I tried using a modified python code to read the flat file, however, the output is a low-res PNG. What would I need to do in order to get a high-res PNG similar to what is the final output images using NUTIL? I am specifically interested in extracting the distinct cerebellar nuclei. If each of these nuclei have different colors, I can use fiji to extract ROI based on color information. However, currently the labeling in the final output of NUTIL yields the same color for all cerebellar nuclei.

 

However, since I do not need object counts, I just obtained the high-res color images using empty segmentation images in the NUTIL workflow. I got the high res maps but the distinct nuclei do not show up. I tried using one of your answers to relabel the label.txt file, but I am unsure how to proceed from here. Because the json file which was exported from Visualign does not open up in visualign itself. So, how would I go about getting only the high-resolution PNGs with each of the cerebellar nuclei (fastigial nucleus, interposed nucleus, and dentate nucleus) distinctly labeled?

 

Best

Aaron