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hkmoon/label_image_from_rois.py

Forked from maweigert/label_image_from_rois.py
Last active July 7, 2021 11:10
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Generate label image from rois in Fiji
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label_image_from_rois.py
#@ ImagePlus imp
#@ OUTPUT ImagePlus result
from ij import IJ
from ij.plugin.frame import RoiManager
result = IJ.createImage("Labeling", "16-bit black", imp.getWidth(), imp.getHeight(), 1)
ip = result.getProcessor()
rm = RoiManager.getInstance()
for index, roi in enumerate(rm.getRoisAsArray()):
ip.setColor(index+1)
ip.fill(roi)
ip.resetMinAndMax()
IJ.run(result, "glasbey inverted", "")
result.show()
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