ilastik

https://www.ilastik.org/

Tools for image segmentation and tracking, leveraging machine learning techniques.

Imaris Viewer

https://imaris.oxinst.com/imaris-viewer

3D rendering of microscopy images

Imaris

https://imaris.oxinst.com/

3D rendering of microscopy images and analysis tools

Micro Manager

https://micro-manager.org/

Image acquisition

Slidebook

https://www.intelligent-imaging.com/slidebook

Image acquisition and analysis

AutoQC

autoQC is an ImageJ plugin for automating microscope quality control routines. It includes four separate workflows:

1. Automatically generating resolution values;
2. Automatically calculating multichannel coalignment via maximum pixel shift;
3. Automatically calculating maximum field of view intensity decrease;
4. Automatically calculating maximum stage drift for stage reproducibility analysis.

The latest plugin release is available from this linkLink opens in a new window

Installation instructions: simply place the JAR file inside the "plugins" folder of your ImageJ/Fiji install.

Source code is also available from hereLink opens in a new window.