Posted by
ajeans on
Sep 04, 2013; 3:03pm
URL: http://imagej.273.s1.nabble.com/Using-ImageJ-to-recognise-synapses-very-grateful-for-any-help-tp5004648.html
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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