Posted by
Krs5 on
URL: http://imagej.273.s1.nabble.com/Find-missing-spots-in-a-grid-of-spots-tp5019879p5019881.html
Dear Cornelius,
If you think of writing a macro I can imagine something like:
- alignment of the images to the standard model containing all spots.
- threshold all images.
- XOR image calculator between images and model creating images of the missing spots.
- Find the Centre of Mass of each spot found to be missing in the results images via Analyze Particles. This step will also allow you to select on size to remove non perfect overlap of spots.
Best wishes
Kees
Dr Ir K.R. Straatman
Senior Experimental Officer
Advanced Imaging Facility
Centre for Core Biotechnology Services
University of Leicester
www.le.ac.uk/advanced-imaging-facility
-----Original Message-----
From: Cornelius Sicker [mailto:
[hidden email]]
Sent: 14 January 2018 18:36
To:
[hidden email]
Subject: Find missing spots in a grid of spots
Dear fellow ImageJ users,
a colleague of mine is looking for an automated solution to find missing spots in a rectangular grid of small spots. The spots are quite uniformly sized and have similar brightness. The grid might be rotated slightly. Only a few spots are expected to be missing in each picture
(<1 % of all grid positions). The grid itself is only virtually created by the visible spots. Apart from the visible spots on dark background there are no distinguishing features in the images. There are thousands of images to be processed, so the solution has to be fully automated.
I think it should be not hard to find the coordinates of the existing spots by some particle analysis plugins in ImageJ. However, given a list of coordinates of visible spots, how would you identify the missing ones? Does anybody know of an existing solution to solve this?
I can provide an example image if it helps, but was not sure how the mailing list policy is about attachments.
Best regards
Cornelius
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