Define region encapsulated by different ROIs as a new ROI


The title might sound vague, but I will try to explain.
Is there an easy way to add a region to the ROI manager that is encapsulated between other ROIs?
For example, 4 lines enclose a square. Is it possible to get the square between those ROIs as a separate new ROI in ROI manager?
The reason I ask this is because I found that the only way to combine lines using the ROI manager commands is by combining them (OR command). However this creates a contour around the line of (several) pixels, which corrupts the original line. This is especially frustrating if I later on want to split the combined line, then it gives a lot of ROIs that are part of the combined line.

below an example of the problem:


Hello Soufiane -

There could be a number of things going on with what you are

If you’re asking specifically how to build a square-shaped ROI
(with interior) from four Line ROIs, I don’t think you can do it
purely at the ROI level, but will have to query the Line ROIs
for their coordinates.

Here is a jython (python) script that illustrates how to do this:

from java.awt import Color

from ij import IJ
from ij.gui import Line
from ij.gui import Overlay
from ij.gui import PolygonRoi
from ij.gui import Roi

# image for displaying overlay (ROIs) 
imp = IJ.createImage ('boundary_roi', '8-bit ramp', 512, 512, 1)

ovl = Overlay()   # Overlay for holding ROIs

# make four Line ROIs
l1 = Line (180, 50, 240, 130)
l2 = Line (240, 130, 160, 190)
l3 = Line (160, 190, 100, 110)
l4 = Line (100, 110, 180, 50)

l1.setStrokeColor (Color.RED)
l2.setStrokeColor (Color.YELLOW)
l3.setStrokeColor (Color.GREEN)
l4.setStrokeColor (Color.BLUE)

ovl.add (l1)
ovl.add (l2)
ovl.add (l3)
ovl.add (l4)

# build PolygonRoi from Line ROIs
fp = l1.getFloatPoints()
x = fp.xpoints[:2]
y = fp.ypoints[:2]
fp = l2.getFloatPoints()
x += fp.xpoints[:2]
y += fp.ypoints[:2]
fp = l3.getFloatPoints()
x += fp.xpoints[:2]
y += fp.ypoints[:2]
fp = l4.getFloatPoints()
x += fp.xpoints[:2]
y += fp.ypoints[:2]
poly = PolygonRoi (x, y, Roi.POLYGON)

# use fill color to show that PolygonRoi includes region enclosed by the four lines
poly.setFillColor (Color.CYAN)

# move PolygonRoi so that it's not on top of Line ROIs
poly.setLocation (poly.getXBase(), poly.getYBase() + 200.0)

ovl.add (poly)

# display the Line and Polygon ROIs (using the Overlay)
imp.setOverlay (ovl)

# flatten the image to save and upload
impFlat = imp.flatten()

IJ.saveAs (impFlat, 'PNG, 'boundary_roi')

[Edit: Changed the first occurrence of fp = l4.getFloatPoints()
in the (previous) above code to fp = l3.getFloatPoints(). This
corrects a bug that didn’t actually affect the result.]

And here is the resulting image that shows the Line ROIs and
the constructed square-shaped ROI:

If this doesn’t address your issue, could you please elaborate on
your question, ideally posting a complete, runnable script that
creates the ROIs you are referring to so we can see the details
of what you are doing?

Thanks, mm

1 Like

Hi mm,
Thank you for your response. I have saved your script.
In the meanwhile I have used analyze particles to achieve my goal, as i used intersections of lines with circles.

Thank you