BrainGlobe : Update Atlas packaging scripts to Altas API v2 (Pranav Kapoor) #44

pranav33317 · 2025-04-02T16:20:43Z

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Please fill out as much of this template as you can, but if you have any problems or questions, just leave a comment and we will help out :)

Description

What is this PR

Bug fix
Addition of a new feature
Other

Why is this PR needed?
My proposal for GSOC 2025
What does this PR do?

References

Please reference any existing issues/PRs that relate to this PR.

How has this PR been tested?

Please explain how any new code has been tested, and how you have ensured that no existing functionality has changed.

Is this a breaking change?

If this PR breaks any existing functionality, please explain how and why.

Does this PR require an update to the documentation?

If any features have changed, or have been added. Please explain how the
documentation has been updated.

Checklist:

The code has been tested locally
Tests have been added to cover all new functionality
The documentation has been updated to reflect any changes
The code has been formatted with pre-commit

adamltyson · 2025-04-02T16:52:57Z

Hi @pranav33317, could you remove the template boilerplate text from your application, it's quite hard to read as it is.

pranav33317

Have made the changes sir . Could you please provide more feedback ?
Thanks

adamltyson · 2025-04-03T12:05:29Z

Hi @pranav33317, there is still some of the template boilerplate text remaining. There is also formatting (e.g. indents that create code blocks) that make it hard to read. Could you view the markdown in the GitHub web interface and make the necessary changes? Thanks!

Could you also restore the deleted template file, so that it isn't removed when this PR is merged?

I fixed the indentation and formatting of the .md file.

pranav33317

Is this fine now sir @adamltyson ?

adamltyson

Hi @pranav33317, I've left a few suggestions. Please note at this stage, we're not able to offer any further feedback. Good luck!

adamltyson · 2025-04-07T09:39:22Z

GSoC-2025/application_template.md

Could you remove all changes to this file? The template should stay as it is for everyone else.

adamltyson · 2025-04-07T09:39:37Z

GSoC-2025/pranav_kapoor.md

Could you rename this file to adhere to the template?

adamltyson · 2025-04-07T09:40:05Z

GSoC-2025/pranav_kapoor.md

+  - PR: [https://github.com/brainglobe/brainglobe-atlasapi/pull/546#pullrequestreview-2729541724](https://github.com/brainglobe/brainglobe-atlasapi/pull/546#pullrequestreview-2729541724)  
+    I tried to disable parallel mesh creation in various files to simplify mesh creation while simultaneously working on [Issue #429](https://github.com/brainglobe/brainglobeatlasapi/issues/429).  
+- **Proposal discussion link:**  
+  - [https://github.com/brainglobe/brainglobe-atlasapi/pull/554](https://github.com/brainglobe/brainglobe-atlasapi/pull/554)  


This should be a link to the discussion about your proposed project, i.e. this PR.

adamltyson · 2025-04-07T09:41:03Z

GSoC-2025/pranav_kapoor.md

+## Project proposal
+
+### Synopsis
+As someone deeply fascinated by the intricate workings of the brain, I have always admired how neuroanatomical atlases empower researchers to navigate complex brain structures with ease. BrainGlobe’s Atlas API stands out as a robust tool that consolidates atlas‑registered data into a unified Python interface. There is now an exciting opportunity to further enhance this system by adopting the OpenMINDS SANDS standard—a community‑driven format that delivers more interoperable brain data. This upgrade will enable researchers to derive deeper, more accurate insights.


While this is nice, it isn't really a synopsis of your project proposal.

adamltyson · 2025-04-07T09:41:26Z

GSoC-2025/pranav_kapoor.md

+### Synopsis
+As someone deeply fascinated by the intricate workings of the brain, I have always admired how neuroanatomical atlases empower researchers to navigate complex brain structures with ease. BrainGlobe’s Atlas API stands out as a robust tool that consolidates atlas‑registered data into a unified Python interface. There is now an exciting opportunity to further enhance this system by adopting the OpenMINDS SANDS standard—a community‑driven format that delivers more interoperable brain data. This upgrade will enable researchers to derive deeper, more accurate insights.
+
+My project aims to enhance the utility of the BrainGlobe ecosystem by updating the atlas packaging scripts so they output data in the OpenMINDS SANDS format. This upgrade is critical for researchers who need consistent, comprehensive data to integrate findings across studies and species. By delivering a modular, well-documented solution complete with rigorous testing, I will enable both seasoned neuroscientists and new entrants in the field, making advanced neuroinformatics more accessible to all.


How exactly will this make advanced neuroinformatics more accessible?

adamltyson · 2025-04-07T09:42:12Z

GSoC-2025/pranav_kapoor.md

+   - Develop comprehensive tests covering all new and modified features.
+   - Update the documentation to guide users on how to generate and utilize OpenMINDS SANDS‑compliant atlases.
+2. **Stretch Goals (if time permits):**
+   - Extend support for additional species or imaging modalities.


Do you mean extend support for additional atlases? Imaging modalities isn't really relevant here.

adamltyson · 2025-04-07T09:43:41Z

GSoC-2025/pranav_kapoor.md

+   - Integrate schema validation using tools like `jsonschema` to ensure full compliance with OpenMINDS SANDS.
+   - Create a conversion utility for existing atlas packages to the new standard.
+3. **Time Commitment:**  
+   I will be devoting 30–35 hours per week towards this GSoC project.


Can you clarify the time commitment (and project size). Here you say 30-35 hours per week, but the timetable implies it's 30 hours every 2 weeks.

adamltyson · 2025-04-07T09:44:16Z

GSoC-2025/pranav_kapoor.md

+|----------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-----------|
+| 1–2      | **Community Bonding & Research:**<br>- Immerse myself in the BrainGlobe Atlas API, current packaging scripts, and OpenMINDS SANDS documentation.<br>- Engage with mentors to clarify requirements and set up a focused development environment.      | 30        |
+| 3–4      | **Design & Planning:**<br>- Map the existing atlas data to the OpenMINDS SANDS schema.<br>- Design a modular function (e.g., `wrapup_atlas_to_openminds`) and create clear wireframes for the conversion workflow.                                      | 30        |
+| 5–6      | **Core Development – Part 1:**<br>- Develop the new wrap‑up function in a separate module (e.g., `openminds_wrapup.py`).<br>- Adapt the Allen Human atlas packaging script to integrate this function and produce the new output.                         | 30        |


Just because the human atlas is a low priority atlas, I would change this to the Allen mouse atlas.

pranav33317 · 2025-04-08T11:37:10Z

Sir I have made the changes you described, sorry for the time irregularities, have fixed them.
Could you please merge my proposal ?
Sorry found some errors , will re - commit in a minute
Thanks a lot for your feedback

adamltyson · 2025-04-08T11:38:45Z

Great. Could you revert your changes to the application template so I can approve and merge this PR? Thanks!

pranav33317 · 2025-04-08T11:42:56Z

Great. Could you revert your changes to the application template so I can approve and merge this PR? Thanks!

Yes sir ,please give me a minute , the renaming deleted my file and I have mistakenly committed the older file. Will re- commit ASAP.
Thanks

pranav33317 · 2025-04-08T12:05:18Z

Yes sir , I am done , have restored the application template to its original state and resolved the errors in my proposal.
Thanks again :)

adamltyson · 2025-04-08T12:32:17Z

Hi @pranav33317, there is still an edit to the application template (which reverts another PR). Could you remove it from this PR?

pranav33317 · 2025-04-08T12:51:10Z

Sir have restored the application template to the main branch :

pranav33317 · 2025-04-08T12:58:45Z

Sir should I submit my proposal in the .md file format ? What format should I use for the proposal pdf, the application template one ?
Thanks

adamltyson · 2025-04-08T13:02:01Z

I think all details will be on the GSoC website. Please follow their instructions.

umaima84 · 2025-04-08T13:14:24Z

Hi @adamltyson,
I'm Umaima, and I'm interested in contributing to the Atlas Packaging Script project for GSoC 2025. I’m currently working on my proposal and would really appreciate it if you could review it before submission. Could you please let me know the best way to share my draft with you?

Also, I couldn’t find a dedicated repository for this specific project. Could you guide me on which repository I should contribute to for this project?

Thanks in advance!

adamltyson · 2025-04-08T13:17:19Z

Hi @umaima84, please ask all questions on the Neuroinformatics Unit Zulip, in the #GSoC channel, otherwise other people are notified if you comment on a PR. All information is in our contributor guidelines but we won't be able to provide any feedback at this late stage.

umaima84 · 2025-04-09T03:46:05Z

I can't submit my proposal as the misunderstanding of time. As late date was 8 April and I was thinking the time will complete after 12pm but it complete at 11pm according to Pakistan It's my biggest mistake. Kindly help me if I can submit my proposal now. Check my proposal. https://docs.google.com/document/d/15NPsAQen7Asi0AYaT1R9RPi8UpfHErJIiR2wGcmNv8E/edit?usp=sharing

…

On Tue, Apr 8, 2025, 6:17 PM Adam Tyson ***@***.***> wrote: Hi @umaima84 <https://github.com/umaima84>, please ask all questions on the Neuroinformatics Unit Zulip, in the #GSoC channel, otherwise other people are notified if you comment on a PR. All information is in our contributor guidelines <https://neuroinformatics.dev/get-involved/gsoc/guidelines.html> but we won't be able to provide any feedback at this late stage. — Reply to this email directly, view it on GitHub <#44 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BMBGKK636EYQRGKTVY3VQPL2YPD7NAVCNFSM6AAAAAB2KAG2NWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDOOBWGQYTANRXHA> . You are receiving this because you were mentioned.Message ID: ***@***.***> *adamltyson* left a comment (neuroinformatics-unit/gsoc#44) <#44 (comment)> Hi @umaima84 <https://github.com/umaima84>, please ask all questions on the Neuroinformatics Unit Zulip, in the #GSoC channel, otherwise other people are notified if you comment on a PR. All information is in our contributor guidelines <https://neuroinformatics.dev/get-involved/gsoc/guidelines.html> but we won't be able to provide any feedback at this late stage. — Reply to this email directly, view it on GitHub <#44 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BMBGKK636EYQRGKTVY3VQPL2YPD7NAVCNFSM6AAAAAB2KAG2NWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDOOBWGQYTANRXHA> . You are receiving this because you were mentioned.Message ID: ***@***.***>

adamltyson · 2025-04-09T08:17:42Z

Unfortunately we cannot consider any applications not submitted through the GSoC system. Please also refrain from commenting on unrelated PRs. I will now lock this conversation.

Pranav Kapoor's proposal

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removed template info

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pranav33317 commented Apr 2, 2025

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pranav33317 and others added 2 commits April 4, 2025 22:22

restored previous file

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Update pranav_kapoor.md

4a66b35

I fixed the indentation and formatting of the .md file.

pranav33317 commented Apr 4, 2025

View reviewed changes

adamltyson reviewed Apr 7, 2025

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pranav33317 added 2 commits April 8, 2025 17:02

final proposal

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final proposal GSOC

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pranav33317 added 2 commits April 8, 2025 17:30

Final proposal

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Final Proposal

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adamltyson mentioned this pull request Apr 8, 2025

BrainGlobe : Adding to Brainglobe's data visualisation tools (Pranav Kapoor) #62

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Revert application_template.md to the version in main

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BrainGlobe : Update Atlas packaging scripts to Altas API v2 (Pranav Kapoor) #44

BrainGlobe : Update Atlas packaging scripts to Altas API v2 (Pranav Kapoor) #44

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BrainGlobe : Update Atlas packaging scripts to Altas API v2 (Pranav Kapoor) #44

BrainGlobe : Update Atlas packaging scripts to Altas API v2 (Pranav Kapoor) #44

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Description

References

How has this PR been tested?

Is this a breaking change?

Does this PR require an update to the documentation?

Checklist:

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