   -
          
-          
-          
-     -
          
-          
-          
-      -
          
-          
-          
-     -
          
-          
-          
-       -
          
-          
-          
-       -
          
-          
-          
-          
-          
-          
-          
-          
-          
-          
-          
-       -
          
-          
-          
-          
-   -
          
-          
-          
-          
-          
-          
-          
-          
-          
-          
-          
-       -
          
-          
-          
-          
-          
-          
-          
-          
-          
-          
-          
-       -
          
-          
-          
-          
-          
-          
-          
-          
-          
-          
-          
-       +
+ + + + + +
Unknown function neurons - - - - - - -    -    - - - - - - - -   -   - - - -    -    -    +Bentley et al. 2016 Peptid. +                
+      +
               
+               
+               
+               
+               
+         +
               
+               
+               
+               
+               
+       +
               
+               
+               
+               
+               
+               
+               
+            +
+ + + + + +
Body wall muscles -           
-          
-          
-   -
          
-          
-          
-   -
- - - -           
-          
-          
-          
-          
-          
-          
-          
-          
-      -
          
-          
-          
-          
-          
-          
-          
-          
-          
+
Cook et al. 2019 Herm +                
+      +
               
+               
+               
+               
+               
+         +
               
+               
+               
+               
+               
+       +
               
+               
+               
+               
+               
+               
+               
+            +
   +                
+               
+               
+               
+               
+               
      -
- -           
-        -
          
-          
-  -
          
-          
-        -
          
-          
-       -
          
-          
-         -
          
-          
-          
-   -
          
-          
-          
-   -
          
-          
-          
-   -
- - - - +                
+               
+         +
               
+               
+       +
+ +
Other muscles - - -     - - - -           
-          
-          
-         -
          
-          
-   -
          
-          
- -
- - - - - - - - - - - - - +Cook et al. 2019 Male +                
+      +
               
+               
+               
+               
+               
+        +
               
+               
+               
+               
+               
+      +
               
+               
+               
+               
+               
+               
+               
+    +
   +                
+               
+               
+               
+               
+               
+      +
               
+        +
               
+               
+   +
               
+               
+               
+               
+               
+               +
               
+               
+        +
              
Other cells -           -       -        - - - -           
-          
-          
+
Cook et al. 2020 +                
+      +
+    + + + +                
+      +
               
       -
          
-          
-          
-   -
          
-          
-  -
-           -           
-  -
          -           
- -
          -           -           -         - - - - - + + + +
Brittin et al. 2021 + +                
+               
+               
+               
+        +
               
+               
+               
+               
+             +
               
+               
+     +
+ + + + + + +
Witvliet et al. 2021 1 (L1) + +                
+               
+               
+               
+  +
               
+               
+               
+               
+         +
               
+               
+   +
+                
+   +
+           + + +
Male specific neurons - - - - - - - -           
-          
-          
-          
-          
-          
-          
-          
-          -
- - - - - - - - - - - - - - +Witvliet et al. 2021 5 (L2) + +                
+               
+               
+               
+        +
               
+               
+               
+               
+             +
               
+               
+      +
+                
+              +
+           + + +
Male specific muscles - - - - - - - -           
-          
-          
-        -
- - - - - - - - - - - - - - +Witvliet et al. 2021 6 (L3) + +                
+               
+               
+               
+        +
               
+               
+               
+               
+              +
               
+               
+     +
  +                
+               
+   +
+           + + + +
Witvliet et al. 2021 8 (Adult) + +                
+               
+               
+               
+          +
               
+               
+               
+               
+               
+ +
               
+               
+       +
+                
+               
+   +
+         + + + +
Randi et al. 2023 +                
+     +
               
+               
+               
+               +
               
+               
+               
+               
+  +
               
+               
+             +
+ + + + + +
Male other cells - - - - - - - -           
-     -
- - - - - - - - - - - - - - +Ripoll Sanchez et al. 2023 ShortRange +                
+      +
               
+               
+               
+               
+               
+         +
               
+               
+               
+               
+               
+       +
               
+               
+               
+               
+               
+               
+               
+            +
   + + + + + +
diff --git a/docs/Full1_Test_data.md b/docs/Full1_Test_data.md index caf4c8d84..1dad01d5d 100644 --- a/docs/Full1_Test_data.md +++ b/docs/Full1_Test_data.md @@ -5,25 +5,25 @@ search: --- -!!! example inline "Choose Dataset" +!!! example "Choose Dataset" White_A White_L4 White_whole Varshney Bentley2016_MA Bentley2016_PEP Cook2019Herm Cook2019Male Cook2020 Brittin2021 Witvliet1 Witvliet2 Witvliet3 Witvliet4 Witvliet5 Witvliet6 Witvliet7 Witvliet8 WormNeuroAtlas Randi2023 RipollSanchezShortRange RipollSanchezMidRange RipollSanchezLongRange Test SSData UpdSSData UpdSSData2 - -!!! tip "Choose View" - Raw Data Neurons Pharynx Social Network Escape Response Circuit Cook 2019 Fig 3 Peptidergic Hubs + Dummy dataset used for testing webpage/graph generation. Do not assume any of these connections are correct!.   Python Reader: TestDataReader - A view of the data set with neurons grouped as in Figure 3 of Cook et al. 2019 -!!! abstract "Choose Graph type" + + +!!! abstract inline "Choose Graph type" Graph - Matrix - Hive plot -

+!!! tip "Choose View" -

Dummy dataset used for testing webpage/graph generation. Do not assume any of these connections are correct!.   Reader: TestDataReader

+ Raw Data Neurons Pharynx Social Network Escape Response Circuit Cook 2019 Fig 3 Peptidergic Hubs + A view of the data set with neurons grouped as in Figure 3 of Cook et al. 2019 === "Chemical"
diff --git a/docs/Full1_Test_data_graph.md b/docs/Full1_Test_data_graph.md index 941f8661b..7cfbd3ffd 100644 --- a/docs/Full1_Test_data_graph.md +++ b/docs/Full1_Test_data_graph.md @@ -5,25 +5,25 @@ search: --- -!!! example inline "Choose Dataset" +!!! example "Choose Dataset" White_A White_L4 White_whole Varshney Bentley2016_MA Bentley2016_PEP Cook2019Herm Cook2019Male Cook2020 Brittin2021 Witvliet1 Witvliet2 Witvliet3 Witvliet4 Witvliet5 Witvliet6 Witvliet7 Witvliet8 WormNeuroAtlas Randi2023 RipollSanchezShortRange RipollSanchezMidRange RipollSanchezLongRange Test SSData UpdSSData UpdSSData2 - -!!! tip "Choose View" - Raw Data Neurons Pharynx Social Network Escape Response Circuit Cook 2019 Fig 3 Peptidergic Hubs + Dummy dataset used for testing webpage/graph generation. Do not assume any of these connections are correct!.   Python Reader: TestDataReader - A view of the data set with neurons grouped as in Figure 3 of Cook et al. 2019 -!!! abstract "Choose Graph type" + + +!!! abstract inline "Choose Graph type" Graph - Matrix - Hive plot -

+!!! tip "Choose View" -

Dummy dataset used for testing webpage/graph generation. Do not assume any of these connections are correct!.   Reader: TestDataReader

+ Raw Data Neurons Pharynx Social Network Escape Response Circuit Cook 2019 Fig 3 Peptidergic Hubs + A view of the data set with neurons grouped as in Figure 3 of Cook et al. 2019 === "Chemical" ```plotly diff --git a/docs/Full1_Test_data_hiveplot.md b/docs/Full1_Test_data_hiveplot.md index 4c4eb751c..bb8e56591 100644 --- a/docs/Full1_Test_data_hiveplot.md +++ b/docs/Full1_Test_data_hiveplot.md @@ -5,25 +5,25 @@ search: --- -!!! example inline "Choose Dataset" +!!! example "Choose Dataset" White_A White_L4 White_whole Varshney Bentley2016_MA Bentley2016_PEP Cook2019Herm Cook2019Male Cook2020 Brittin2021 Witvliet1 Witvliet2 Witvliet3 Witvliet4 Witvliet5 Witvliet6 Witvliet7 Witvliet8 WormNeuroAtlas Randi2023 RipollSanchezShortRange RipollSanchezMidRange RipollSanchezLongRange Test SSData UpdSSData UpdSSData2 - -!!! tip "Choose View" - Raw Data Neurons Pharynx Social Network Escape Response Circuit Cook 2019 Fig 3 Peptidergic Hubs + Dummy dataset used for testing webpage/graph generation. Do not assume any of these connections are correct!.   Python Reader: TestDataReader - A view of the data set with neurons grouped as in Figure 3 of Cook et al. 2019 -!!! abstract "Choose Graph type" + + +!!! abstract inline "Choose Graph type" Graph - Matrix - Hive plot -

+!!! tip "Choose View" -

Dummy dataset used for testing webpage/graph generation. Do not assume any of these connections are correct!.   Reader: TestDataReader

+ Raw Data Neurons Pharynx Social Network Escape Response Circuit Cook 2019 Fig 3 Peptidergic Hubs + A view of the data set with neurons grouped as in Figure 3 of Cook et al. 2019 === "Chemical"
diff --git a/docs/Neurons_Test_data.md b/docs/Neurons_Test_data.md index 7e8cc7a71..4f5845bf3 100644 --- a/docs/Neurons_Test_data.md +++ b/docs/Neurons_Test_data.md @@ -5,25 +5,25 @@ search: --- -!!! example inline "Choose Dataset" +!!! example "Choose Dataset" White_A White_L4 White_whole Varshney Bentley2016_MA Bentley2016_PEP Cook2019Herm Cook2019Male Cook2020 Brittin2021 Witvliet1 Witvliet2 Witvliet3 Witvliet4 Witvliet5 Witvliet6 Witvliet7 Witvliet8 WormNeuroAtlas Randi2023 RipollSanchezShortRange RipollSanchezMidRange RipollSanchezLongRange Test SSData UpdSSData UpdSSData2 - -!!! tip "Choose View" - Raw Data - Neurons - Pharynx - Social Network - Escape Response Circuit - Cook 2019 Fig 3 - Peptidergic Hubs - + Dummy dataset used for testing webpage/graph generation. Do not assume any of these connections are correct!.   Python Reader: TestDataReader - All 302 hermaphrodite neurons (whether present or not in the connectome dataset) -!!! abstract "Choose Graph type" + + +!!! abstract inline "Choose Graph type" Graph - Matrix - Hive plot -

+!!! tip "Choose View" -

Dummy dataset used for testing webpage/graph generation. Do not assume any of these connections are correct!.   Reader: TestDataReader

+ Raw Data - Neurons - Pharynx - Social Network - Escape Response Circuit - Cook 2019 Fig 3 - Peptidergic Hubs - + All 302 hermaphrodite neurons (whether present or not in the connectome dataset) === "Chemical Exc"
diff --git a/docs/Neurons_Test_data_graph.md b/docs/Neurons_Test_data_graph.md index a1a8db5c9..96d859281 100644 --- a/docs/Neurons_Test_data_graph.md +++ b/docs/Neurons_Test_data_graph.md @@ -5,25 +5,25 @@ search: --- -!!! example inline "Choose Dataset" +!!! example "Choose Dataset" White_A White_L4 White_whole Varshney Bentley2016_MA Bentley2016_PEP Cook2019Herm Cook2019Male Cook2020 Brittin2021 Witvliet1 Witvliet2 Witvliet3 Witvliet4 Witvliet5 Witvliet6 Witvliet7 Witvliet8 WormNeuroAtlas Randi2023 RipollSanchezShortRange RipollSanchezMidRange RipollSanchezLongRange Test SSData UpdSSData UpdSSData2 - -!!! tip "Choose View" - Raw Data - Neurons - Pharynx - Social Network - Escape Response Circuit - Cook 2019 Fig 3 - Peptidergic Hubs - + Dummy dataset used for testing webpage/graph generation. Do not assume any of these connections are correct!.   Python Reader: TestDataReader - All 302 hermaphrodite neurons (whether present or not in the connectome dataset) -!!! abstract "Choose Graph type" + + +!!! abstract inline "Choose Graph type" Graph - Matrix - Hive plot -

+!!! tip "Choose View" -

Dummy dataset used for testing webpage/graph generation. Do not assume any of these connections are correct!.   Reader: TestDataReader

+ Raw Data - Neurons - Pharynx - Social Network - Escape Response Circuit - Cook 2019 Fig 3 - Peptidergic Hubs - + All 302 hermaphrodite neurons (whether present or not in the connectome dataset) === "Chemical Exc" ```plotly diff --git a/docs/Neurons_Test_data_hiveplot.md b/docs/Neurons_Test_data_hiveplot.md index 44e6d7ff3..18a766bcb 100644 --- a/docs/Neurons_Test_data_hiveplot.md +++ b/docs/Neurons_Test_data_hiveplot.md @@ -5,25 +5,25 @@ search: --- -!!! example inline "Choose Dataset" +!!! example "Choose Dataset" White_A White_L4 White_whole Varshney Bentley2016_MA Bentley2016_PEP Cook2019Herm Cook2019Male Cook2020 Brittin2021 Witvliet1 Witvliet2 Witvliet3 Witvliet4 Witvliet5 Witvliet6 Witvliet7 Witvliet8 WormNeuroAtlas Randi2023 RipollSanchezShortRange RipollSanchezMidRange RipollSanchezLongRange Test SSData UpdSSData UpdSSData2 - -!!! tip "Choose View" - Raw Data - Neurons - Pharynx - Social Network - Escape Response Circuit - Cook 2019 Fig 3 - Peptidergic Hubs - + Dummy dataset used for testing webpage/graph generation. Do not assume any of these connections are correct!.   Python Reader: TestDataReader - All 302 hermaphrodite neurons (whether present or not in the connectome dataset) -!!! abstract "Choose Graph type" + + +!!! abstract inline "Choose Graph type" Graph - Matrix - Hive plot -

+!!! tip "Choose View" -

Dummy dataset used for testing webpage/graph generation. Do not assume any of these connections are correct!.   Reader: TestDataReader

+ Raw Data - Neurons - Pharynx - Social Network - Escape Response Circuit - Cook 2019 Fig 3 - Peptidergic Hubs - + All 302 hermaphrodite neurons (whether present or not in the connectome dataset) === "Chemical Exc"
diff --git a/docs/Nonpharyngeal_Test_data.md b/docs/Nonpharyngeal_Test_data.md new file mode 100644 index 000000000..58ae41c5d --- /dev/null +++ b/docs/Nonpharyngeal_Test_data.md @@ -0,0 +1,363 @@ +--- +title: "Dataset: Test" +search: + exclude: true +--- + + +!!! example "Choose Dataset" + + White_A White_L4 White_whole Varshney Bentley2016_MA Bentley2016_PEP Cook2019Herm Cook2019Male Cook2020 Brittin2021 Witvliet1 Witvliet2 Witvliet3 Witvliet4 Witvliet5 Witvliet6 Witvliet7 Witvliet8 WormNeuroAtlas Randi2023 RipollSanchezShortRange RipollSanchezMidRange RipollSanchezLongRange Test SSData UpdSSData UpdSSData2 + + Dummy dataset used for testing webpage/graph generation. Do not assume any of these connections are correct!.   Python Reader: TestDataReader + + + + +!!! abstract inline "Choose Graph type" + + Graph - Matrix - Hive plot + + +!!! tip "Choose View" + + Raw Data - Neurons - Pharynx - Nonpharyngeal Neurons - Social Network - Escape Response Circuit - Cook 2019 Fig 3 - Peptidergic Hubs - + + All **hermaphrodite** neurons except those in the pharynx +=== "Chemical Exc" + +
+ ```plotly + { "file_path": "./assets/Test_Nonpharyngeal_Chemical_Exc.json" } + ``` + +=== "Chemical Inh" + +
+ ```plotly + { "file_path": "./assets/Test_Nonpharyngeal_Chemical_Inh.json" } + ``` + +=== "Electrical" + +
+ ```plotly + { "file_path": "./assets/Test_Nonpharyngeal_Electrical.json" } + ``` + + +### Neurons (herm) (18) +
Full list of Neurons (hermaphrodite only) in this dataset +ASHR + | ASKR + | AVBL + | AWBR + | DB4 + | DD4 + | DVA + | I5 + | M1 + | M4 + | PVCL + | RMGR + | VA3 + | VA6 + | VB2 + | VB6 + | VD3 + | VD6 + +
+ +### Missing neurons (284) +
Full list of Missing neurons (known hermaphrodite neurons not present) +ADAL + | ADAR + | ADEL + | ADER + | ADFL + | ADFR + | ADLL + | ADLR + | AFDL + | AFDR + | AIAL + | AIAR + | AIBL + | AIBR + | AIML + | AIMR + | AINL + | AINR + | AIYL + | AIYR + | AIZL + | AIZR + | ALA + | ALML + | ALMR + | ALNL + | ALNR + | AQR + | AS1 + | AS10 + | AS11 + | AS2 + | AS3 + | AS4 + | AS5 + | AS6 + | AS7 + | AS8 + | AS9 + | ASEL + | ASER + | ASGL + | ASGR + | ASHL + | ASIL + | ASIR + | ASJL + | ASJR + | ASKL + | AUAL + | AUAR + | AVAL + | AVAR + | AVBR + | AVDL + | AVDR + | AVEL + | AVER + | AVFL + | AVFR + | AVG + | AVHL + | AVHR + | AVJL + | AVJR + | AVKL + | AVKR + | AVL + | AVM + | AWAL + | AWAR + | AWBL + | AWCL + | AWCR + | BAGL + | BAGR + | BDUL + | BDUR + | CANL + | CANR + | CEPDL + | CEPDR + | CEPVL + | CEPVR + | DA1 + | DA2 + | DA3 + | DA4 + | DA5 + | DA6 + | DA7 + | DA8 + | DA9 + | DB1 + | DB2 + | DB3 + | DB5 + | DB6 + | DB7 + | DD1 + | DD2 + | DD3 + | DD5 + | DD6 + | DVB + | DVC + | FLPL + | FLPR + | HSNL + | HSNR + | I1L + | I1R + | I2L + | I2R + | I3 + | I4 + | I6 + | IL1DL + | IL1DR + | IL1L + | IL1R + | IL1VL + | IL1VR + | IL2DL + | IL2DR + | IL2L + | IL2R + | IL2VL + | IL2VR + | LUAL + | LUAR + | M2L + | M2R + | M3L + | M3R + | M5 + | MCL + | MCR + | MI + | NSML + | NSMR + | OLLL + | OLLR + | OLQDL + | OLQDR + | OLQVL + | OLQVR + | PDA + | PDB + | PDEL + | PDER + | PHAL + | PHAR + | PHBL + | PHBR + | PHCL + | PHCR + | PLML + | PLMR + | PLNL + | PLNR + | PQR + | PVCR + | PVDL + | PVDR + | PVM + | PVNL + | PVNR + | PVPL + | PVPR + | PVQL + | PVQR + | PVR + | PVT + | PVWL + | PVWR + | RIAL + | RIAR + | RIBL + | RIBR + | RICL + | RICR + | RID + | RIFL + | RIFR + | RIGL + | RIGR + | RIH + | RIML + | RIMR + | RIPL + | RIPR + | RIR + | RIS + | RIVL + | RIVR + | RMDDL + | RMDDR + | RMDL + | RMDR + | RMDVL + | RMDVR + | RMED + | RMEL + | RMER + | RMEV + | RMFL + | RMFR + | RMGL + | RMHL + | RMHR + | SAADL + | SAADR + | SAAVL + | SAAVR + | SABD + | SABVL + | SABVR + | SDQL + | SDQR + | SIADL + | SIADR + | SIAVL + | SIAVR + | SIBDL + | SIBDR + | SIBVL + | SIBVR + | SMBDL + | SMBDR + | SMBVL + | SMBVR + | SMDDL + | SMDDR + | SMDVL + | SMDVR + | URADL + | URADR + | URAVL + | URAVR + | URBL + | URBR + | URXL + | URXR + | URYDL + | URYDR + | URYVL + | URYVR + | VA1 + | VA10 + | VA11 + | VA12 + | VA2 + | VA4 + | VA5 + | VA7 + | VA8 + | VA9 + | VB1 + | VB10 + | VB11 + | VB3 + | VB4 + | VB5 + | VB7 + | VB8 + | VB9 + | VC1 + | VC2 + | VC3 + | VC4 + | VC5 + | VC6 + | VD1 + | VD10 + | VD11 + | VD12 + | VD13 + | VD2 + | VD4 + | VD5 + | VD7 + | VD8 + | VD9 + +
+ +### Muscles (0) + +### Other cells (0) diff --git a/docs/Nonpharyngeal_Test_data_graph.md b/docs/Nonpharyngeal_Test_data_graph.md new file mode 100644 index 000000000..67e3d3402 --- /dev/null +++ b/docs/Nonpharyngeal_Test_data_graph.md @@ -0,0 +1,360 @@ +--- +title: "Dataset: Test" +search: + exclude: true +--- + + +!!! example "Choose Dataset" + + White_A White_L4 White_whole Varshney Bentley2016_MA Bentley2016_PEP Cook2019Herm Cook2019Male Cook2020 Brittin2021 Witvliet1 Witvliet2 Witvliet3 Witvliet4 Witvliet5 Witvliet6 Witvliet7 Witvliet8 WormNeuroAtlas Randi2023 RipollSanchezShortRange RipollSanchezMidRange RipollSanchezLongRange Test SSData UpdSSData UpdSSData2 + + Dummy dataset used for testing webpage/graph generation. Do not assume any of these connections are correct!.   Python Reader: TestDataReader + + + + +!!! abstract inline "Choose Graph type" + + Graph - Matrix - Hive plot + + +!!! tip "Choose View" + + Raw Data - Neurons - Pharynx - Nonpharyngeal Neurons - Social Network - Escape Response Circuit - Cook 2019 Fig 3 - Peptidergic Hubs - + + All **hermaphrodite** neurons except those in the pharynx +=== "Chemical Exc" + + ```plotly + { "file_path": "./assets/Test_Nonpharyngeal_Chemical_Exc_graph.json" } + ``` + +=== "Chemical Inh" + + ```plotly + { "file_path": "./assets/Test_Nonpharyngeal_Chemical_Inh_graph.json" } + ``` + +=== "Electrical" + + ```plotly + { "file_path": "./assets/Test_Nonpharyngeal_Electrical_graph.json" } + ``` + + +### Neurons (herm) (18) +
Full list of Neurons (hermaphrodite only) in this dataset +ASHR + | ASKR + | AVBL + | AWBR + | DB4 + | DD4 + | DVA + | I5 + | M1 + | M4 + | PVCL + | RMGR + | VA3 + | VA6 + | VB2 + | VB6 + | VD3 + | VD6 + +
+ +### Missing neurons (284) +
Full list of Missing neurons (known hermaphrodite neurons not present) +ADAL + | ADAR + | ADEL + | ADER + | ADFL + | ADFR + | ADLL + | ADLR + | AFDL + | AFDR + | AIAL + | AIAR + | AIBL + | AIBR + | AIML + | AIMR + | AINL + | AINR + | AIYL + | AIYR + | AIZL + | AIZR + | ALA + | ALML + | ALMR + | ALNL + | ALNR + | AQR + | AS1 + | AS10 + | AS11 + | AS2 + | AS3 + | AS4 + | AS5 + | AS6 + | AS7 + | AS8 + | AS9 + | ASEL + | ASER + | ASGL + | ASGR + | ASHL + | ASIL + | ASIR + | ASJL + | ASJR + | ASKL + | AUAL + | AUAR + | AVAL + | AVAR + | AVBR + | AVDL + | AVDR + | AVEL + | AVER + | AVFL + | AVFR + | AVG + | AVHL + | AVHR + | AVJL + | AVJR + | AVKL + | AVKR + | AVL + | AVM + | AWAL + | AWAR + | AWBL + | AWCL + | AWCR + | BAGL + | BAGR + | BDUL + | BDUR + | CANL + | CANR + | CEPDL + | CEPDR + | CEPVL + | CEPVR + | DA1 + | DA2 + | DA3 + | DA4 + | DA5 + | DA6 + | DA7 + | DA8 + | DA9 + | DB1 + | DB2 + | DB3 + | DB5 + | DB6 + | DB7 + | DD1 + | DD2 + | DD3 + | DD5 + | DD6 + | DVB + | DVC + | FLPL + | FLPR + | HSNL + | HSNR + | I1L + | I1R + | I2L + | I2R + | I3 + | I4 + | I6 + | IL1DL + | IL1DR + | IL1L + | IL1R + | IL1VL + | IL1VR + | IL2DL + | IL2DR + | IL2L + | IL2R + | IL2VL + | IL2VR + | LUAL + | LUAR + | M2L + | M2R + | M3L + | M3R + | M5 + | MCL + | MCR + | MI + | NSML + | NSMR + | OLLL + | OLLR + | OLQDL + | OLQDR + | OLQVL + | OLQVR + | PDA + | PDB + | PDEL + | PDER + | PHAL + | PHAR + | PHBL + | PHBR + | PHCL + | PHCR + | PLML + | PLMR + | PLNL + | PLNR + | PQR + | PVCR + | PVDL + | PVDR + | PVM + | PVNL + | PVNR + | PVPL + | PVPR + | PVQL + | PVQR + | PVR + | PVT + | PVWL + | PVWR + | RIAL + | RIAR + | RIBL + | RIBR + | RICL + | RICR + | RID + | RIFL + | RIFR + | RIGL + | RIGR + | RIH + | RIML + | RIMR + | RIPL + | RIPR + | RIR + | RIS + | RIVL + | RIVR + | RMDDL + | RMDDR + | RMDL + | RMDR + | RMDVL + | RMDVR + | RMED + | RMEL + | RMER + | RMEV + | RMFL + | RMFR + | RMGL + | RMHL + | RMHR + | SAADL + | SAADR + | SAAVL + | SAAVR + | SABD + | SABVL + | SABVR + | SDQL + | SDQR + | SIADL + | SIADR + | SIAVL + | SIAVR + | SIBDL + | SIBDR + | SIBVL + | SIBVR + | SMBDL + | SMBDR + | SMBVL + | SMBVR + | SMDDL + | SMDDR + | SMDVL + | SMDVR + | URADL + | URADR + | URAVL + | URAVR + | URBL + | URBR + | URXL + | URXR + | URYDL + | URYDR + | URYVL + | URYVR + | VA1 + | VA10 + | VA11 + | VA12 + | VA2 + | VA4 + | VA5 + | VA7 + | VA8 + | VA9 + | VB1 + | VB10 + | VB11 + | VB3 + | VB4 + | VB5 + | VB7 + | VB8 + | VB9 + | VC1 + | VC2 + | VC3 + | VC4 + | VC5 + | VC6 + | VD1 + | VD10 + | VD11 + | VD12 + | VD13 + | VD2 + | VD4 + | VD5 + | VD7 + | VD8 + | VD9 + +
+ +### Muscles (0) + +### Other cells (0) diff --git a/docs/Nonpharyngeal_Test_data_hiveplot.md b/docs/Nonpharyngeal_Test_data_hiveplot.md new file mode 100644 index 000000000..a778494f1 --- /dev/null +++ b/docs/Nonpharyngeal_Test_data_hiveplot.md @@ -0,0 +1,363 @@ +--- +title: "Dataset: Test" +search: + exclude: true +--- + + +!!! example "Choose Dataset" + + White_A White_L4 White_whole Varshney Bentley2016_MA Bentley2016_PEP Cook2019Herm Cook2019Male Cook2020 Brittin2021 Witvliet1 Witvliet2 Witvliet3 Witvliet4 Witvliet5 Witvliet6 Witvliet7 Witvliet8 WormNeuroAtlas Randi2023 RipollSanchezShortRange RipollSanchezMidRange RipollSanchezLongRange Test SSData UpdSSData UpdSSData2 + + Dummy dataset used for testing webpage/graph generation. Do not assume any of these connections are correct!.   Python Reader: TestDataReader + + + + +!!! abstract inline "Choose Graph type" + + Graph - Matrix - Hive plot + + +!!! tip "Choose View" + + Raw Data - Neurons - Pharynx - Nonpharyngeal Neurons - Social Network - Escape Response Circuit - Cook 2019 Fig 3 - Peptidergic Hubs - + + All **hermaphrodite** neurons except those in the pharynx +=== "Chemical Exc" + +
+ ```plotly + { "file_path": "./assets/Test_Nonpharyngeal_Chemical_Exc_hiveplot.json" } + ``` + +=== "Chemical Inh" + +
+ ```plotly + { "file_path": "./assets/Test_Nonpharyngeal_Chemical_Inh_hiveplot.json" } + ``` + +=== "Electrical" + +
+ ```plotly + { "file_path": "./assets/Test_Nonpharyngeal_Electrical_hiveplot.json" } + ``` + + +### Neurons (herm) (18) +
Full list of Neurons (hermaphrodite only) in this dataset +ASHR + | ASKR + | AVBL + | AWBR + | DB4 + | DD4 + | DVA + | I5 + | M1 + | M4 + | PVCL + | RMGR + | VA3 + | VA6 + | VB2 + | VB6 + | VD3 + | VD6 + +
+ +### Missing neurons (284) +
Full list of Missing neurons (known hermaphrodite neurons not present) +ADAL + | ADAR + | ADEL + | ADER + | ADFL + | ADFR + | ADLL + | ADLR + | AFDL + | AFDR + | AIAL + | AIAR + | AIBL + | AIBR + | AIML + | AIMR + | AINL + | AINR + | AIYL + | AIYR + | AIZL + | AIZR + | ALA + | ALML + | ALMR + | ALNL + | ALNR + | AQR + | AS1 + | AS10 + | AS11 + | AS2 + | AS3 + | AS4 + | AS5 + | AS6 + | AS7 + | AS8 + | AS9 + | ASEL + | ASER + | ASGL + | ASGR + | ASHL + | ASIL + | ASIR + | ASJL + | ASJR + | ASKL + | AUAL + | AUAR + | AVAL + | AVAR + | AVBR + | AVDL + | AVDR + | AVEL + | AVER + | AVFL + | AVFR + | AVG + | AVHL + | AVHR + | AVJL + | AVJR + | AVKL + | AVKR + | AVL + | AVM + | AWAL + | AWAR + | AWBL + | AWCL + | AWCR + | BAGL + | BAGR + | BDUL + | BDUR + | CANL + | CANR + | CEPDL + | CEPDR + | CEPVL + | CEPVR + | DA1 + | DA2 + | DA3 + | DA4 + | DA5 + | DA6 + | DA7 + | DA8 + | DA9 + | DB1 + | DB2 + | DB3 + | DB5 + | DB6 + | DB7 + | DD1 + | DD2 + | DD3 + | DD5 + | DD6 + | DVB + | DVC + | FLPL + | FLPR + | HSNL + | HSNR + | I1L + | I1R + | I2L + | I2R + | I3 + | I4 + | I6 + | IL1DL + | IL1DR + | IL1L + | IL1R + | IL1VL + | IL1VR + | IL2DL + | IL2DR + | IL2L + | IL2R + | IL2VL + | IL2VR + | LUAL + | LUAR + | M2L + | M2R + | M3L + | M3R + | M5 + | MCL + | MCR + | MI + | NSML + | NSMR + | OLLL + | OLLR + | OLQDL + | OLQDR + | OLQVL + | OLQVR + | PDA + | PDB + | PDEL + | PDER + | PHAL + | PHAR + | PHBL + | PHBR + | PHCL + | PHCR + | PLML + | PLMR + | PLNL + | PLNR + | PQR + | PVCR + | PVDL + | PVDR + | PVM + | PVNL + | PVNR + | PVPL + | PVPR + | PVQL + | PVQR + | PVR + | PVT + | PVWL + | PVWR + | RIAL + | RIAR + | RIBL + | RIBR + | RICL + | RICR + | RID + | RIFL + | RIFR + | RIGL + | RIGR + | RIH + | RIML + | RIMR + | RIPL + | RIPR + | RIR + | RIS + | RIVL + | RIVR + | RMDDL + | RMDDR + | RMDL + | RMDR + | RMDVL + | RMDVR + | RMED + | RMEL + | RMER + | RMEV + | RMFL + | RMFR + | RMGL + | RMHL + | RMHR + | SAADL + | SAADR + | SAAVL + | SAAVR + | SABD + | SABVL + | SABVR + | SDQL + | SDQR + | SIADL + | SIADR + | SIAVL + | SIAVR + | SIBDL + | SIBDR + | SIBVL + | SIBVR + | SMBDL + | SMBDR + | SMBVL + | SMBVR + | SMDDL + | SMDDR + | SMDVL + | SMDVR + | URADL + | URADR + | URAVL + | URAVR + | URBL + | URBR + | URXL + | URXR + | URYDL + | URYDR + | URYVL + | URYVR + | VA1 + | VA10 + | VA11 + | VA12 + | VA2 + | VA4 + | VA5 + | VA7 + | VA8 + | VA9 + | VB1 + | VB10 + | VB11 + | VB3 + | VB4 + | VB5 + | VB7 + | VB8 + | VB9 + | VC1 + | VC2 + | VC3 + | VC4 + | VC5 + | VC6 + | VD1 + | VD10 + | VD11 + | VD12 + | VD13 + | VD2 + | VD4 + | VD5 + | VD7 + | VD8 + | VD9 + +
+ +### Muscles (0) + +### Other cells (0) diff --git a/docs/PeptidergicHubs_Test_data.md b/docs/PeptidergicHubs_Test_data.md index f9ff0368f..0b319963a 100644 --- a/docs/PeptidergicHubs_Test_data.md +++ b/docs/PeptidergicHubs_Test_data.md @@ -5,25 +5,25 @@ search: --- -!!! example inline "Choose Dataset" +!!! example "Choose Dataset" White_A White_L4 White_whole Varshney Bentley2016_MA Bentley2016_PEP Cook2019Herm Cook2019Male Cook2020 Brittin2021 Witvliet1 Witvliet2 Witvliet3 Witvliet4 Witvliet5 Witvliet6 Witvliet7 Witvliet8 WormNeuroAtlas Randi2023 RipollSanchezShortRange RipollSanchezMidRange RipollSanchezLongRange Test SSData UpdSSData UpdSSData2 - -!!! tip "Choose View" - Raw Data - Neurons - Pharynx - Social Network - Escape Response Circuit - Cook 2019 Fig 3 - Peptidergic Hubs - + Dummy dataset used for testing webpage/graph generation. Do not assume any of these connections are correct!.   Python Reader: TestDataReader - Peptidergic hubs as outlined in in [Ripoll-Sánchez et al. 2023](../RipollSanchez_2023.md), Fig 7E -!!! abstract "Choose Graph type" + + +!!! abstract inline "Choose Graph type" Graph - Matrix - Hive plot -

+!!! tip "Choose View" -

Dummy dataset used for testing webpage/graph generation. Do not assume any of these connections are correct!.   Reader: TestDataReader

+ Raw Data - Neurons - Pharynx - Social Network - Escape Response Circuit - Cook 2019 Fig 3 - Peptidergic Hubs - + Peptidergic hubs as outlined in in [Ripoll-Sánchez et al. 2023](../RipollSanchez_2023.md), Fig 7E === "Chemical Exc"
diff --git a/docs/PeptidergicHubs_Test_data_graph.md b/docs/PeptidergicHubs_Test_data_graph.md index 59be69ec1..c647d294d 100644 --- a/docs/PeptidergicHubs_Test_data_graph.md +++ b/docs/PeptidergicHubs_Test_data_graph.md @@ -5,25 +5,25 @@ search: --- -!!! example inline "Choose Dataset" +!!! example "Choose Dataset" White_A White_L4 White_whole Varshney Bentley2016_MA Bentley2016_PEP Cook2019Herm Cook2019Male Cook2020 Brittin2021 Witvliet1 Witvliet2 Witvliet3 Witvliet4 Witvliet5 Witvliet6 Witvliet7 Witvliet8 WormNeuroAtlas Randi2023 RipollSanchezShortRange RipollSanchezMidRange RipollSanchezLongRange Test SSData UpdSSData UpdSSData2 - -!!! tip "Choose View" - Raw Data - Neurons - Pharynx - Social Network - Escape Response Circuit - Cook 2019 Fig 3 - Peptidergic Hubs - + Dummy dataset used for testing webpage/graph generation. Do not assume any of these connections are correct!.   Python Reader: TestDataReader - Peptidergic hubs as outlined in in [Ripoll-Sánchez et al. 2023](../RipollSanchez_2023.md), Fig 7E -!!! abstract "Choose Graph type" + + +!!! abstract inline "Choose Graph type" Graph - Matrix - Hive plot -

+!!! tip "Choose View" -

Dummy dataset used for testing webpage/graph generation. Do not assume any of these connections are correct!.   Reader: TestDataReader

+ Raw Data - Neurons - Pharynx - Social Network - Escape Response Circuit - Cook 2019 Fig 3 - Peptidergic Hubs - + Peptidergic hubs as outlined in in [Ripoll-Sánchez et al. 2023](../RipollSanchez_2023.md), Fig 7E === "Chemical Exc" ```plotly diff --git a/docs/PeptidergicHubs_Test_data_hiveplot.md b/docs/PeptidergicHubs_Test_data_hiveplot.md index 3d8017afd..f475e8d5d 100644 --- a/docs/PeptidergicHubs_Test_data_hiveplot.md +++ b/docs/PeptidergicHubs_Test_data_hiveplot.md @@ -5,25 +5,25 @@ search: --- -!!! example inline "Choose Dataset" +!!! example "Choose Dataset" White_A White_L4 White_whole Varshney Bentley2016_MA Bentley2016_PEP Cook2019Herm Cook2019Male Cook2020 Brittin2021 Witvliet1 Witvliet2 Witvliet3 Witvliet4 Witvliet5 Witvliet6 Witvliet7 Witvliet8 WormNeuroAtlas Randi2023 RipollSanchezShortRange RipollSanchezMidRange RipollSanchezLongRange Test SSData UpdSSData UpdSSData2 - -!!! tip "Choose View" - Raw Data - Neurons - Pharynx - Social Network - Escape Response Circuit - Cook 2019 Fig 3 - Peptidergic Hubs - + Dummy dataset used for testing webpage/graph generation. Do not assume any of these connections are correct!.   Python Reader: TestDataReader - Peptidergic hubs as outlined in in [Ripoll-Sánchez et al. 2023](../RipollSanchez_2023.md), Fig 7E -!!! abstract "Choose Graph type" + + +!!! abstract inline "Choose Graph type" Graph - Matrix - Hive plot -

+!!! tip "Choose View" -

Dummy dataset used for testing webpage/graph generation. Do not assume any of these connections are correct!.   Reader: TestDataReader

+ Raw Data - Neurons - Pharynx - Social Network - Escape Response Circuit - Cook 2019 Fig 3 - Peptidergic Hubs - + Peptidergic hubs as outlined in in [Ripoll-Sánchez et al. 2023](../RipollSanchez_2023.md), Fig 7E === "Chemical Exc" No plottable connections of this type... === "Chemical Inh" diff --git a/docs/Pharynx_Test_data.md b/docs/Pharynx_Test_data.md index b65b4ef3e..91d8711e8 100644 --- a/docs/Pharynx_Test_data.md +++ b/docs/Pharynx_Test_data.md @@ -5,25 +5,25 @@ search: --- -!!! example inline "Choose Dataset" +!!! example "Choose Dataset" White_A White_L4 White_whole Varshney Bentley2016_MA Bentley2016_PEP Cook2019Herm Cook2019Male Cook2020 Brittin2021 Witvliet1 Witvliet2 Witvliet3 Witvliet4 Witvliet5 Witvliet6 Witvliet7 Witvliet8 WormNeuroAtlas Randi2023 RipollSanchezShortRange RipollSanchezMidRange RipollSanchezLongRange Test SSData UpdSSData UpdSSData2 - -!!! tip "Choose View" - Raw Data - Neurons - Pharynx - Social Network - Escape Response Circuit - Cook 2019 Fig 3 - Peptidergic Hubs - + Dummy dataset used for testing webpage/graph generation. Do not assume any of these connections are correct!.   Python Reader: TestDataReader - Only the 20 neurons of the pharynx (whether present or not in the connectome dataset) -!!! abstract "Choose Graph type" + + +!!! abstract inline "Choose Graph type" Graph - Matrix - Hive plot -

+!!! tip "Choose View" -

Dummy dataset used for testing webpage/graph generation. Do not assume any of these connections are correct!.   Reader: TestDataReader

+ Raw Data - Neurons - Pharynx - Social Network - Escape Response Circuit - Cook 2019 Fig 3 - Peptidergic Hubs - + Only the 20 neurons of the pharynx (whether present or not in the connectome dataset) === "Chemical Exc"
diff --git a/docs/Pharynx_Test_data_graph.md b/docs/Pharynx_Test_data_graph.md index ee1d97272..daf756de2 100644 --- a/docs/Pharynx_Test_data_graph.md +++ b/docs/Pharynx_Test_data_graph.md @@ -5,25 +5,25 @@ search: --- -!!! example inline "Choose Dataset" +!!! example "Choose Dataset" White_A White_L4 White_whole Varshney Bentley2016_MA Bentley2016_PEP Cook2019Herm Cook2019Male Cook2020 Brittin2021 Witvliet1 Witvliet2 Witvliet3 Witvliet4 Witvliet5 Witvliet6 Witvliet7 Witvliet8 WormNeuroAtlas Randi2023 RipollSanchezShortRange RipollSanchezMidRange RipollSanchezLongRange Test SSData UpdSSData UpdSSData2 - -!!! tip "Choose View" - Raw Data - Neurons - Pharynx - Social Network - Escape Response Circuit - Cook 2019 Fig 3 - Peptidergic Hubs - + Dummy dataset used for testing webpage/graph generation. Do not assume any of these connections are correct!.   Python Reader: TestDataReader - Only the 20 neurons of the pharynx (whether present or not in the connectome dataset) -!!! abstract "Choose Graph type" + + +!!! abstract inline "Choose Graph type" Graph - Matrix - Hive plot -

+!!! tip "Choose View" -

Dummy dataset used for testing webpage/graph generation. Do not assume any of these connections are correct!.   Reader: TestDataReader

+ Raw Data - Neurons - Pharynx - Social Network - Escape Response Circuit - Cook 2019 Fig 3 - Peptidergic Hubs - + Only the 20 neurons of the pharynx (whether present or not in the connectome dataset) === "Chemical Exc" ```plotly diff --git a/docs/Pharynx_Test_data_hiveplot.md b/docs/Pharynx_Test_data_hiveplot.md index 7fa3c4e1c..c7cde136c 100644 --- a/docs/Pharynx_Test_data_hiveplot.md +++ b/docs/Pharynx_Test_data_hiveplot.md @@ -5,25 +5,25 @@ search: --- -!!! example inline "Choose Dataset" +!!! example "Choose Dataset" White_A White_L4 White_whole Varshney Bentley2016_MA Bentley2016_PEP Cook2019Herm Cook2019Male Cook2020 Brittin2021 Witvliet1 Witvliet2 Witvliet3 Witvliet4 Witvliet5 Witvliet6 Witvliet7 Witvliet8 WormNeuroAtlas Randi2023 RipollSanchezShortRange RipollSanchezMidRange RipollSanchezLongRange Test SSData UpdSSData UpdSSData2 - -!!! tip "Choose View" - Raw Data - Neurons - Pharynx - Social Network - Escape Response Circuit - Cook 2019 Fig 3 - Peptidergic Hubs - + Dummy dataset used for testing webpage/graph generation. Do not assume any of these connections are correct!.   Python Reader: TestDataReader - Only the 20 neurons of the pharynx (whether present or not in the connectome dataset) -!!! abstract "Choose Graph type" + + +!!! abstract inline "Choose Graph type" Graph - Matrix - Hive plot -

+!!! tip "Choose View" -

Dummy dataset used for testing webpage/graph generation. Do not assume any of these connections are correct!.   Reader: TestDataReader

+ Raw Data - Neurons - Pharynx - Social Network - Escape Response Circuit - Cook 2019 Fig 3 - Peptidergic Hubs - + Only the 20 neurons of the pharynx (whether present or not in the connectome dataset) === "Chemical Exc"
diff --git a/docs/Resources.md b/docs/Resources.md index e33c17fca..8e7b5e09b 100644 --- a/docs/Resources.md +++ b/docs/Resources.md @@ -1,4 +1,4 @@ -# Connectome resources +# Connectome Resources The following are other resources which have been developed by the community for sharing information related to _C. elegans_ connectomics. @@ -30,7 +30,7 @@ Introductory chapters on a number of aspects of worm biology, including [neurobi ## NemaNode -[NemaNode](https://nemanode.org) is ... +[NemaNode](https://nemanode.org) is an open source software package developed by the Zhen Lab and is used to visualise the datasets presented in [Witvliet et al. 2021](Witvliet_2021.md). ## parsetrakem2 @@ -53,6 +53,9 @@ Introductory chapters on a number of aspects of worm biology, including [neurobi [NemaMod](http://nemamod.org/) is an application for intuitive and rapid visualisation of neuropeptide connections in _C. elegans_. The data shown in the app was generated for the paper [Ripoll-Sanchez et al. 2023](RipollSanchez_2023.md). +## FunCoNN (Beta) +[FunCoNN](https://funconn.princeton.edu/) is an interactive browser of functional connectivity measurements of _C.elegans_ that is overlaid on top of connectomics data present within [NemaNode](https://nemanode.org). The functional data shown in the app was generated for the paper [Randi et al. 2023](Randi_2023.md). + diff --git a/docs/Social_Test_data.md b/docs/Social_Test_data.md index a881c0ad3..f6e6baccd 100644 --- a/docs/Social_Test_data.md +++ b/docs/Social_Test_data.md @@ -5,25 +5,25 @@ search: --- -!!! example inline "Choose Dataset" +!!! example "Choose Dataset" White_A White_L4 White_whole Varshney Bentley2016_MA Bentley2016_PEP Cook2019Herm Cook2019Male Cook2020 Brittin2021 Witvliet1 Witvliet2 Witvliet3 Witvliet4 Witvliet5 Witvliet6 Witvliet7 Witvliet8 WormNeuroAtlas Randi2023 RipollSanchezShortRange RipollSanchezMidRange RipollSanchezLongRange Test SSData UpdSSData UpdSSData2 - -!!! tip "Choose View" - Raw Data - Neurons - Pharynx - Social Network - Escape Response Circuit - Cook 2019 Fig 3 - Peptidergic Hubs - + Dummy dataset used for testing webpage/graph generation. Do not assume any of these connections are correct!.   Python Reader: TestDataReader - Hub and spoke circuit for social behavior as in Macosko et al. 2009 -!!! abstract "Choose Graph type" + + +!!! abstract inline "Choose Graph type" Graph - Matrix - Hive plot -

+!!! tip "Choose View" -

Dummy dataset used for testing webpage/graph generation. Do not assume any of these connections are correct!.   Reader: TestDataReader

+ Raw Data - Neurons - Pharynx - Social Network - Escape Response Circuit - Cook 2019 Fig 3 - Peptidergic Hubs - + Hub and spoke circuit for social behavior as in Macosko et al. 2009 === "Chemical Exc"
diff --git a/docs/Social_Test_data_graph.md b/docs/Social_Test_data_graph.md index 4a5633f27..506b84658 100644 --- a/docs/Social_Test_data_graph.md +++ b/docs/Social_Test_data_graph.md @@ -5,25 +5,25 @@ search: --- -!!! example inline "Choose Dataset" +!!! example "Choose Dataset" White_A White_L4 White_whole Varshney Bentley2016_MA Bentley2016_PEP Cook2019Herm Cook2019Male Cook2020 Brittin2021 Witvliet1 Witvliet2 Witvliet3 Witvliet4 Witvliet5 Witvliet6 Witvliet7 Witvliet8 WormNeuroAtlas Randi2023 RipollSanchezShortRange RipollSanchezMidRange RipollSanchezLongRange Test SSData UpdSSData UpdSSData2 - -!!! tip "Choose View" - Raw Data - Neurons - Pharynx - Social Network - Escape Response Circuit - Cook 2019 Fig 3 - Peptidergic Hubs - + Dummy dataset used for testing webpage/graph generation. Do not assume any of these connections are correct!.   Python Reader: TestDataReader - Hub and spoke circuit for social behavior as in Macosko et al. 2009 -!!! abstract "Choose Graph type" + + +!!! abstract inline "Choose Graph type" Graph - Matrix - Hive plot -

+!!! tip "Choose View" -

Dummy dataset used for testing webpage/graph generation. Do not assume any of these connections are correct!.   Reader: TestDataReader

+ Raw Data - Neurons - Pharynx - Social Network - Escape Response Circuit - Cook 2019 Fig 3 - Peptidergic Hubs - + Hub and spoke circuit for social behavior as in Macosko et al. 2009 === "Chemical Exc" ```plotly diff --git a/docs/Social_Test_data_hiveplot.md b/docs/Social_Test_data_hiveplot.md index 1c9be898b..243e5f354 100644 --- a/docs/Social_Test_data_hiveplot.md +++ b/docs/Social_Test_data_hiveplot.md @@ -5,25 +5,25 @@ search: --- -!!! example inline "Choose Dataset" +!!! example "Choose Dataset" White_A White_L4 White_whole Varshney Bentley2016_MA Bentley2016_PEP Cook2019Herm Cook2019Male Cook2020 Brittin2021 Witvliet1 Witvliet2 Witvliet3 Witvliet4 Witvliet5 Witvliet6 Witvliet7 Witvliet8 WormNeuroAtlas Randi2023 RipollSanchezShortRange RipollSanchezMidRange RipollSanchezLongRange Test SSData UpdSSData UpdSSData2 - -!!! tip "Choose View" - Raw Data - Neurons - Pharynx - Social Network - Escape Response Circuit - Cook 2019 Fig 3 - Peptidergic Hubs - + Dummy dataset used for testing webpage/graph generation. Do not assume any of these connections are correct!.   Python Reader: TestDataReader - Hub and spoke circuit for social behavior as in Macosko et al. 2009 -!!! abstract "Choose Graph type" + + +!!! abstract inline "Choose Graph type" Graph - Matrix - Hive plot -

+!!! tip "Choose View" -

Dummy dataset used for testing webpage/graph generation. Do not assume any of these connections are correct!.   Reader: TestDataReader

+ Raw Data - Neurons - Pharynx - Social Network - Escape Response Circuit - Cook 2019 Fig 3 - Peptidergic Hubs - + Hub and spoke circuit for social behavior as in Macosko et al. 2009 === "Chemical Exc"
diff --git a/docs/Test_data.md b/docs/Test_data.md index 00e981053..938e5e857 100644 --- a/docs/Test_data.md +++ b/docs/Test_data.md @@ -5,25 +5,25 @@ search: --- -!!! example inline "Choose Dataset" +!!! example "Choose Dataset" White_A White_L4 White_whole Varshney Bentley2016_MA Bentley2016_PEP Cook2019Herm Cook2019Male Cook2020 Brittin2021 Witvliet1 Witvliet2 Witvliet3 Witvliet4 Witvliet5 Witvliet6 Witvliet7 Witvliet8 WormNeuroAtlas Randi2023 RipollSanchezShortRange RipollSanchezMidRange RipollSanchezLongRange Test SSData UpdSSData UpdSSData2 - -!!! tip "Choose View" - Raw Data - Neurons - Pharynx - Social Network - Escape Response Circuit - Cook 2019 Fig 3 - Peptidergic Hubs - + Dummy dataset used for testing webpage/graph generation. Do not assume any of these connections are correct!.   Python Reader: TestDataReader - All of the cells present in the original connectome dataset -!!! abstract "Choose Graph type" + + +!!! abstract inline "Choose Graph type" Graph - Matrix - Hive plot -

+!!! tip "Choose View" -

Dummy dataset used for testing webpage/graph generation. Do not assume any of these connections are correct!.   Reader: TestDataReader

+ Raw Data - Neurons - Pharynx - Social Network - Escape Response Circuit - Cook 2019 Fig 3 - Peptidergic Hubs - + All of the cells present in the original connectome dataset === "Chemical"
diff --git a/docs/Test_data_graph.md b/docs/Test_data_graph.md index f4046b626..aad87d948 100644 --- a/docs/Test_data_graph.md +++ b/docs/Test_data_graph.md @@ -5,25 +5,25 @@ search: --- -!!! example inline "Choose Dataset" +!!! example "Choose Dataset" White_A White_L4 White_whole Varshney Bentley2016_MA Bentley2016_PEP Cook2019Herm Cook2019Male Cook2020 Brittin2021 Witvliet1 Witvliet2 Witvliet3 Witvliet4 Witvliet5 Witvliet6 Witvliet7 Witvliet8 WormNeuroAtlas Randi2023 RipollSanchezShortRange RipollSanchezMidRange RipollSanchezLongRange Test SSData UpdSSData UpdSSData2 - -!!! tip "Choose View" - Raw Data - Neurons - Pharynx - Social Network - Escape Response Circuit - Cook 2019 Fig 3 - Peptidergic Hubs - + Dummy dataset used for testing webpage/graph generation. Do not assume any of these connections are correct!.   Python Reader: TestDataReader - All of the cells present in the original connectome dataset -!!! abstract "Choose Graph type" + + +!!! abstract inline "Choose Graph type" Graph - Matrix - Hive plot -

+!!! tip "Choose View" -

Dummy dataset used for testing webpage/graph generation. Do not assume any of these connections are correct!.   Reader: TestDataReader

+ Raw Data - Neurons - Pharynx - Social Network - Escape Response Circuit - Cook 2019 Fig 3 - Peptidergic Hubs - + All of the cells present in the original connectome dataset === "Chemical" ```plotly diff --git a/docs/Test_data_hiveplot.md b/docs/Test_data_hiveplot.md index 9143745cd..9b3aeb518 100644 --- a/docs/Test_data_hiveplot.md +++ b/docs/Test_data_hiveplot.md @@ -5,25 +5,25 @@ search: --- -!!! example inline "Choose Dataset" +!!! example "Choose Dataset" White_A White_L4 White_whole Varshney Bentley2016_MA Bentley2016_PEP Cook2019Herm Cook2019Male Cook2020 Brittin2021 Witvliet1 Witvliet2 Witvliet3 Witvliet4 Witvliet5 Witvliet6 Witvliet7 Witvliet8 WormNeuroAtlas Randi2023 RipollSanchezShortRange RipollSanchezMidRange RipollSanchezLongRange Test SSData UpdSSData UpdSSData2 - -!!! tip "Choose View" - Raw Data - Neurons - Pharynx - Social Network - Escape Response Circuit - Cook 2019 Fig 3 - Peptidergic Hubs - + Dummy dataset used for testing webpage/graph generation. Do not assume any of these connections are correct!.   Python Reader: TestDataReader - All of the cells present in the original connectome dataset -!!! abstract "Choose Graph type" + + +!!! abstract inline "Choose Graph type" Graph - Matrix - Hive plot -

+!!! tip "Choose View" -

Dummy dataset used for testing webpage/graph generation. Do not assume any of these connections are correct!.   Reader: TestDataReader

+ Raw Data - Neurons - Pharynx - Social Network - Escape Response Circuit - Cook 2019 Fig 3 - Peptidergic Hubs - + All of the cells present in the original connectome dataset === "Chemical"
diff --git a/docs/api/cect/Analysis.md b/docs/api/cect/Analysis.md new file mode 100644 index 000000000..21fd48ecb --- /dev/null +++ b/docs/api/cect/Analysis.md @@ -0,0 +1 @@ +::: cect.Analysis diff --git a/docs/api/summary.md b/docs/api/summary.md index 9fcd48de7..26b8a6591 100644 --- a/docs/api/summary.md +++ b/docs/api/summary.md @@ -1,4 +1,5 @@ * [cect](cect/index.md) + * [Analysis](cect/Analysis.md) * [BrittinDataReader](cect/BrittinDataReader.md) * [CellInfo](cect/CellInfo.md) * [Cells](cect/Cells.md) diff --git a/docs/assets/Test_Neurons_Chemical_Exc_graph.json b/docs/assets/Test_Neurons_Chemical_Exc_graph.json index 32f5a41b5..81530bea8 100644 --- a/docs/assets/Test_Neurons_Chemical_Exc_graph.json +++ b/docs/assets/Test_Neurons_Chemical_Exc_graph.json @@ -11,12 +11,12 @@ "textposition": "middle center", "type": "scatter", "x": [ - -0.877932, - -0.923915 + -0.988656, + -0.986776 ], "y": [ - 0.00289, - 0.028945 + 0.129635, + 0.086008 ] }, { @@ -30,12 +30,12 @@ "textposition": "middle center", "type": "scatter", "x": [ - -0.923915, - -0.991058 + -0.986776, + -1.0 ], "y": [ - 0.028945, - 0.044005 + 0.086008, + 0.032089 ] }, { @@ -49,12 +49,12 @@ "textposition": "middle center", "type": "scatter", "x": [ - -0.233329, - -0.194552 + -0.454996, + -0.386672 ], "y": [ - -0.159622, - -0.190212 + 0.521158, + 0.448148 ] }, { @@ -68,12 +68,12 @@ "textposition": "middle center", "type": "scatter", "x": [ - -0.303647, - -0.233329 + -0.541474, + -0.454996 ], "y": [ - -0.14207, - -0.159622 + 0.438789, + 0.521158 ] }, { @@ -87,12 +87,12 @@ "textposition": "middle center", "type": "scatter", "x": [ - 0.243629, - 0.309722 + 0.157617, + 0.206195 ], "y": [ - 0.177089, - 0.20449 + -0.172821, + -0.117865 ] }, { @@ -106,12 +106,12 @@ "textposition": "middle center", "type": "scatter", "x": [ - 0.309722, - 0.272293 + 0.206195, + 0.159815 ], "y": [ - 0.20449, - 0.242361 + -0.117865, + -0.084205 ] }, { @@ -125,12 +125,12 @@ "textposition": "middle center", "type": "scatter", "x": [ - 0.309722, - 0.382934 + 0.206195, + 0.283683 ], "y": [ - 0.20449, - 0.175592 + -0.117865, + -0.131037 ] }, { @@ -144,12 +144,12 @@ "textposition": "middle center", "type": "scatter", "x": [ - 0.309722, - 0.342223 + 0.206195, + 0.247485 ], "y": [ - 0.20449, - 0.269449 + -0.117865, + -0.05039 ] }, { @@ -163,12 +163,12 @@ "textposition": "middle center", "type": "scatter", "x": [ - 0.382934, - 0.364804 + 0.283683, + 0.27528 ], "y": [ - 0.175592, - 0.260144 + -0.131037, + -0.053691 ] }, { @@ -182,12 +182,12 @@ "textposition": "middle center", "type": "scatter", "x": [ - 0.382934, - 0.429849 + 0.283683, + 0.332007 ], "y": [ - 0.175592, - 0.158962 + -0.131037, + -0.150907 ] }, { @@ -201,12 +201,12 @@ "textposition": "middle center", "type": "scatter", "x": [ - 0.342223, - 0.364804 + 0.247485, + 0.27528 ], "y": [ - 0.269449, - 0.260144 + -0.05039, + -0.053691 ] }, { @@ -220,12 +220,12 @@ "textposition": "middle center", "type": "scatter", "x": [ - 0.496116, - 0.429849 + 0.401292, + 0.332007 ], 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