PPBI
PPBI - Portuguese Platform of BioImaging
National Research Infrastructure for Open-access to Bioimaging resources
Member of Portuguese Roadmap for Research Infrastructures of Strategic Interest
PPBI Euro-BioImaging Node
Tissue Clearing Online Workshop
18-20 May 2021 | ONLINE
Tissue clearing is a technique that enables visualization of opaque organs and tissues in 3-dimensions (3-D) by turning tissue transparent. The major challenge that underlies most of the unsuccessful applications of tissue clearing is that every application requires its own protocol and optimization approach.
This 3 days online workshop will cover various topics in tissue clearing, from protocol optimization, light-sheet microscopy imaging to 3D visualization and quantification. This is an opportunity for participants to learn and discuss tissue clearing protocols and applications and to contact with state-of-the-art light microscopy systems for imaging of the cleared tissue samples, guided by an experienced staff. Participants will also explore processing and image analysis workflows to extract the best information from the data.
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
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