ImageJ How-To Guides

Step-by-step guides for common ImageJ workflows — and how IJPB handles each one in plain English.

How to Measure Fluorescence Intensity in ImageJ

Step-by-step guide to measuring mean, integrated, and corrected fluorescence intensity in ImageJ — and how IJPB automates the whole process.

April 29, 2026

How to Count Cells in ImageJ

Step-by-step guide to counting cells in ImageJ using thresholding and Analyze Particles — and how IJPB does it in one sentence.

April 29, 2026

How to Batch Process Images in ImageJ

How to run the same analysis pipeline across a folder of images in ImageJ using macros and the built-in batch processor — and how IJPB handles it in one step.

April 29, 2026