About | People | Services | Projects | Training | Publications


Function StackMeasure is a plugin for ImageJ which can identify features of interest and measure the distance between them.
Language Java (>=v1.5)
Requirements ImageJ and Java3D
Code Maturity Legacy - this code is no longer being developed but we will fix any bugs which are found
Code Released Yes, under GPL v3 or later.
Initial Contact Simon Andrews

Download Now

StackMeasure is a plugin for the ImageJ image analysis platform. It is designed to identify features of interest and allow you to measure the distance between them.

Interesting features are groups of spatially clustered voxels with the same (or similar) colour. StackMeasure can work with either with a single RGB image file, with separate black and white TIFF files (one for each channel), or with Zeiss lsm files. With RGB files you can set how much flexibility you want to allow in colour matching but with the other formats the channels are completely separated.

StackMeasure with then identify a set of features and give you details of their position and volume. It will generate a composite image stack, and can render a 3D version of your stack so you can better visualise the features.

Once you have defined your features you can measure the distances between them. You can do this either from their centre of mass, or from their closest boundary. You can also choose to merge all features in a channel and find the closest distance between any 2 channels.


I've put together a help document which should provide all of the essential information you need to run StackMeasure. Please let me know if you feel that anything useful is missing from it.