PPBI
Batch analysis and macro development in ImageJ/Fiji: going beyond the basics | 2nd edition
9, 10, 11, 14 and 15 December 2020 | ONLINE COURSE
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.
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.
More information and registration: https://www.i3s.up.pt/training?v=118
Introduction to digital bioimage analysis, 2nd Edition
September 23-25 and 28-30, 2020 | ONLINE COURSE
With the advent of the digital era, nowadays images are multidimensional numerical data that can be processed and analyzed quantitatively to extract more information. With this course, we intend to give a general introduction to ImageJ/Fiji (imagej.net/), show how to use it to extract quantitative data and how to write simple macros. This edition will be online (ZOOM) sessions with a practical approach.
CONTENTS
- Principles, techniques and ethics of digital bioimage processing.
- Basic commands of ImageJ/Fiji software.
- Working with multidimensional (2D, 3D, time-lapse, position) bioimages.
- Enhancement and processing of images.
- Extract quantitative numerical data.
- Design of simple workflows for automation of image analysis with ImageJ macros.
More information and registration: https://www.i3s.up.pt/training?v=119
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