We know how frustrating it can be when you start Icy for the first time and you have absolutely no idea about how to use it. On this page, we list all training material we are aware of. If you would like to list your own material here, please contact us.
If you are currently stuck with a specific issue with the Icy software, in addition to exploring these training resources, we suggest reading also our blog post “How to get help on Icy“ and taking a look at our cheat sheets.
We regularly give trainings, webinars and add new blog posts on our website with tips on how to use Icy. To be informed of all these events, please follow the Icy software Twitter account
Slides only
Here we list courses for which we only have slides. In the paragraph below, we list webinars available on Youtube, with the slides, if they are available.
Our own course and tutorial
License: Creative Commons Attribution Share Alike 4.0 International
- Icy – Introduction (PDF)
- Icy – Protocols (PDF)
- Icy – Script (PDF)
- Icy – Micro-Manager (PDF)
- Icy – Plugin development (PDF)
- Icy – Keyboard shortcuts (PDF)
- Complete courses ZIP package (PDF, images, protocols, scripts…)
Other training material
Please check license rights with the authors prior to re-use.
- Slides about Colocalisation Studio plugin, by Romain Guiet, EPFL
Webinars available on Youtube
Please check license rights with the authors prior to re-use.
In English
- Bioimage Analysis with Icy, webinar from the NEUBIAS Academy, general introduction to Icy
- Bioimage Analysis with Icy bioimaging, lecture by Robert Haase with associated exercises, general introduction to Icy
- Introduction to Icy, slides of the presentation given at the Biomedaqu Summer School n°3
- Advanced SMLM colocalization webinar from the NEUBIAS Academy. Part 2 by Thibault Lagache (at 00:47:39) is on Statistical tools for analyzing the spatial distribution of objects with a demo on the SODA plugin.
- Developing your own Icy plugins, tutorial for Icy plugin developers from I2K 2020 online conference (see the Icy tutorial program of this tutorial on the I2K webpage program) with the associated slides.
In French
- Colocalisation analysis with the Icy plugin SODA, webinar from the RT MFM network, with explanations on the SODA plugin
- 3D deconvolution microscopy, webinar from the RT MFM network, with explanations on the EpiDEMIC plugin
- Analyses d’images avec le logiciel Icy, general introduction to Icy, webinar from the RT MFM network with corresponding slides.
Some more resources
We list here complementary resources related to image analysis.
Resources in image analysis
- List of reading and viewing recommendations on Bioimage Analysis on the image.sc forum (in English)
- MOOC on the FUN platform “ImageInLife – Imaging the Vertebrate embryo: from biological material to modelling“, from image acquisition to data analysis, with a focus on mouse and zebrafish organisms (in English)
- MOOC on the FUN platform “Introduction au traitement des images“, with a bit of Python programming (in French)
- Reproducible image handling and analysis, The EMBO journal (2021)
Resources to help making figures
- Creating clear and informative image-based figures for scientific publications, Plos Biology (2021)
- SuperPlots: Communicating reproducibility and variability in cell biology, JCB (2020)
Resources about microscopy image acquisition
- Designing a rigorous microscopy experiment: Validating methods and avoiding bias, JCB (2019)
- A beginner’s guide to rigor and reproducibility in fluorescence imaging experiments, MBoC (2018)