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.

Install the plugins

• How to install OMERO plugins for Fiji/ImageJ

Manual Analysis

• Crop and import
• Analyze, save ROIs and measurements
• Manual Segmentation

Automated Analysis

• Segment using ImageJ Macro language
• Segment using Groovy script

Fiji and Zarr

• 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.