How to run TMA dearrayer for fluorescent image

Usage & Issues
#1

Hi guys,
It is my first trial to work with TMAs in Qupath. In v0.2.0-m9 I am not able to make a grid for fluorescent TMAs(*.qptiff, 5 channels). When I run TMA dearrayer, only one TMA annotation appears. What I’ve tried:

  1. two different TMA files (with 6 and 50 cores),
  2. older QuPath versions,
  3. Increased memory up to 8GB,
  4. made a full image annotation prior to TMA dearrayer.
  5. deselected all channels but DAPI.

Still I see only one blue circle in the middle of image. Please see printscreen attached.

Screen Shot 2020-04-17 at 15.06.45
Screen Shot 2020-04-17 at 15.06.451680×1050 313 KB

What else can I try?

Thanks,
Alice

#2

Did you try adjusting the diameter of the core during detection?

Sometimes the dearrayer can be very sensitive to the diameter being (almost) correct. You can draw a line across a core to see what an appropriate value would be.

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#3

Thanks Pete. It worked, when I entered the precise number of the core diameter.

1 Like