Hello,
I’m currently developing a custom ImageJ macro to segment synapses in 2D
neuronal cultures that have been fixed and immunostained using
antibodies against pre- and post-synaptic markers.
The SynQuantSimple plugin <https://github.com/freemanwyz/SynQuantSimple>
has proven to be highly efficient for detecting the relevant puncta.
I've found that adjusting its parameters — such as |zscore_thres|,
|MinSize|, |MaxSize|, |minFill|, |maxWHRatio|, and |zAxisMultiplier
noiseStd| — allows for effective customization to suit our image data.
When I run the plugin manually, the results are very good with a
specific parameter configuration. However, when I try to apply those
same parameters within an ImageJ macro, /SynQuantSimple/ appears to
revert to its default settings instead.
Is there a way to pass custom parameter values to /SynQuantSimple/ via
macro?
Any guidance would be greatly appreciated.
Best regards,
Javier
F Javier Diez-Guerra, PhD
Servicio de Microscopía Óptica Avanzada (SMOA)
Centro de Biologia Molecular
C/ Nicolás Cabrera, 1
UAM, Campus de Cantoblanco
28049 Madrid
SPAIN
Tel +34 91 196 4612
e-mail:[email protected]
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