ImageJ_Macros_For_Batch_Analysis

Using Jython (Python) for creating Macros using the ImageJ module for automating tasks

Projects

1. Automating Cell Counts and Percent Area:

2. Batch Image Merger

Instructions

Notes:

1. The utils directory is only for editing. To locally use the macros on ImageJ please move this directory to the C:\fiji-win64\Fiji.app\jars\Lib directory.

Project 1: CD3CD45 Quick Merge

The CD3CD45 Quick Merge is a Macros to create a merged image of any file.

Steps:

1. After installing the macros on the FIJI ImageJ application, open the script on the Macros --> Run tab.
2. Hit Run located below the script box.
3. Click on the desired channels (blue, green, red) to merge
4. There is a option to remove or subtract one of the three channels from the rest.
5. The Process All Images will merge the channels into one (regardless of whether the subtraction checkbox was checked), then maximize the window for easier visualization.