peggyscshu / myotome-volume-nucleus-count-and-color-analysis Goto Github PK

The tools in this repository are designed to analyze the confocal images of zebrafish myotome whose membrane is labeled by the multicolor cell barcode (ref1). Three types of analysis done by five scripts are included in this repository. The first application is used to process the zebrafish myotome image before 3D volume quantification. Second, a stack image with the center of each nucleus is built. Therefore, the nucleus number can be counted along with myofibers. Third, the unique color of the multicolor labeling was extracted iteratively from images which constitute a single myotome. At the end, the python tool is used to project the identified color to a 3D plot with gray value RGB as axes to draw the representative result image.

License: Apache License 2.0