Posted by
G. Esteban Fernandez on
Oct 15, 2015; 5:20pm
URL: http://imagej.273.s1.nabble.com/Only-count-cells-that-contain-nuclei-or-holes-in-the-binarized-image-tp5014650p5014652.html
Also, solidity is higher if there are no holes. Maybe there's a
cutoff Solidity value above which are all your nuclei without holes,
so you would be able to run Analyze Particles with Shape Descriptors
activated (under Analyze > Set Measurements) and just see how many
nuclei there are above your cutoff Solidity (sort the list by Solidity
in Excel).
-Esteban
On Thu, Oct 15, 2015 at 10:13 AM, G. Esteban Fernandez
<
[hidden email]> wrote:
> I'd run Analyze Particles WITHOUT "Include holes" then again WITH
> "Include holes" activated and compare the Results to count the ones
> for which the Area changed.
>
> -Esteban
>
> On Thu, Oct 15, 2015 at 8:38 AM, kirbyfloss <
[hidden email]> wrote:
>> Hi - is there a way to only count the cells in the attached binarized image
>> that contain "holes"?
>> <
http://imagej.1557.x6.nabble.com/file/n5014650/workingCopy.png>
>>
>> I am trying to analyze slides with muscle stained with H&E - and would like
>> to count the number of regenerating muscle fibers, which are distinguished
>> by dark nuclei in the interior of the cell bodies (rather than on the
>> periphery).
>>
>> This is the pipeline I have set up thus far:
>> 1) Apply colour deconvolution (using plugin by G. Landini)
>> 2) Set threshold to binarize the resulting image in channel 2
>> 3) Analyze particles
>>
>> This works reasonably well to count all the cells in an image, but is there
>> any way to only count the cells that contain a hole (or multiple holes)
>> automatically? I'm aware of more manual tools, like Cell Counter, but was
>> hoping for the most automated solution possible.
>>
>> Thanks!
>>
>>
>>
>> --
>> View this message in context:
http://imagej.1557.x6.nabble.com/Only-count-cells-that-contain-nuclei-or-holes-in-the-binarized-image-tp5014650.html>> Sent from the ImageJ mailing list archive at Nabble.com.
>>
>> --
>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html--
ImageJ mailing list:
http://imagej.nih.gov/ij/list.html