Posted by
Straub, Volko A. (Dr.) on
Sep 04, 2013; 3:53pm
URL: http://imagej.273.s1.nabble.com/Using-ImageJ-to-recognise-synapses-very-grateful-for-any-help-tp5004648p5004650.html
Hi Alex,
If you have already thresholded your images, you can just simply combine the two thresholded images with an "AND" operator (Process>Image Calculator). You can then use the resulting image as the seed for a binary reconstruction using Gabriel Landini collection of morphological operators for ImageJ (
http://www.dentistry.bham.ac.uk/landinig/software/software.html). Following the reconstruction that should restore the original size of the particles based on the image that you selected as the Mask image which contain an overlapping region. You can then use the Particle Analyser for your measurements.
I hope this helps,
Volko
-----Original Message-----
From: ImageJ Interest Group [mailto:
[hidden email]] On Behalf Of Alex Jeans
Sent: 04 September 2013 16:03
To:
[hidden email]
Subject: Using ImageJ to recognise synapses - very grateful for any help
Hello all,
Can anyone help a relatively inexperienced user with suggestions on how to do the following with plugins or *very* simple macros:
I am a neuroscientist and have been trying to identify synapses in images of nerve cells which have been labelled up with two different coloured markers. Essentially, both of the markers exist as variously-sized puncta scattered across the whole image, and in various places different coloured puncta will overlap. I want to identify and analyse only those puncta from one channel (red as it stands) which have any overlap at all with any of the puncta from the other (green) channel. If a red punctum has overlap with a green one, I want to select that whole red punctum, not just the overlapping part, for analysis. The analysis of selected puncta is just simple diameter and average fluorescence measurement.
I have got as far as thresholding the raw images and using the particle analyzer to define the puncta themselves. How to identify that subset which has overlap with another channel is the bit I am stuck on.
I've tried lots of Google searches which give lots of variations of colocalisation analysis, but that's not really what I'm looking for. I just want to use the presence or absence of colocalisation as a binary filter to sort red channel puncta for analysis or not.
Does anybody have any thoughts, or know of a plugin or macro that could do something like this? Any help very gratefully accepted!
Thanks very much,
Alex Jeans
Oxford, UK
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