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Jul 22, 2020  11:07 PM | Francesco Vanzi
Mapping segmented neurons onto a registered stack
I am registering a zebrafish larva brain onto a reference brain and I get the registration parameters.
Along with the intensity data stack (which I use for the registration), I segment the larva brain and produce a stack where the intensity distribution of each neuron is replaced with its id number in all the pixels occupied by that neuron. I need to map these numbers onto the registered brain. I have used reformatx and it works ok as far as the spatial distribution but it also scales the "intensity" which in my case should actually stay unchanged since it tells me the neuron id number.
I have seen the option of mapping the coordinates of the neurons and transforming those with streamxform but I would much prefer having a registered stack with all the neurons numbered, if possible.
Thank you very much for your help!!
Jul 23, 2020  01:07 PM | Greg Jefferis
RE: Mapping segmented neurons onto a registered stack
Dear Francesco,

You need to change the interpolation method to pv or nn. See below excerpt from reformatx docs.

reformatx is what you need if you have a volume to reformat. If you have individual points e.g. because you have traced your neurons then you can use streamxform. If you plan to do much work with traced neurons, then I would definitely recommend you look into the natverse xform toolchain (

All the best,


Image interpolation method.
Supported values: "linear", "nn", "cubic", "pv", "sinc-cosine",
"sinc-hamming", where the default is "linear", or use one of the

--linear Trilinear interpolation
[This is the default]
--nn Nearest neighbor interpolation
--cubic Tricubic interpolation
--pv Partial volume interpolation
Jul 23, 2020  02:07 PM | Francesco Vanzi
RE: Mapping segmented neurons onto a registered stack
Hi Greg,
I followed your suggestion and ran pv. It works great!
Thanks again for all your help!!!