Fiji is a popular and versatile image analysis software. This course will introduce basic concepts in bioimage analysis and how to apply them in Fiji.
Instructor: Mélodie Ambroset, MicroPICell core facility, University of Nantes, melodie.ambroset@univ-nantes.fr
Helper: Héloïse Monnet, Collège de France
Outline
- Introduction to bioimage analysis, fundamental concepts
- Hands-on
- Getting to know basic commands in Fiji
- 2D segmentation workflow examples
Preparation
- Fiji: please download /!\ a fresh version of /!\ Fiji for your Operating System here. Unzip it somewhere where you have full read/write permissions.
- Note: If you have a previous version of Fiji and like it, you do not have to delete it, two Fiji can co-exist! But I would ask everyone to follow the course on a fresh version to prevent any issues.
- For Windows: "Caution: “Program Files” not recommended! On Windows, we strongly recommend that you store your Fiji.app directory somewhere in your user space (e.g., C:\Users[your name]\Fiji.app) rather than in C:\Program Files or other system-wide directory. If you move Fiji.app to such a directory, modern versions of Windows will deny Fiji write permission to its own directory structure, preventing it from being able to update."
- For Apple: it may be necessary to move the app to another folder when things are not working properly. "MacOS 10.12 (Sierra) and later have a security feature called Path Randomization that can cause ImageJ to not work as expected. Path randomization is in effect if the "ImageJ home" path shown in the Image>Show Info window starts with "/private" and plugins are not installed in the Plugins menu. You can disable path randomization by dragging ImageJ.app to another folder and then (optionally) dragging it back."
- Data: Download the dataset here.
Remark: Image analysis with a trackpad can get quite uncomfortable, please bring your mouse!