ImageJ Macro Scripting – Automatic Image Analysis with Fiji

ImageJ Macro Scripting for Analysis Automation

Introduction

Fiji Installation

Creating a Macro from Scratch

The ImageJ Macro Language

Macro Recording and Script Editor

Error messages and Error Handling

File download

Macro Project - Part 1: Macro Recording

Scripting basics

Macro Project - Part 2: Variables and their Usage

Using print() to log and trouble shoot

Handling Windows - Part 3: Selection and Closing

Automate Specific Analyses (introducing FOR loops)

Analysis Intro - Detecting Spots in Images

The FOR-Loop

Macro Project - Part 4: Run Analyses in Independent ROIs

Directories and Saving Data

Read and Create Directories

Save different File Types

Macro Project - Part 5: Folder Creation and File Saving

User Interaction in Macros

Analysis Introduction - Quantitative Background Subtraction

Dialogs - Part 1: Pop-Ups and Interaction

Measurements without Tables

Read and Write Tables

Macro Project - Part 6: Measurements and Tables

Second Level Analysis - Object Classification (introducing IF-ELSE)

Condition Testing (IF - ELSE - ELSE IF)

Macro Project - Part 7: Object Classification Example

Macro Project - Part 8: Analysis Fine Tuning and Saving Remaining Data

File and Batch Processing

Introduction to Arrays

Simple File Reader using Arrays

Processing Decisions for Relevant Files (and Folders)

Macro Project - Part 9: Create a Basic File Processor

Writing Reusable Code - Custom Functions

Learning Functions over a Coffee

Macro Project - Part 10: Creating a Flexible File Processor

Combining Analysis and Batch Processing

Macro Project - Part 11: Marriage of File Processor and Analysis

Fine Tuning Macros

The WHILE Loop

Macro Project - Part 12: Unique Output Folders and Convenience Improvement

Saving Tables Options (Exporting Excel Tables)

Saving Excel Tables (using Macro Extensions)

Adding Images to Excel Tables

Adding Custom Dialogs

Dialogs - Part 2: Different Dialog Types in Fiji

Generic Dialogs

Dialogs via Scripting Parameters

Final Macro Download

Bonus Lessons

Creating Date Stamps for Saving

Create Reusable Macros and your own Macro Library

Creating your own Menu

Creating Macro Tool Menus with Icons

Batch Processing Bio-Formats >160 File Type

ImageJ Macro Scripting for Automatic Image Analysis

ImageJ Macro Scripting

Introduction

Course Overview

The Trainer

Dr. Jan Brocher - BioVoxxel

BioVoxxel was founded in 2012 by Dr. Jan Brocher and since then offers widely accepted individualized workshops in image proper image integrity and publication figure creation, image analysis and analysis automation for undergraduates, PhD students and PostDocs in life sciences worldwide.

These courses understandably transmit in-depth methodologies according to high scientific standards to enable researchers to successfully apply those to solve individual image analysis challenges and create publication figures efficiently.

Besides teaching, BioVoxxel offers customized trainings, 1:1-coaching sessions, automated solutions and customized programming of image processing and analyses tools challenges for customers as well as scientific illustration services.

Expertise

Bio-Image Analyst with expertise in scientific image analysis since 2010
Until 2025 over 400 live workshops for over 5000 students delivered
PhD in Molecular Biology
10 years experience in international academic science
Experience in very diverse light microscopy techniques
Professional teaching as freelance scientific trainer since 2012
Scientific image analysis software developer since 2013
Bio-Image analysis consultant for academia and industry since 2013
Programming experience: IJ Macro, Java, Groovy, Python

Considerations for the Course

It is recommended to do the course step-by-step in the order the lectures are presented.

Mostly, individual lectures are building up on prior ones. If you have already programming experience, the beginning will be very easy and you can obviously speed up the videos. I won't blame you, I love 1.5x video speed when learning something, I'm partially familiar with .

The confirmation "stops" at the end of some sections are included, to actually ensure, that you follow the sequence initially. Once you finish the course, you can jump between the lectures and pick which lesson you want to repeat.

If you follow the coding examples hands-on and receive error messages, read them and try to find out what the reason for the error might be. There is also an error handling section included in the course content!

Mostly, it is a typo, a missing semicolon in the code and any other step that is not exactly as shown. This way you practice how to locate mistakes or issues in macros. Trouble shooting a macro is minimally as important as learning how to write a macro.