Access to:
- Over 8.5 hours of video content (~30 videos) and follow-along exercises
- Over 30 downloadable example macros and files
- Learn all ImageJ macro concepts easy understandable
- Access for 2 years including all updates
- General file processor macro for free (automate image analysis for over 160 image file types)
- Course certificate
- Official invoice after purchase
- Basic ImageJ macro recording of a general image analysis pipeline
- Step-by-step extending an analysis pipeline with increasing complexity
- Basics about variables and macro command and how to use them
- Looping over image files, table data, ROIs
- Interaction between user and macro
- Automatic customized measurements
- Creating and interacting with customized tables
- Automatically creating folders and flexibly saving data as needed
- Testing conditions and creating automatic macro decisions
- Creating reusable functions and an own macro function library
- Creating different customized dialogs for user input
- Making your own ImageJ menu with your own macros
- Create Macro Tool Menus
Category:
Hard Skill
Venue:
The workshop will be held as a virtual live event via Zoom. Login information and preparation instructions will be send in advance.
Duration:
Over 8.5h video material and additional written explanations
Main Target Group:
Life or Natural Scientists (optimally around PhD student level and above), imaging experience is helpful, some basic image analysis knowledge is assumed to understand the example analysis in full! However, you can even do this course also without prior image analysis knowledge.
Difficulty Level:
The difficulty level is medium to advanced but easy to follow in step-by-step procedures and in-depth explanation of the necessary background to the individual methods. NO prior programming knowledge is assumed or necessary.
Software:
During the course you will use exclusively Fiji (ImageJ bundle) in a customized setup. Prior experience with Fiji and image analysis is helpful.
Disclaimer:
This course is not in-depth explaining how image analysis works. It merely shows how you can automate pretty much everything about image processing and analyses you can do in Fiji.
Access Period:
- 36 months from day of purchase (extendable on request)
Course plan
Introduction
Creating a Macro from Scratch
Scripting basics
Automate Specific Analyses (introducing FOR loops)
Directories and Saving Data
User Interaction in Macros
Second Level Analysis - Object Classification (introducing IF-ELSE)
File and Batch Processing
Writing Reusable Code - Custom Functions
Combining Analysis and Batch Processing
Fine Tuning Macros
Saving Tables Options (Exporting Excel Tables)
Adding Custom Dialogs
Bonus Lessons
ImageJ Macro Scripting for Automatic Image Analysis
