Future plan for `cellfinder-visualize`

[adamltyson]

cellfinder-visualise is a useful tool to analyse and visualise data output from the cellfinder command-line tool at a group level.

Maintenance of this repo hasn't been happening, and I think it's hard to do so because:

• It's currently broken (partly due to brainrender issues)
• The cellfinder CLI isn't a top priority for us
• It's a bit different to our other tools (stand-alone GUI)

I've been thinking about what to do with it. I was thinking:

• Close all issues
• Archive
• Create an issue detailing what features we would eventually like to support in the future. Likely some combination of:
  • Scripts to analyse in brainglobe-workflows
  • GUI for exploratory plotting & visualisation (maybe in brainrender-napari)

Any thoughts @brainglobe/active-devs?

[willGraham01]

Why not merge the visualisation functionality into cellfinder-napari (or new cellfinder post v1) if it's meant to be used on cellfinder outputs? Or is this another "cellfinder" historical naming thing?

But I agree, particularly with cellfinder-CLI moving to workflows, it makes sense for the scripts to do this analysis to move there too. Even if they are only surviving in issue form for now.

[adamltyson]

Why not merge the visualisation functionality into cellfinder-napari (or new cellfinder post v1) if it's meant to be used on cellfinder outputs? Or is this another "cellfinder" historical naming thing?

Partly a history thing, it requires cell detection & registration. More generally though, cellfinder should just "find cells", and other tools can do other types of more specialised analysis workflow.

[adamltyson]

cellfinder-visualize has been archived, and a note about its future added to the readme