Java

Orbit Image Analysis is a free open source software with the focus to quantify big images like whole slide scans.

It can connect to image servers, e.g. Omero.
Analysis can be done on your local computer or via scaleout functionality in a distrubuted computing environment like a Spark cluster.

Sophisticated image analysis algorithms incl. tissue quantification using machine learning, object segmentation and classification are build in. In addition a versatile API allows you to enhance Orbit and to run your own scripts.

LimeSeg: A coarsed-grained lipid membrane simulation for 3D image segmentation

Download instruction:

There is no download but you can easily install this plugin via ImageJ update site. If you reallu need to download the jar file, access the file in the update site repository (Link)

automated open-source image acquisition and on-the-fly analysis pipeline (initially developped for analysis of mitotic defects in fission yeast)

MaMuT is an end user plugin that combines the BigDataViewer and TrackMate to provide an application that allow browsing, annotating and curating annotations for large image data.

Reconstruct big images from overlapping tiled images on a Spark cluster.

The code is based on the Stitching plugin for Fiji https://github.com/fiji/Stitching