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Defense-Circuits-Lab / findmycells

An end-to-end bioimage analysis pipeline with state-of-the-art tools for non-coding experts
https://defense-circuits-lab.github.io/findmycells/
GNU General Public License v3.0
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No quantification is carried out #49

Open NataliaFavila opened 6 months ago

NataliaFavila commented 6 months ago

Dear findmycells developers,

we are having issues with the GUI based jupyter notebook application of findmycells.

We are testing the gui using the cfos dummy data provided. All steps from preprocessing to segmentation work well. However, after that when quantification is run, nothing is created in the quantified_segmentations and thus, when asked to save the data to excel, nothing is output either.

Any idea why this might be happening?

This is happening to us in both Windows and Linux, and we tried using both firefox and chrome. We have access to a GPU and all steps before quantification, that is the segmentation (both instance and semantic) part, work well with it.

Best regards,

Natalia

KonKob commented 11 hours ago

Dear Natalia, I'm very sorry that you encountered an error when using findmycells and that it took such a long time to answer you. I assume, you installed findmycells locally on your server, is that correct? As you did not mention the postprocessing step, I just want to make sure you did run it as well before quantification? I checked the findmycells on Google colab just now and apart from two versioning issues, that you will have to fix when using Google Colab or a recent findmycells installation, I was able to run the full pipeline and create the result sheets.