/Pathology-1BI047

ImageJ macros for pathology course

Primary LanguageImageJ Macro

Pathology-1BI047 ImageJ Macros

Two ImageJ macros I used to automate histology frame analysis labwork for my pathology course.

folder_sort.ijm sorts your main histology images folder into several smaller folders based on the marker.

batch_analyze.ijm can then be used on one of those marker folders to batch process/analyze all images using a specified sequence of filters and functions (specified by our lab compendium, in this case) and output the summarized data into an Excel sheet using the "Read and Write Excel" plugin. Configurable variables are max threshold and watershed on/off.