Bioimage analysis with Icy

Short description

This webinar is part the serie of webinars from the NEUBIAS Academy @home

Recording: https://www.youtube.com/watch?v=5SJqhKjCbMQ&feature=youtu.be .

Slides: https://marionlouveaux.github.io/bioimage_analysis_with_icy/

and GitHub repository: https://github.com/marionlouveaux/bioimage_analysis_with_icy

Q&A: https://forum.image.sc/t/neubias-academy-home-webinar-bioimage-analysis…

About the software

Icy (http://icy.bioimageanalysis.org/) is a general all-purpose bioimage analysis software that exists since almost ten years. It was developed with three major goals in mind:

1) be a software suite that covers a large variety of biological applications (microscopy, particle tracking, high content screening, digital pathology, animal behavior,…) and users (biologist, bioimage analyst, physicist, developer),

2) be the platform where computer vision specialists can deliver their solutions, including cutting-edge algorithms to non experts in a user-friendly manner,

3) promote and facilitate the use of reproducible quantitative approaches in bioimage analysis.

Icy now provides more than 400 dedicated Java based plugins covering a wide range of image analysis methods such as active contours, colocalisation analyses based on spatial statistics and a wide range of biological applications. Anyone can add new plugins to Icy and is encouraged to share them through Icy’s website (http://icy.bioimageanalysis.org). Plugins provide convenient graphical interface for end users to use algorithms developped by specialists. Bioimage analysis often requires the use of several plugins one after the other. Each plugin can be seen as a component and the ensemble of steps constitute a workflow. Icy provides a graphical programming interface called « protocols » (http://icy.bioimageanalysis.org/plugin/protocols/) that gives the possibility to anyone to assemble plugins blocks and build bioimage analysis workflows without any programming knowledge. With this tool, Icy fully reaches its goal to be the platform where computer vision specialists meet end-users biologists and bioimage analysts and to promote and facilitate the use of reproducible quantitative approaches in bioimage analysis.

Webinar content

In this webinar, we will:

- introduce the graphical user interface

- detail an example of use of the graphical programming interface called « protocols »

- talk about the community around Icy and how to get involved

Learning outcomes

After this session, you will know:

- how to navigate in the graphical interface of Icy,

- how to create a protocol: concept of blocks and connectors, automation of workflow on several images (batch mode), tips and tricks to make life easier and go further in terms of complexity,

- how to get involved in the Icy community: share a protocol, report bugs & ask for help, cite Icy and the protocols and plugins, contribute to documentation and teaching resources.