This repository contains scripts to transform EM-based neuron skeleton provided by neuPrint into the image format that can be used for color depth MIP mask search.
- SWC files can be downloaded from the "Skeleton" view in neuPrint, which should be stored by cell types under /swc/whateverCellName directories.
- To generate color depth MIP compatible images, you need to download the LUT file from the ColorMIP_Mask_Search repository, and save it as psychedelicrainbow.mat containing a 256 x 3 matrix called psychedelicrainbow.
- Color depth MIP search itself runs on Fiji.
- generateColorDepthMIPfromSWC is the main function.
- This is an ongoing work and might require significant amount of calibration before it actually works.