Re: Segmentation of oligodendrocyte (cell) staining - DAB

Posted by dpoburko on Feb 11, 2010; 2:34pm
URL: http://imagej.273.s1.nabble.com/Segmentation-of-oligodendrocyte-cell-staining-DAB-tp3689428p3689431.html

Hi Jacqui,

  Have a look the Houch Circles plugin (
http://rsb.info.nih.gov/ij/plugins/hough-circles.html ). With some
patience trying to the appropriate parameters, this approach should
probably be able to identify the rings around the oligodendrocytes. Your
student will have to threshold their images first. They might be able to
reduce some of the non-ring staining with Bandpass filters of various
sizes, or by using the Subtract Background function built into IJ.

Hope that get you somewhere.

Cheers,
Damon



--

Damon Poburko, PhD
Postdoctoral Research Fellow
Stanford University School of Medicine
Dept. of Molecular & Cellular Physiology
279 Campus Dr., Beckman B103, Stanford, CA 94305
Ph: 650 725 7564, fax: [phone]




Jacqui Ross 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: [phone] Ext 87438
> Fax: [phone]
>
> http://www.fmhs.auckland.ac.nz/sms/biru/
> <http://www.fmhs.auckland.ac.nz/sms/biru/>
>