Tube formation analysis

I would like to quantify tube formation assay on Matrigel - I am interested mostly in the number of branching points, total length of tubes and maybe the average width of the tubes. My pictures are done with phase-contrast microscope and look similar to part A on mct.aacrjournals.org/content/6/1 … .large.jpg
Is it possible to perform such analysis using cell profiler?
Karolina

Hi Karolina,

This is possible, however not at all straightforward:
(1) You would need to segment the tubes from the background, and with phase contrast, that can be a lot harder than it appears. Inverting the image is necessary, since the edges are darker than the background, but then the interior of the tube is dark, so you may end up with only the edges. If you can get a fluorescent image, that would help tremendously.
(2) We have built in a MeasureNeurons module, which could be used here to measure branchpoint counts, total length, etc, however it is not in the released, compiled version. If you have Matlab and know how to access our SVN repository, you can download the newest version and run it from within Matlab. Or you can wait for the next (and final) release of the Matlab version of CP, or the 2.0 version which will have these features as well.
(2a) Also, the MeasureNeurons module requires a primary object to seed from, like a nucleus, however that is not apparent in the images, though you might be able to fake one or more depending on your needs.

Let us know if you want to pursue this and we can try to help.
Dave