only save outlines/overlay as skeleton?

[Mrc010]

Hi there,

thanks a lot for your useful plugin. Instead of saving a JPG image with the original image and the outlined ROIs, I'd rather only store the outlined ROIs (aka skeleton/binary image) to be able to further process these skeleton images in another software. I will look into your python script ( # Section Save jpg with outlines) whether I can modify it accordingly. But any suggestions would be much appreciated.

[Mrc010]

Okay, the following modification worked for me...

original code:

                   # Section Save jpg with outlines
                   path_to_multiple_outline = os.path.join(str(gvars['path_multiple_image_directory']),original_name + "_Erosion_" +str(self.pix_erosion_mult)+ "px_" + "Outlines.jpg")
                   outlines_image = original_image.flatten()
                   IJ.saveAs(outlines_image, "JPG", path_to_multiple_outline)

modified code:

                   # Section Save jpg with outlines
                   path_to_multiple_outline = os.path.join(str(gvars['path_multiple_image_directory']),original_name + "_Erosion_" +str(self.pix_erosion_mult)+ "px_" + "Outlines.jpg")
                   IJ.run(original_image, "Select All", "");
                   IJ.setBackgroundColor(0, 0, 0);
                   IJ.run(original_image, "Clear", "slice");
                   outlines_image = original_image.flatten()
                   IJ.saveAs(outlines_image, "JPG", path_to_multiple_outline)