Fiji

Fiji is a popular free open-source image processing package based on ImageJ, https://imagej.net/Fiji. We demonstrate how to use Fiji User Interface and OMERO and we also demonstrate how to analyze data in OMERO using Fiji scripting facility.

Contents:

• How to install the OMERO plugin for Fiji/ImageJ
• Analyze manually OMERO data using the OMERO plugin for Fiji/ImageJ
• Segment manually OMERO data using Fiji/ImageJ
• Segment OMERO data using the Scripting editor in Fiji
• Segment OMERO data using Fiji run headlessly in notebook
• Use ImageJ in Python
• View zarr file using MoBIE and BDV

Contribute

Changes to the documentation or the materials should be made directly in the omero-guide-fiji repository.