-
Dear all,
I am trying to classify a slide from a colon cancer FFPE stained with a lymphocytic marker labelled with DAB, counterstained with Hematoxylin and scanned at 20X with Hamamatsu scanner. M…
-
Hello,
I am using the following command to call the variants. My intention here is to speed up this process while retaining all the variant information that is needed.
```
samtools mpileup
…
-
Hi,
I am working with whole tissue slides and have several slides of the same (consecutive) slides with different stainings per case. I would like to select a ROI (tumor area) and copy this to the…
-
Hey,
first of all,I totally like your software. But I need your help, maybe you have an idea...:
I´m trying to get the measurements of the area which I already classified as stroma or tumor.
Maybe …
-
Thanks for sharing this excellent program!! Is there a way to expand the subcellular detection categories to 4? Perhaps 1-3, 4-9, 10-15 and >15 spots per cell to correspond with the RNAscope scoring s…
-
I would like to create a Hot Spot analyses of my IF images that i have classified in QuPath. i have never done this before and was hoping for some insight into what might be the best way to go about t…
-
H-DAB Ki67 labeled tissue,
celldetection of negative blue nuclei works best, with Hematoxylin OD Nucleus Detection.
Drawback is lack of recognition of DAB positive cells.
Recognition of DAB po…
-
Hi, my name is Luis and I was wondering if there is a way of training an additional classifier that takes into account an image that has been cell-type classified. For example, if an image of a tumour…
-
Dear @petebankhead
Hope this finds you well. I am back again for your input on an issue.
First, let me tell briefly about **my task with the QuPath**. I stained slides of different mouse tissue…
-
Hello, we are using VEP in GDC-like pipeline after VarScan step.
This is our VEP launch command:
`/soft/ensembl-vep-95/vep --fork 14 --input_file Test.all.all.hc.fp-filtered-D3.Somatic.vcf --format …