Border Exclusion in Fiji

Have you ever tried to remove labels or ROIs from a dedicated region, but struggled to exclude the objects you were interested in?

Then this plugin is for you!

• ✅ Works on 2D label images
• ✅ Works on 2D binary masks
• ✅ Works on 2D ROIs
• ✅ Fast on large images when interpolated
• ❎ 3D labels/ROIs

Parameters:

• Keep Overlaps: If true, this will keep any labels/rois overlapping with the boundary. Otherwise, all overlaps are excluded.
• Interpolation: For oval/freehand ROIs, interpolating the selection can speed up the functionality by converting your ROI into a polygon shape prior to border exclusion.

Using Border Exclusion on Label Images

Exclude_Labels_Example.mp4

Interpolation acceleration

By setting the interpolation interval, an OvalRoi or Freehand ROI is no longer subpixel-accurate, but the speed increase is substantial for resolving label images.

The test below was used on a binary image of 2480 by 2512 pixels, using an oval ROI of size (w 1431,h 1281).

Original Image	Speed Increase via Interpolation

Interpolation results:

Post Removal (no interpolation)	Post Removal (interpolation = 50)

Scripting with Border Exclusion

A few examples of how to remove ROIs from the Fiji/ImageJ script editor. The below example is compatible with Jython/Python:

#@ LogService ls
from net.ianfc import BorderExclusion
from ij import IJ, Prefs
from ij.gui import OvalRoi

test_code = True # Set to False to work on your own images
if test_code:
	IJ.run("Close All")
	imp = IJ.openImage("http://imagej.net/images/blobs.gif");
	imp.setAutoThreshold("Default no-reset");
	Prefs.blackBackground = True;
	IJ.run(imp, "Convert to Mask", "");
	roi = OvalRoi(50,47,100,156)
	BorderExclusion.remove_external(imp, roi, ls, True, 2)
	imp.show()
else:
	imp = IJ.getImage()
	roi = imp.getRoi()
	if not roi:
		IJ.log("Set an ROI first!")
	else:
		BorderExclusion.remove_external(imp, roi, ls, False, 0) # keep_overlaps: False, interpolation: 0

Installation

For now, simply place the border-exclusion-0.2.1-SNAPSHOT.jar file into your Fiji.app/jars directory.

Contributions

Any contributions are very welcome! Please file any issues or send a pull-request if you have suggestions.

I hope you enjoy this plugin!