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)))

Hello!
I am trying to use this code to run stardist on all the pics in the directory but I am getting this error,
SyntaxError: no viable alternative at input ‘=’

does anyone know how to fix it.

thank you

`#@ DatasetIOService io
#@ CommandService command

theinput = "C:\Users\abdel\Downloads\8bitgreen";
output = "C:\Users\abdel\Downloads\try";
print (theinput)

setBatchMode(true);
list = getFileList(theinput);
print (list)

for (i = 0; i < lengthof(list); i+=){
IJ.run(list[i], "8-bit", "");
run("Command From Macro", "command=[de.csbdresden.stardist.StarDist2D], args=['input':'list[i]', 'modelChoice':'Versatile (fluorescent nuclei)', 'normalizeInput':'true', 'percentileBottom':'1.0', 'percentileTop':'99.8', 'probThresh':'0.15000000000000002', 'nmsThresh':'0.3', 'outputType':'Both', 'modelFile':'C:\\Users\\abdel\\Downloads\\dsb2018_heavy_augment.zip', 'nTiles':'5', 'excludeBoundary':'2', 'roiPosition':'Automatic', 'verbose':'false', 'showCsbdeepProgress':'false', 'showProbAndDist':'false'], process=[false]");
rm.runCommand(list[i],"Measure");
IJ.saveAs("Results", output + filename);
}
setBatchMode(false);
`

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