How to normalize overall area, and anyway to select large area to manually de-object


I identify nucs, use them as a seed for the secondary object. so far so good. The goal is to count the number of secondary objects (using very stringent (1.6) conditions).

I have 2 issues:

  1. A large swathe of each overall image (brain slices) is not wanted. However, there is no way to crop it out during acquisition. I tied manual Crop in CP, but it only gives me geometric shapes. I lose too much of the wanted area. Also, using coordinates is impossible because each slice is a bit diff.
    So I tried manual select object after secondary object, but there are hundreds of cells, to click on - not realistic to work this way,
  2. Unfortunately, during acquisition of the 30 slides, the student (I did not catch this in time), tiled sometimes 4 sometimes up to 8 tiles. So counting is now a problem. Any ideas how to normalize? (Maybe measure overall image size and do some calculation from there?)

(Defined as new user on this newish forum, though I been here since 2010, so can’t upload my pipeline)


Hi Avi_Jacob,
Just reply to this , just say hi! or anything. Then you will be able to upload anything.

Hi Avi,

At least for your first issue, you could first use the module IdentifyObjectsManually to freehand draw a shape then you can freehand draw any shape then use it to Crop your image by setting the set to crop to the object you just drew.


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Cool thanks Laura, I’ll try that.
(I solved the normalization issue by adding a count of the nucs and ratioing)

hi! or anything. (need to hit 20 char…) :slight_smile:

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