Posted by
Joel Sheffield on
Feb 11, 2010; 4:53pm
URL: http://imagej.273.s1.nabble.com/Segmentation-of-oligodendrocyte-cell-staining-DAB-tp3689428p3689429.html
---------- Forwarded message ----------
From: JOEL B. SHEFFIELD <
[hidden email]>
Date: Thu, Feb 11, 2010 at 10:06 AM
Subject: Re: Segmentation of oligodendrocyte (cell) staining - DAB
To: Jacqui Ross <
[hidden email]>
Hi Jacqui
I suppose that it depends on how much error you can tolerate, but here is a
relatively simple approach. The newer versions of IJ include an
experimental threshold routine, in the image>adjust menu, that allows an
enormous range of selections. I chose to use the saturation parameter in
HSB imaging. When I did this, I was able to crudely threshold the cell
bodies, with some scattered bits of other material. I then converted the
RGB image, with the threshold to 8-bit, so that I could use the analyze
particles routine to count the cells. I restricted the routine to just
count cells larger than a given value. I through the I might be able to use
circularity as a second parameter, but the images were actually too
irregular. I ticked "include holes", as well.
Joel
On Thu, Feb 11, 2010 at 12:43 AM, Jacqui Ross <
[hidden email]>wrote:
> Dear All,
>
>
>
> One of the graduate students here needs to count the number of
> oligodendrocytes stained in his sections. The staining is
> immunohistochemistry with DAB substrate.
>
>
>
> This labelling not only stains the area around the cell but also the
> cell processes. However, he just needs to know how many cells are
> stained not the area occupied by fibres, etc.
>
>
>
> He has a large number of images to analyse so we have been trying to see
> if we can segment out the cell body staining which looks like a ring
> around the cell in order to then batch-process.
>
>
>
> I have tried a few things with varied success and would really value
> some assistance on this. At the moment, my conclusion is that some
> processing to enhance the image with subsequent manual counting may be
> the only solution.
>
>
>
> I have put 3 examples on our website here:
>
http://www.fmhs.auckland.ac.nz/sms/biru/links/imagej.aspx which vary
> from easy to hard!
>
>
>
> There are 3 cropped images with the full sized image also available to
> download below. The images do look blue (probably lamp temperature
> issue) but the staining is reasonably clear.
>
>
>
> I have put arrowheads on one of the images to indicate what the student
> needs to measure.
>
>
>
> All suggestions welcome!
>
>
>
> Kind regards,
>
>
>
> Jacqui
>
>
>
> Jacqueline Ross
>
> Biomedical Imaging Microscopist
> Biomedical Imaging Research Unit
> School of Medical Sciences
> Faculty of Medical & Health Sciences
> The University of Auckland
> Private Bag 92019
> Auckland, NEW ZEALAND
>
> Tel: 64 9 373 7599 Ext 87438
> Fax: 64 9 373 7484
>
>
http://www.fmhs.auckland.ac.nz/sms/biru/> <
http://www.fmhs.auckland.ac.nz/sms/biru/>
>
--
Joel B. Sheffield, Ph.D
Department of Biology
Temple University
Philadelphia, PA 19122
Voice: 215 204 8839
e-mail:
[hidden email]
URL:
http://astro.temple.edu/~jbs <
http://astro.temple.edu/%7Ejbs>
--
Joel B. Sheffield, Ph.D
Department of Biology
Temple University
Philadelphia, PA 19122
Voice: 215 204 8839
e-mail:
[hidden email]
URL:
http://astro.temple.edu/~jbs