Nucleii + micro nucleii identification

i’m using the previous pipeline on a new branch of cells and i seem to be having issues when aquiring the secondary objects

any ideas?

2011_03_14.cp (13.2 KB)

Try the the following changes:

  • Some of the nuclei are being missed because the upper size limit is too small and is therefore throwing off the cell detection as well. Increase the upper size limit in both IdentifyPrimary modules, from 60 to ,say, 100.

  • The illumination aberration is also throwing off secondary object detection so use the CorrBlue in IdentifySecondary instead of OrigBlue, and change the Otsu method from Background to Foreground.

Note that these adjustments seem to work for the three images posted for this question. I’ll leave it to you to try it with the other images.


[quote=“Tomb”]if you look at the images logarithmically you will see some lovely bright streaks across the image. It is different for each image.

I believe it is adding bias to my detection of bi-nucleated cells as it is altering the intensity readings.[/quote]

You might be able to use EnhanceOrSupressFeatures to pre-processing the image using Speckles as the feature and setting the feature size to at least the size of the least single nucleus you expect to encounter. This pre-processing may help somewhat with nuclei detection and intensity measurements. But I would recommend you check your microscope settings and see if you can further optimize the image acquisition from that end.