Tracing neurites in brightfield images



I need to measure the length and branch-points of neurites in treated and untreated neurons. The images are phase contrast images, although the nuclei are labelled with Hoechst. I used NeuronJ for tracing the neurites and it works perfectly. However my problem is that it is manual and since we do high throughput screens, its not useful in context of analysis of large amount of images. Does anybody know how I can automate this ? Is there a tool available which I am unaware of or if I can use a trainable tool?

Looking forward to hear back. Thank you very much in advance for your help.

Best wishes,



You can try out Simple Neurite Tracer - a plugin by @tferr & @mhl. :slight_smile: There is also another tool called NeuriteTracer you can check out that is apparently automate-able. Hopefully, that gives you a start!



Thank you for the help, I thought these plugins are for florescence images, I will try.



Ha! @Manmeet_Bedi - that’s a good point! I didn’t realize that you were working with phase images (overlooked that one - my bad!)… still read up on those two options and see if they’d be compatible with such images. Perhaps if you were still able to segment your neurons and create a binary mask - they might be useful still?