Where Ideas grow

Batch analysis and macro development in ImageJ/Fiji:
going beyond the basics | 2nd edition

18-20 November 2020 | i3S - Instituto de Investigação e Inovação em Saúde

 

This 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 course will focus 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, 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. At the 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:
- Basic knowledge in image analysis and some experience with ImageJ/Fiji for simple tasks
- Laptop for course sessions.

Organizers:
Eduardo Conde-Sousa | Paulo de Castro Aguiar

 

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.
  • 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.

 

Program

To be announced

Course approximate duration: 18 hours

Registration

Registration fee includes coffee breaks and course material.

  Early Bird Late registration
Registration period Until 4th September from 5th September until 23rd October
Payment deadline 11th September  30th October 
i3S members with previous
participation in Image Analysis courses*
90€ 135€
i3S members 100€ 150€
External participants with previous
participation in Image Analysis courses*
117€ 175,5€ 
External participants 130€ 195€

 

* Applicable to candidates that have enrolled the following i3S courses:
- Introduction to digital image analysis with ImageJ/ Fiji / Introduction to digital bioimage analysis;
- MATLAB: Data analysis & image processing
- Course on Optical Microscopy Imaging for Biosciences
- High Throughput Screening and Image Analysis for BioSciences

 

Limited number of participants: 15

Sponsors


More Information:
Advanced Training Unit | E-mail: training@i3s.up.pt | Tel: +351 226 074 900