cellpose segments cells in images using GPU-accelerated deep learning
Input
name:type
description
pattern
meta{:bash}
:map
Groovy Map containing sample information
(sample id)
image{:bash}
:file
tif file ready for segmentation
*.{tif,tiff}
model{:bash}
:file
Optional custom cellpose model file. When provided, passed as
—pretrained_model to cellpose. Pass [] (empty list) to use the
default model (cpsam in cellpose 4).
*
Output
name:type
description
pattern
mask{:bash}
meta{:bash}
:map
Groovy Map containing sample information
[sample id]
${prefix}/*masks.tif{:bash}
:file
labelled mask output from cellpose in tif format
${prefix}/*masks.tif
flows{:bash}
meta{:bash}
:map
Groovy Map containing sample information
[sample id]
${prefix}/*flows.tif{:bash}
:file
cell flow output from cellpose
${prefix}/*flows.tif
cells{:bash}
meta{:bash}
:map
Groovy Map containing sample information
[sample id]
