Nuclear morphometry analysis


I am attempting to export scanned H&E style images from Aperio Webscope as Tiff files to conduct measurements on a large volume of nuclei. My desired measurements are: Area, perimeter, min/max diameter, and shape factor, axis ratio, compactness, and similar.


Is there a way to automate this process (I need to analyze approximately 5,000 nuclei)? If so how can I calibrate Image J to identify nuclei properly?

I need my output results in units of um, how can I convert pixels to um in way that is calibrated/scaled to my images?


Hi @mraza10 and welcome to the forum!

may I suggest for you to use Qupath instead of ImageJ for your project?

In a Nutshell, Quapth is a free and open source software targeted at the analysis of whole slide images / histological stainigs. For example, you do not need to export your images as Tiff, as Qupath likely understands directly the *.svs file format that is saved by he Aperio Webscope. Thus, you will not need to scale your images manually afterwards, they should already be scaled properly.

Qupath is extremely well documented and also has a youtube channel with guides.

To count and measure nuclei, you may simply use the build-in “detecting objects” functionality:
Follow the guide by starting with drawing an annotation around your area of interest, then Run the Analyze → Cell analysis → Positive cell detection command.