MATLAB code for neural tracing in Brainbow images
The method follows a segmentation-tracing pipeline.
Run BM4D to denoise the image, code can be downloaded from here.
Run mainScript.m in brainbowSegmentation folder to get the segmentation results. You can either use kernel k-means or GMM. Both the skeleton and segmentation will be saved in the directory specified.
Run testMain.m in linkagebriding folder to process the skeletons towards compact tracings and then generate the SWC files.
Some codes are heavily borrowed from Lorenzo Tortorella, Philip Kollmannsberger, Mo Chen, and Uygar Sümbül, especially for supervoxelization and skeletonization. Thanks for their wonderful implementations.