Development of LabelsToROIs FIJI/ImageJ plugin

Development of LabelsToROIs plugin

There have been many recent machine learning tools created for image segmentation and object detection that work astoundingly well, such as the amazing #cellpose . In many cases, these algorithms generate their output in the form of labeled images. For a computer scientist or a user well versed in image analysis using programming languages, the use of label images is common practice, and thus they can rapidly incorporate these algorithms into their everyday routines. However, other users without this specific knowledge are significantly more limited in taking advantage of these tools.

I created this simple ImageJ plugin to convert labeled images into ImageJ ROIs. The plugin, written in Jython, incorporates a tool to erode/dilate the ROIs, which can be useful to “adjust” the segmentations, especially when area-related measurements are intended. It also allows to easily save the ROIs, measurement tables, jpg-image of the original image+overlaid ROIs, and batch conversion and measurement of many images at the same time.

The intention was to make these kinds of analyses easier for users without programming skills.
You can find the plugin and a tutorial in the GitHub page below.

Any comments are very much welcome!