ImageJ_Macros

This repository is an assortment of ImageJ macros developed for various people around Warwick Medical School. They include:

• a macro for saving split channels and the Z-projections thereof for all images in a directory;
• a macro for saving XY coordinates of cell shapes as a CSV file;
• a macro for automatically detecting, counting and saving measurements of cells;
• a macro for counting cells, the number of foci per cell and the distances between foci in the same cell;
• a macro for measuring 3D distances between a user-defined point and detected particles in a multichannel image.

Some of those are written in IJ macro language, some in Python (Jython, in this case). They are all extremely custom and there's plenty information hardcoded: they are provided as is in the hopes of being useful as templates for someone else!