Positive pixel count question

[Vetdocjim1]

Good morning:

I am trying to do a positive pixel count on the enclosed image. I have adjusted the detection parameters so qupath can see the Fast Red chromagen. When I run a test analysis on a small box within the image, the software generates exactly the data I am trying to measure. However, when I request analysis on the entire annotated area, the software does not report a result. I wonder if the annotated area is too large, if my computer does not have sufficient resources, or if there is some way to adjust the software to take full advantage of the computer resources? I am running a Lenovo ThinkPad with an I5 processor 2.3 GHz with 8GB of RAM.

Thanks,

Jim

[micros...@gmail.com]

The area is probably too large, I usually create annotation tiles and sum the results for any positive pixel detection.

See here: https://groups.google.com/forum/#!topic/qupath-users/U6ee_WJ_Wp0

The links to the scripts I wrote have been moved to here: https://gist.github.com/Svidro/6171d6d24a85539d3af5d417bc928d50

There is still a 1.3 version as well.

But the first few lines show that I was splitting the annotations into 1000um tiles.

runPlugin('qupath.lib.algorithms.TilerPlugin', '{"tileSizeMicrons": 1000.0, "trimToROI": true, "makeAnnotations": true, "removeParentAnnotation": false}');
 

selectAnnotations();

The thread also has some nice uses of the positive pixel detection with regards to what is considered positive and negative.

[micros...@gmail.com]

I want to emphasize that the "red" was the primary color in that script (which is the "negative" measurement) and "brown" was used to detect background color. That probably will not quite be the same in your case, though you can do something similar to summarize the measurements.

[Vetdocjim1]

Hi Micros:

Thanks! I'll try that!

Jim