stardist_script.py

#@ DatasetIOService io
#@ CommandService command

""" This example runs stardist on all tif files in a folder

Full list of Parameters: 

res = command.run(StarDist2D, False,
			 "input", imp, "modelChoice", "Versatile (fluorescent nuclei)",
			 "modelFile","/path/to/TF_SavedModel.zip",
			 "normalizeInput",True, "percentileBottom",1, "percentileTop",99.8,
			 "probThresh",0.5, "nmsThresh", 0.3, "outputType","Label Image",
			 "nTiles",1, "excludeBoundary",2, "verbose",1, "showCsbdeepProgress",1, "showProbAndDist",0).get();			

"""

from de.csbdresden.stardist import StarDist2D 
from glob import glob
import os

# run stardist on all tiff files in <indir> and save the label image to <outdir>
indir   = os.path.expanduser("~/Tmp/images/")
outdir  = os.path.expanduser("~/Tmp/labels/")

for f in sorted(glob(os.path.join(indir,"*.tif"))):
	print "processing ", f
  
	imp = io.open(f)
  
	res = command.run(StarDist2D, False,
			"input", imp,
			"modelChoice", "Versatile (fluorescent nuclei)",
			).get()
	label = res.getOutput("label")
  
	io.save(label, os.path.join(outdir,"label."+os.path.basename(f)))

@Bassetyabrag You cross-posted this also at the image.sc forum, where I replied to you.