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