cell counting on an image with python

When Python is the interpreter, what is a good
design for the interface to the basic NEURON
concepts.

Moderator: hines

Post Reply
fpointeau
Posts: 2
Joined: Mon Apr 13, 2020 11:17 am
Location: Bordeaux

cell counting on an image with python

Post by fpointeau »

Hello everyone,
I have to work on a code to count number of neurons on an image and to automated it for multiples images.
Do you have any tool guide to provide to me ?
Sincerely yours
ted
Site Admin
Posts: 5793
Joined: Wed May 18, 2005 4:50 pm
Location: Yale University School of Medicine
Contact:

Re: cell counting on an image with python

Post by ted »

That's an interesting problem, but far outside of the scope of the NEURON Forum. You might try doing a web search for "automated neuron counting". I just now did that with Duck Duck Go, and saw three or four possibly useful hits on the first page of results.
fpointeau
Posts: 2
Joined: Mon Apr 13, 2020 11:17 am
Location: Bordeaux

Re: cell counting on an image with python

Post by fpointeau »

hello ted,
thank you for your answer.
So i made a mistake when i wrote my post sorry.
I have brain slices with fluorescent signal ( i.e :eYFP) and i would like to count the number of pixels corresponding to the fluo signal. So it is not counting cells.
Sorry for the mistake.
regards
ted
Site Admin
Posts: 5793
Joined: Wed May 18, 2005 4:50 pm
Location: Yale University School of Medicine
Contact:

Re: cell counting on an image with python

Post by ted »

With regard to "neuron counting" (and might even be relevant to your question), MicroBrightField is presenting a 1 hour webinar on stereology on April 21 starting at 11 AM EDT. It's free but registration is required--see https://register.gotowebinar.com/regist ... 8440137741
gladonias
Posts: 6
Joined: Thu Feb 28, 2019 5:24 am
Location: Waterford Institute of Technology

Re: cell counting on an image with python

Post by gladonias »

fpointeau wrote: Wed Apr 15, 2020 5:23 am hello ted,
thank you for your answer.
So i made a mistake when i wrote my post sorry.
I have brain slices with fluorescent signal ( i.e :eYFP) and i would like to count the number of pixels corresponding to the fluo signal. So it is not counting cells.
Sorry for the mistake.
regards
This seems like a Digital Image Processing kind of problem. Would you be able to show us one of those images? Maybe with some pointers in it showing what is what in the image?
Post Reply