Area ratio for brightfield image


#1

Hi all.

We want to measure the area that occupies the light blue area with regard to the whole tissue area. Could I process brightfield image with a program? I suppose it’s no need for scale, if I need a area ratio.

Thanks in advance.



#2

Hi,

Indeed, yes you can do this easily enough. The attached pipeline

  • Unmixes the colors (but you didn’t say what the stains were, so I guessed)
  • Segments the blue regions
  • Measures the area occupied by the blue objects, in pixels
  • Calculates the percentage of pixels in the whole image

Hope that helps!
David
DL_area_ratio.cppipe (8.42 KB)


#3

Hi.
Thanks a lot David.
Please, could you modify your pipeline to get red and white areas also measured? I suppose, the white one could be calculated as a difference between all area and (blue+red) areas. Of course if no any other colors is presented.
Thanks in advance,
Konstantin


#4

Hi,

Did you make any progress with this? I haven’t tried, but it ought to be easy enough to segment the red area analogous to the blue. And yes, the white might be simply the rest of the area.

David


#5

Yes, it works OK. Thanks a lot.


#6

Dear David. I’d prefer don’t make updates on PC, but nevertheless it happens. Some Java or some Windows updates made CellProfiler inusable. So, I had to install the new version you have for download. But the pipeline you prepared presents some problem. I put them in


Could you, please, correct it. If it is possible, please, could you add the red and white areas estimated also.

Bu the way, why the data stored as a csv file? The problem is when I open them in Excel all they appeared in a only one table cell and I have to divide in column trying not to make an error. Could the data be stored as a Excel format file directly?