Apparently, people who have actually had to sit down and think about
colocalization (programmers) have a dim view of how biologists report
colocalization, so I'm attempting to do this as close to correctly as I can
and would appreciate any clues. I'm imaging zebrafish larva motor axons and
duel staining axon membrane (znp-1) and acetylcholine receptors (alpha
bungarotoxin). Red and green. Want to count synapses. I've got masked
axons made from tracing with Simple Neurite Tracer, filling it out, and
making ROI of the fill. I could stop there, according to what I see
published in similar studies, all I'm seeing is pretty pictures, but I'd
really like to be able to show some graphs and numbers. I'm thinking that
Pearson's coeffients done for the whole axon aren't going to help me alot.
I'm thinking I need to count the number of true colocalized voxels within
the ROI. This is where I'm stumped. I can use something like the Color
Pixel Counter to just count yellow pixels, but is there a way of selecting
pixels with a certain yellow threshold and using Coloc2 to get a Pearson's
statistic on each yellow blob in the ROI so that I have some sort of
evidence that I'm not just monkeying around with the gain?
Thanks,
Mike Holloway
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