Imaris Viewer

3D rendering of microscopy images

Imaris

3D rendering of microscopy images and analysis tools

ilastik

Image analysis tool

Micro Manager

Microscope control

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.