Hello,
I've written a number of plugins for ImageJ in Java that: trace pixel
neighborhoods on a greyscale image to try to find the nearest local maxima,
search skeletal branchings for the nearest "node", as well as looked at
mesh/particle components. So I strongly suspect what you are trying to do
can be done within ImageJ.
I think generally the best advice at this stage would be for you to post a
few links to some of your images that represent a good sample of what you
have. Then I can at least respond more completely. If you're tracing along
neuron network connections, then I can almost definately help you. :-)
If your pictured neurons are isolated, my first guess would be to use the
Particle Analyzer to identify the exact single-coordinate centers of each
neuron, construct a list of those centers, and then at that point a first
year Informatics student could pair up all the closest neurons :-)
Cheers,
-Mike Miller
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----- Original Message -----
From: "David W. Robinson" <
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To: <
[hidden email]>
Sent: Thursday, November 02, 2006 4:43 PM
Subject: Nearest Neighbour Analysis
> Hi there,
>
> We have 2D images of neurons and we would like to conduct a nearest
> neighbor analysis. We can use point picker to get the XY coordinates of
> the cell bodies we wish to analyze but have not yet found a plugin or
> method for using ImageJ to compute the nearest neighbor value. Does anyone
> know how we can achieve this in either ImageJ or with some other program?
>
> Thank you
>
> David
>
> --
> David W. Robinson, Ph.D.
> Vice Provost for Academic Technology
> Assistant Professor and Director, Educational Communications
> Center for Research on Occupational and Environmental Toxicology, L606
> Oregon Health & Science University
> 3181 Sam Jackson Park Road
> Portland OR 97239
>
> Tel 503-494-7361
> Fax 503-494-4352
>
>
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