Posted by
vbindokas on
Feb 11, 2010; 4:20pm
URL: http://imagej.273.s1.nabble.com/Segmentation-of-oligodendrocyte-cell-staining-DAB-tp3689428p3689430.html
Dear Jacqui,
Try using the Template Matching plugin,
http://rsb.info.nih.gov/ij/plugins/template-matching.html . You can
draw a ROI around a good example, then use the 'crop template from
image' or just use the 'create circular template' routine. Define
thresholds and sizes to match the range you want, then press the
"perform statstica correlation' button. It will output a correlation
image that encodes how all features matched your template. Threshold
this to something like 0.6-1.0 (60-100% match range], and count those
[analyze particles or use binary_find maxima for similar tolerance
range]. This plugin converts data to 32bit [b/w], so you may want to
tweak color settings or do it yourself vs automatic mode.
It seemed to do a reasonable job.
regards,
On 2/10/2010 11:43 PM, 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: 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/>
>
--
__
Vytas Bindokas, Ph.D.
Research Assoc. / Assoc. Prof.,
Director, BSD Light Microscopy Core Facility
Dept Neurobiol Pharmacol Physiol MC0926
947 E 58th Street
The University of Chicago
Chicago IL 60637
Room Abbott 129
773-702-4875
email
[hidden email]
web site for LMCF:
http://digital.uchicago.edu/index.html