Manual annotation and measurements

[Jack Cleutjens]

Dear Qupath users,

I am not that skilled yet with qupath, but I have a question because for the measurements I have to do the classification is no option.

What I want to do is:

1. Detect the tissue ( no problem with the simple tissue detection option)
2. Mark the areas of peritumoral and tumor tissue (orange and yellow areas in the picture) manually.
3. Count the nerves manually using the point tool in the total tissue

Measurements:

1. areas: total tissue, tumor, peritumoral and rest of the stromal tissue
2. Number of nerves in all of the areas above

Is there anybody who can help me with this?

Best regards,

Jack Cleutjens

[micros...@gmail.com]

As noted at the top of the google group, the forum location is now here: https://forum.image.sc/tags/qupath

In general, area measurements are included in the annotations, and you can sum the areas of same classes by modifying scripts like this, while subtracting the sub-areas (sum tissue - sum peritumoral area = blue, sum peritumoral-sum tumor = peritumoral area, etc). That is provided your area types are always in the same size order. It looks like they always would be. The points would be slightly more complicated since they are annotations, and do not really stack well in terms of being "inside" stacked annotations. You would need a script to check .contains for this, I think, though that may have changed if you are using 0.2.0. I would recommend including the version number if you re-post on the QuPath forum for further help.

[micros...@gmail.com]

Oh, and there you did! Good. Will try to help more there.