blog about new mouse atlases #281

alessandrofelder · 2025-02-05T18:28:33Z

Description

What is this PR

Bug fix
Addition of a new feature
Other

What does this PR do?

I've kept things as simple as possible, just to give a top-level idea of the new mouse atlases we've recently added.

alessandrofelder · 2025-02-05T18:30:40Z

@carlocastoldi this is a WIP blog - but just flagging that I'd like your review on the KimDevCCF part (which is currently the only one that is fleshed out) and the confirmation you're happy to be a co-author, when you have a moment, thanks!

adamltyson

Some notes just because I happened to be taking a look. I'll review properly when it's done :)

docs/source/blog/mouse-atlases-added.md

carlocastoldi · 2025-02-10T15:30:42Z

Hi!

I am sorry for my late reply, i had some busy days.
That said, I like the tone and that it's a quick post, but covers the main question. Namely, why adding an additional developmental mouse atlas.

Lately, however, I have been thinking whether making an atlas for each reference image was the correct approach. Only recently I discovered that BrainGlobe API also support for additional_references. Using them feels like the better and correct approach, don't you think?

adamltyson · 2025-02-10T15:37:08Z

Lately, however, I have been thinking whether making an atlas for each reference image was the correct approach. Only recently I discovered that BrainGlobe API also support for additional_references. Using them feels like the better and correct approach, don't you think?

Yes, that probably would have been better. It would depend on the size of the atlases though. The "original" version of the P56 dev atlas was split up into different atlases because otherwise the packaged atlas was too large (>10 GB).

Co-authored-by: Adam Tyson <[email protected]>

adamltyson

This is really nice @alessandrofelder, thanks! Quite a few comments though, sorry!

docs/source/blog/mouse-atlases-added.md

adamltyson · 2025-02-20T12:04:26Z

docs/source/blog/mouse-atlases-added.md

+
+**Figure 3. A visualisation of both the LSFM (top row) and MRI (bottom row) templates and their annotations contained in Gubra's multimodal mouse brain atlas. Note that both modes are available at 25um, but the LSFM is slightly smaller due to shrinkage effects of sample preparation for LSFM.**
+
+[Perens et al](https://doi.org/10.1007/s12021-023-09623-9) created a multimodal atlas of the mouse brain, in collaboration with Gubra, a Danish biotech company. It contains both a MRI and a LSFM template at 25 micrometer resolution (`perens_stereotaxic_mri_mouse_25um` and `perens_multimodal_lsfm_25um`, respectively), with annotations based on the Allen Mouse Brain atlas. This atlas enables the linking of in-vivo (MRI) data with ex-vivo (LSFM) data in atlas space.


Some changes because a) Johanna (Perens) works for Gubra, so it's not really "in collaboration with", and also because these atlases are in different coordinate spaces, it doesn't (yet) allow the user to link in/ex vivo within BrainGlobe.

Suggested change

[Perens et al](https://doi.org/10.1007/s12021-023-09623-9) created a multimodal atlas of the mouse brain, in collaboration with Gubra, a Danish biotech company. It contains both a MRI and a LSFM template at 25 micrometer resolution (`perens_stereotaxic_mri_mouse_25um` and `perens_multimodal_lsfm_25um`, respectively), with annotations based on the Allen Mouse Brain atlas. This atlas enables the linking of in-vivo (MRI) data with ex-vivo (LSFM) data in atlas space.

[Perens et al.](https://doi.org/10.1007/s12021-023-09623-9) created a multimodal atlas of the mouse brain containing both an MRI and an LSFM template at 25 micrometer resolution (`perens_stereotaxic_mri_mouse_25um` and `perens_multimodal_lsfm_25um`, respectively), with annotations based on the Allen Mouse Brain atlas.

I would also like a line highlighting that the MRI atlas is stereotaxic.

"The MRI template is in flat skull position, and is able to be used for planning stereotaxic surgeries."

Also makes me think one day stereotaxic atlases in braingllobe should perhaps have a bregma and lambda metadata field but that's something to consider in the future.

Hey @PolarBean - I've added a sentence along those lines. Are you happy for this to be merged now?

adamltyson · 2025-02-20T12:04:55Z

docs/source/blog/mouse-atlases-added.md

+
+## Gubra's Multimodal 3D mouse brain atlas
+
+```{image} ./images/gubra_multimodal.png


This image isn't super useful. You can't really see anything in the MRI and LSFM templates. I would stick with a 2D version.

docs/source/blog/mouse-atlases-added.md

adamltyson · 2025-02-20T12:07:52Z

docs/source/blog/mouse-atlases-added.md

+
+**Figure 1. LSFM templates for embryonic developmental stages (from left to right: E11.5, E13.5, E15.5, E18.5) available in the Kim DevCCF.**
+
+![Coronal sections for all templates for Kim DevCCF template at E18.5](./images/kim_dev_embryonic_18_all_modalities_2d.png)


Can this figure be cropped a bit to make the brains bigger? Also, the bottom right image (ADC?) should be adjusted a bit, you can't see anything in the brain!

docs/source/blog/mouse-atlases-added.md

Co-authored-by: Adam Tyson <[email protected]> Co-authored-by: Harry Carey <[email protected]>

PolarBean

Looks great. Minor feedback.

PolarBean · 2025-02-20T13:07:39Z

docs/source/blog/mouse-atlases-added.md

+
+**Figure 3. A visualisation of both the LSFM (top row) and MRI (bottom row) templates and their annotations contained in Gubra's multimodal mouse brain atlas. Note that both modes are available at 25um, but the LSFM is slightly smaller due to shrinkage effects of sample preparation for LSFM.**
+
+[Perens et al](https://doi.org/10.1007/s12021-023-09623-9) created a multimodal atlas of the mouse brain, in collaboration with Gubra, a Danish biotech company. It contains both a MRI and a LSFM template at 25 micrometer resolution (`perens_stereotaxic_mri_mouse_25um` and `perens_multimodal_lsfm_25um`, respectively), with annotations based on the Allen Mouse Brain atlas. This atlas enables the linking of in-vivo (MRI) data with ex-vivo (LSFM) data in atlas space.


I would also like a line highlighting that the MRI atlas is stereotaxic.

"The MRI template is in flat skull position, and is able to be used for planning stereotaxic surgeries."

Also makes me think one day stereotaxic atlases in braingllobe should perhaps have a bregma and lambda metadata field but that's something to consider in the future.

carlocastoldi · 2025-02-21T09:06:06Z

Thank you all for the amazing work!

draft kimdevccf + intro for mouse blog

540680e

adamltyson reviewed Feb 6, 2025

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Demba dev mouse brainglobe/brainglobe-atlasapi#492

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alessandrofelder and others added 6 commits February 19, 2025 17:14

Apply suggestions from code review

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Co-authored-by: Adam Tyson <[email protected]>

simple description of the australian mouse brain

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spell out abbreviation

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describe Gubra, improve Australian mouse atlas paragraph

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make Gubra image span 100% width, needed due to its different shape

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fix typo in mouse blog

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alessandrofelder marked this pull request as ready for review February 20, 2025 11:50

alessandrofelder requested review from adamltyson and PolarBean February 20, 2025 11:50

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Co-authored-by: Adam Tyson <[email protected]> Co-authored-by: Harry Carey <[email protected]>

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improve images and text as per code review

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alessandrofelder changed the title ~~Mouse blog~~ blog about new mouse atlases Feb 20, 2025

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alessandrofelder requested a review from PolarBean February 20, 2025 13:52

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Document the addition of the perens MRI atlas #273

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adamltyson merged commit 909919c into main Feb 20, 2025
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adamltyson deleted the mouse-blog branch February 20, 2025 17:02

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blog about new mouse atlases #281

blog about new mouse atlases #281

alessandrofelder commented Feb 5, 2025 •

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carlocastoldi commented Feb 21, 2025


		Figure 3. A visualisation of both the LSFM (top row) and MRI (bottom row) templates and their annotations contained in Gubra's multimodal mouse brain atlas. Note that both modes are available at 25um, but the LSFM is slightly smaller due to shrinkage effects of sample preparation for LSFM.

		[Perens et al](https://doi.org/10.1007/s12021-023-09623-9) created a multimodal atlas of the mouse brain, in collaboration with Gubra, a Danish biotech company. It contains both a MRI and a LSFM template at 25 micrometer resolution (`perens_stereotaxic_mri_mouse_25um` and `perens_multimodal_lsfm_25um`, respectively), with annotations based on the Allen Mouse Brain atlas. This atlas enables the linking of in-vivo (MRI) data with ex-vivo (LSFM) data in atlas space.


		## Gubra's Multimodal 3D mouse brain atlas

		```{image} ./images/gubra_multimodal.png


		Figure 1. LSFM templates for embryonic developmental stages (from left to right: E11.5, E13.5, E15.5, E18.5) available in the Kim DevCCF.

		![Coronal sections for all templates for Kim DevCCF template at E18.5](./images/kim_dev_embryonic_18_all_modalities_2d.png)

blog about new mouse atlases #281

blog about new mouse atlases #281

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