Cell and nuclear segmentation with star-convex shapes
Input
name:type
description
pattern
meta
:map
Groovy Map containing sample information
e.g. [ id:'sample1' ]
image
:file
Single channel nuclear image
*.{tiff,tif}
model_name
:string
Name of a pretrained StarDist model (e.g. ‘2D_versatile_fluo’,
‘2D_versatile_he’). Used when model_path is not provided.
Pass ” (empty string) if providing a custom model path or
passing -m via ext.args.
model_path
:file
Optional path to a custom StarDist model directory. When provided,
takes precedence over model_name. Pass [] (empty list) to use a
pretrained model name instead.
*
Output
name:type
description
pattern
mask
meta
:map
Groovy Map containing sample information
e.g. [ id:'sample1' ]
*.stardist.tif
:file
labelled mask output from stardist in tif format.
*.{tiff,tif}
versions_stardist
${task.process}
:string
The name of the process
stardist
:string
The name of the tool
pip show stardist | sed -n 's/^Version: //p'
:eval
The expression to obtain the version of the tool
versions_python
${task.process}
:string
The name of the process
python
:string
The name of the tool
python --version | sed 's/Python //'
:eval
The expression to obtain the version of the tool
versions_tensorflow
${task.process}
:string
The name of the process
tensorflow
:string
The name of the tool
pip show tensorflow | sed -n 's/^Version: //p'
:eval
The expression to obtain the version of the tool
versions_tifffile
${task.process}
:string
The name of the process
tifffile
:string
The name of the tool
pip show tifffile | sed -n 's/^Version: //p'
:eval
The expression to obtain the version of the tool
Topics
name:type
description
pattern
versions
${task.process}
:string
The name of the process
stardist
:string
The name of the tool
pip show stardist | sed -n 's/^Version: //p'
:eval
The expression to obtain the version of the tool
${task.process}
:string
The name of the process
python
:string
The name of the tool
python --version | sed 's/Python //'
:eval
The expression to obtain the version of the tool
${task.process}
:string
The name of the process
tensorflow
:string
The name of the tool
pip show tensorflow | sed -n 's/^Version: //p'
:eval
The expression to obtain the version of the tool
${task.process}
:string
The name of the process
tifffile
:string
The name of the tool
pip show tifffile | sed -n 's/^Version: //p'
:eval
The expression to obtain the version of the tool
Tools
stardist
BSD 3-Clause
Stardist is an cell segmentation tool developed in Python by Martin Weigert and Uwe Schmidt
