[Feature] Output files for Brainmapper without cell classification

[Eddymorphling]

Hi folks,
A really naive questions here. I am simply doing registration and cell detection without any cell classification using the CLI. But it does not create any of the output files when doing so that is mentioned over here. I end up with an error that said cell classification.xml not found and the run completes. Any chance we can still get these output files with doing cell classification?
Thanks!

[adamltyson]

Hi @Eddymorphling do you get an actual error message, or does it just say that classification isn't running (as you want)? But no, if you skip parts of the pipeline, it will only do the analysis that can be done based on the results it has (e.g. it needs classified cells). If you want to create custom pipeline, then I would use either the Python APIs or the napari plugins. If you have any usage questions, please ask over at https://forum.image.sc/, tagging your question with both "brainglobe" and the tool you're using (e.g. "brainmapper").

[Eddymorphling]

Thank you @adamltyson. I deleted my logs hence I don't have the error message for you. Let me try via the python API. I would simply want to run cell detection + generate the out analysis files. Thanks for reminding me about the ImageJ forum, I keep forgetting about it, apologies.

[adamltyson]

The easiest way is to use the napari plugins for brainreg, cellfinder & then brainmapper. However, this may not the simple, headless automated workflow you're after. I've transferred this issue to track the idea of generating the analysis files without the classification step within the brainmapper CLI.

[Eddymorphling]

Ah ok. Thank you. I prefer to use the API to custom build this. Would you happen to have any documentation to build a python API that allows me to jump from brainreg>>cell detection>>analysis files?

[adamltyson]

No, but that's basically what brainmapper is. Shouldn't be too hard to adapt:
https://github.com/brainglobe/brainglobe-workflows/blob/main/brainglobe_workflows/brainmapper/main.py

Alternatively, you could submit a PR to brainglobe-workflows to add the options to brainmapper that you need?

[Eddymorphling]

Got it. Let me see if I do tweak this. Thank you.

[Eddymorphling]

Also, just a small question @adamltyson . Is it possible to have labels highlighting for all the brain region in the atlas that I used for registration when opening brainmapper output files in napari?

[adamltyson]

Sorry to be a pain, but would you mind asking new questions on image.sc? That way we can keep this issue for the new feature to add to brainmapper.

[Eddymorphling]

Ah yes. Will do!

[Eddymorphling]

No, but that's basically what brainmapper is. Shouldn't be too hard to adapt: https://github.com/brainglobe/brainglobe-workflows/blob/main/brainglobe_workflows/brainmapper/main.py

Alternatively, you could submit a PR to brainglobe-workflows to add the options to brainmapper that you need?

Hi @adamltyson I havent been able to work on this yet. Do you know if you had a chance to work on this as a feature yet? Sorry to be a bother. Thank you.

[adamltyson]

Hi @Eddymorphling, unfortunately no, it's quite far down our list of priorities I'm afraid.