help with atlas based segmentation

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ginevra bargigli

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Jan 25, 2024, 10:49:57 AMJan 25
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Hello everyone,

I'm a molecular biology student, and I'm trying to segment a TIFF hyperstack (x, y, z, t) from fluorescence neuroimaging in zebrafish. I want to use the Z-brain atlas as a reference, which I downloaded from https://zebrafishexplorer.zib.de/home/. The downloaded TIFF file is named after the transgenic fish lines I'm using, and I'm unsure whether I also need to download a mask file.

If I understand correctly, I should use the cmtk.call function from the nat package to invoke the asegment function with the parameters input_image.nii, atlas_image.nii, atlas_labels.nii, and output_labels.nii. Since I have very little coding experience, I would appreciate help understanding how to properly use these functions, which parameters need to be specified, and how to execute them in RStudio. Currently, I only have two TIFF files, and I'm not sure if they are compatible with the asegment function or what characteristics the TIFF files should have to be compatible.

I apologize for my lack of expertise, but I'm hopeful to find assistance. Thank you in advance!

Sebastien Tourbier

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Jan 26, 2024, 4:21:37 AMJan 26
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Dear Ginevra,

I am sorry to tell you but this is a Google group dedicated to the support of the Connectome Mapping Toolkit (CMTK) for the human brain.

Good luck for your project,

Sébastien
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