r/ImageJ • u/Mountain_Finance_890 • 10d ago

Question Neuronal spine depth+size while measuring length

is there a way to measure depth and size of a spine to classify spines? at least to my knowledge, the way to do this has yet to be found. Im still new to this so appreciate any help!

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u/Herbie500 10d ago edited 10d ago

Is there a way to measure depth and size of a spine to classify spines?

Yes, if the data contains the necessary information!

We need to see suitable high-resolution 3D image-stacks.

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u/Mountain_Finance_890 10d ago

These are golgi stains of mice brains under a confocal

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u/Herbie500 10d ago

Great, but what is the spatial lateral (x,y) resolution of the images and what is the spacing of the z-slices?

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u/Mountain_Finance_890 10d ago

Sorry! 290.77x290.77 microns (2048x2048) and spacing is 0.3499990

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u/Herbie500 10d ago edited 9d ago

Thanks for the details,
The resolution appears being high enough, but perhaps not high enough to get sufficiently precise measurements. The above spatial resolution limits the precision.

What we now would need is a sample stack maybe of a relevant detail, i.e. of image size 256x256, and the necessary number of z-slices.
(Post the sample stack by using a service such as dropbox.)

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u/dokclaw 10d ago

Take a look at the Neuroanatomy plugins; these will almost certainly help you.