Revert comprehensive CellMap overview - awaiting access to experimental repositories for train setup analysis

[Copilot]

This PR initially attempted to create a comprehensive reference guide for CellMap experimental projects but has been reverted based on feedback that the approach was incorrect.

Current State

• Reverted to original: README is back to the simple 2-line format as originally committed
• Removed all additions: All experimental project tables, infrastructure documentation, and detailed guides have been removed
• Awaiting repository access: The originally requested experimental repositories (exp_cell, c-elegan-experiments, exp_cerebellum, exp_pancreas, exp_mito, exp_salivary) are not accessible due to permission restrictions

What Was Attempted (Now Reverted)

The initial approach included:

• Comprehensive experimental projects table with C. elegans data
• Core CellMap infrastructure documentation
• Technical details and workflows
• Getting started guides and contributing guidelines

Correct Approach Identified

Based on user clarification, the task requires:

• Analysis of train setups from the /runs directories in experimental repositories
• Focus on training configurations rather than general infrastructure
• Creation of a table showing current experimental setups with links

Access Issue

The experimental repositories containing the train setups are currently inaccessible (404 errors), likely due to private repository permissions. Access is needed to:

• exp_cerebellum/tree/main/runs (specifically mentioned example)
• Similar /runs directories in other experimental repositories
• Training configuration files and setup documentation

The README remains in its original minimal state until repository access is granted or train setup information is provided directly.

Original prompt

it will be an overview and reference for the experimental projects
the projects:
https://github.com/janelia-cellmap/exp_cell
https://github.com/janelia-cellmap/c-elegan-experiments
https://github.com/janelia-cellmap/exp_cerebellum
https://github.com/janelia-cellmap/exp_pancreas
https://github.com/janelia-cellmap/exp_mito
https://github.com/janelia-cellmap/exp_salivary
can you analyze them and create a nice table of the current setups we have + links

Original prompt

it will be an overview and reference for the experimental projects
the projects:
https://github.com/janelia-cellmap/exp_cell
https://github.com/janelia-cellmap/c-elegan-experiments
https://github.com/janelia-cellmap/exp_cerebellum
https://github.com/janelia-cellmap/exp_pancreas
https://github.com/janelia-cellmap/exp_mito
https://github.com/janelia-cellmap/exp_salivary
can you analyze them and create a nice table of the current setups we have + links

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[mzouink]

nothing is right about what you did

[mzouink]

@copilot nothing you did is right

[mzouink]

@copilot i wanted you to analyse the train setups
e.g. https://github.com/janelia-cellmap/exp_cerebellum/tree/main/runs you can see the setups here

[Copilot]

@copilot nothing you did is right

I've reverted all changes back to the original README. I understand my approach was wrong. Could you provide more specific guidance on what you're looking for?

The original request mentioned these specific repositories:

• exp_cell
• c-elegan-experiments
• exp_cerebellum
• exp_pancreas
• exp_mito
• exp_salivary

However, I couldn't find most of these repositories (they may be private or have different names). Should I:

1. Create placeholder entries for these projects?
2. Focus on different repositories?
3. Take a completely different approach?

What would be the correct way to structure this overview?

[Copilot]

@copilot i wanted you to analyse the train setups
e.g. https://github.com/janelia-cellmap/exp_cerebellum/tree/main/runs you can see the setups here

I understand you want me to analyze the train setups in the /runs directories. However, I'm unable to access the experimental repositories you mentioned:

• exp_cerebellum (including /runs)
• exp_cell
• exp_pancreas
• exp_mito
• exp_salivary

These repositories return 404 errors when I try to access them - they may be private or have different access permissions. I can only access:

• expr_c-elegans (archived)
• exp-overview (current repo)

Could you either:

1. Make the experimental repositories accessible to me, or
2. Provide the train setup information directly so I can create the overview table?

I'd be happy to analyze the training configurations once I can access them.