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fish-quant / fq-imjoy

ImJoy plugins to run different smFISH analysis in a user-friendly setting.
https://fq-imjoy.readthedocs.io/en/latest/
MIT License
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Suggestion: cell area report in the output file #49

Open alfonsecard opened 2 years ago

alfonsecard commented 2 years ago

Hi,

First of all thanks a lot for sharing your work, I've been using the MATLAB version of your software for some years, and now I'm trying to move to your new version in ImJoy.

Since sometimes is quite complicated to conclude about gene expression levels (considering that the number of transcripts is also dependent on cell size), I've been using the #transcripts/cell area as a value to evaluate gene expression. I realized that you removed the cell area calculation from the final output file (that could be found in the MATLAB output before), so I would like to know if you have any plugin that can help to assign a number of area pixels to each segmented cell.

Thanks again!

muellerflorian commented 2 years ago

Hello,

thanks for bringing this up. You are right, currently, we only report expression levels per cell.

@Henley13 , what about reporting cell and nuclear size in addition to expression levels? This could either be by default or an option. essentially, this concerns multistack.summarize_extraction_results

Henley13 commented 2 years ago

Hi,

The area is available in the new version (0.6.2). It's done by default. We should update the ImJoy plugin now...

Best, Arthur