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labsyspharm / mcmicro

Multiple-choice microscopy pipeline
https://mcmicro.org/
MIT License
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segementation using cell pose #547

Open yas92 opened 3 months ago

yas92 commented 3 months ago

I used cell pose for segmentation using MCMICRO and found that some cells are undersegmented while viewing in segmentation mask. Is there any threshold to adjust in param.yml file.

Your response will be very appreciated. param.yml.txt

kbestak commented 3 months ago

Hi, I would suggest adjusting the diameter, flow_threshold and cellprob_threshold parameters for Cellpose. Here, you can find the explanations of those three parameters. You can provide the parameters to the pipeline with the options block in the params file, like this: 

workflow:
  start-at: segmentation
  stop-at: downstream
  viz: true
  segmentation-recyze: false
  segmentation: cellpose
  downstream: scimap
options:
  cellpose: --pretrained_model cyto --no_npy --diameter 20 --flow_threshold 0.6