biovoxxel
ImageJ Macro Scripting for Analysis Automation
Introduction
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
Analysis Introduction - Quantitative Background Subtraction
Here the second analysis will be introduced and shortly explained for a better understanding. It is clear that not everybody taking this course wants to or needs to do pixel intensity measurements but since it represents our example, you should also fully understand some scientific considerations and(or pitfalls and how to solve them in a macro.
