Obtaining nuclei outline coordinates


I have segmented cells and drawn outlines using CellProfiler, but I was wondering if there’s a way to retrieve the pixel coordinates of the outline without post-processing in matlab or some other software. We are trying to track changes in cell morphology in consecutive tissue slices in order to track cell migration. After CellProfiler has identified primary objects and drawn an outline, are the coordinates of the outline not accessible somehow, like by finding where pixel intensities are 1 vs 0?

Thank you

CellProfiler isn’t designed to export pixel-by-pixel data- you can export images of the outlines, and you can measure and export a large number of morphological features of the objects that you’ve drawn, but as of now I can’t think of a way in CP to just list which pixels the outlines cover. Sorry!

Just wanted to be sure you’re at least aware that you could use SaveImages to save images displaying only the outlines of your objects of interest on a black background.

You could write a new custom module in CellProfiler to do what you like very easily, using each image as essentially a look up table for the values you want to export.

Even if you don’t have much programming experience, you may be able to put together a module that does what you want, or find a friend who can help. See the instructions here: https://github.com/CellProfiler/CellProfiler/wiki/Module-structure-and-data-storage-retrieval

You’d have only one input: Select an image, and the output would be whatever format you want - you could even save that data to a spreadsheet or database from within your custom module.