PPBI
Introduction to digital bioimage analysis, 2nd Edition
September 23-25, 2020 | i3S
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. Also, the design of typical workflows to automate image analysis will be addressed not only in Fiji but also with Cellprofiler (cellprofiler.org). This course will be focused on the analysis of light microscopy images but is targeted to all people engaged in research.
Participants are invited to submit in advance an analysis problem/data of their interest that might be addressed in the course as an individual mini-project (with the help of the tutors).
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.
- Introduction to Cellprofiler.
REGISTRATION
Early Registration until 15th June 2020
Late Registration until 1st September 2020
More information and registration: https://www.i3s.up.pt/training?v=119
Batch analysis and macro development in ImageJ/Fiji: going beyond the basics | 2nd edition
November 18-20, 2020 | i3S
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.
REGISTRATION
Early Registration until 4th September 2020
Late Registration until 23rd October 2020
More information and registration: https://www.i3s.up.pt/training?v=118
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