Batch analysis and macro development in ImageJ/Fiji: going beyond the basics

13-15 November 2019 | i3S - Instituto de Investigação e Inovação em Saúde

About the course: Is designed for ImageJ/Fiji users who want to go beyond the basics and progress to more intermediate/advanced analysis with this software. The focus of this course is on how to automate routine tasks (for conditions where many images need to be processed), as well as how to deal with more complex image analysis situations as to maximize information extraction. Although ImageJ can be used with its graphical user interface, the implementation of a workflow to multiple images requires the development of macros and/or scripts for batch processing. In this course, this process is tackled by building up from the development of very simple macros to more complex workflows, where images are processed and information acquired in an automated or semi-automated way. Previous knowledge on the basics of bioimage analysis is recommended, but no prior experience in ImageJ macro development is required or assumed, nor any prior programming skills.

Target Audience: Researchers who want to go beyond the basics and progress to more intermediate/advanced analysis with ImageJ/Fiji

Requirements: Participants should have basic knowledge in image analysis and some experience with ImageJ/Fiji for simple tasks.

The participant should bring a personal laptop for the sessions.

Course contents:

.          Introduction to batch analysis: from macro recorder to simple scripts.

.          ImageJ macro language syntax.

.          From GUI (graphical user interface) workflows to scripts: exploring ImageJ’s built-in functions and developing user-defined functions.

.          Automatic data loading: access list of files in a given directory and filter it by text patterns in file name or by extension.

.          Batch processing from scripts.

.          Combine multi-dimensional information: programmatically identifying image pairs (e.g. multichannel, time-lapse) and combine information.

.          From Image data to tables: extract information to tables and personalize output variables on output tables (data logging).

.          Export sample images and customized tables to a directory.

Early bird registration: until 8th October 2019 (payment deadline: 10th October 2019)

Late registration: from 9th October until 28th October 2019 (payment deadline: 30th October 2019)

For more information and registration:  https://www.i3s.up.pt/training?v=100