Add new tutorials and update existing guides

[petersenpeter]

Added new tutorials covering behavioral paradigms, electrophysiology workflow, managing data storage, setting up lab infrastructure, and two-photon imaging workflow. Updated existing tutorials to reference new guides, expanded instructions for personal attributes, group and project management, and API usage. These changes improve documentation coverage and provide step-by-step guidance for users on experimental setup, data management, and programmatic access.

[Copilot]

Pull Request Overview

This pull request significantly expands BrainSTEM's tutorial documentation by adding five new comprehensive tutorials and updating existing guides to provide better cross-referencing and expanded instructional content. The changes improve documentation coverage for experimental workflows, infrastructure setup, and data management.

• Added comprehensive tutorials for behavioral paradigms, electrophysiology workflow, data storage management, lab infrastructure setup, and two-photon imaging workflow
• Updated existing tutorials with expanded instructions for personal attributes, group/project management, and API usage
• Enhanced cross-referencing between tutorials with "Next Steps" sections linking related workflows

Reviewed Changes

Copilot reviewed 13 out of 13 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
docs/tutorials/two-photon-imaging-workflow.md	New comprehensive tutorial covering complete two-photon calcium imaging experiments from setup to analysis
docs/tutorials/setting-up-lab-infrastructure.md	New detailed guide for establishing lab foundations including setups, equipment, and inventories
docs/tutorials/managing-data-storage.md	New tutorial covering data storage configuration and dynamic linking for analysis workflows
docs/tutorials/electrophysiology-workflow.md	New complete workflow tutorial for electrophysiology experiments with spatial learning paradigms
docs/tutorials/behavioral-paradigms.md	New tutorial explaining behavioral paradigm creation and management
docs/tutorials/submit-resource-and-taxonomies.md	Updated with expanded guidelines and "Next Steps" section
docs/tutorials/sharing-project-publicly.md	Added "Next Steps" section linking to related tutorials
docs/tutorials/managing-projects.md	Added "Next Steps" section with workflow integration
docs/tutorials/managing-groups.md	Expanded content and added "Next Steps" section
docs/tutorials/python-api-tool.md	Enhanced with error handling, examples, and "Next Steps"
docs/tutorials/matlab-api-tool.md	Improved with troubleshooting and "Next Steps" section
docs/tutorials/get_started.md	Expanded personal attributes section with detailed instructions
docs/tutorials.md	Updated main tutorial index with new tutorial links

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[petersenpeter]

Hi Mingze

Have you had time to review the new tutorials and fix the ephys tutorial? The 2p tutorial is not ready - I can continue working on it.

[MingzeDou]

Hi peter,

I only reformatted the ephys md file, nothing is changed otherwise. I think the API tutorials could be improved a bit. I am working on it now. Also I am checking the updates we made recently, then to make sure our API tutorials are up-to-date.

[MingzeDou]

Hi Peter,

I moved your API tools in tutorial section to api tools section since it's redundant to have 2 different tutorials. But I still left the tutorial files, directing to the api tools page.

[petersenpeter]

Hi Mingze,

That's fine as long as they cover the same topics. I see you included a lot on the Python tool page, but the MATLAB API tool page doesn't cover the same content.

If we proceed with this, I think we should simply remove the two empty tool tutorials and references to them. Furthermore, there are tutorials within the GitHub repositories that we could link to instead.

[MingzeDou]

Hi peter, you mean remove the api tools in tutorial? If you think it's redundant then of course we can delete it. (Because you put them in the tutorial I didn't know if it's intentional) I have added the link directing to api repo. And I think it would be a good idea to also have an md file with code block as what we made. So our users wont always have to go to the ipynb or m file.

[petersenpeter]

Let's discuss it in person tomorrow

[MingzeDou]

Hi Peter,

I think this is ready to be merged. I added an import tool doc and a 2fa doc