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Apply Pixie to Codex dataset #1065
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Hey @RYY0722, I would recommend looking at the pixel cluster output to ensure that everything you included in the CD31 cluster expresses CD31, and that you didn't miss any. If the individual pixels in the CD31 cluster are not actually expressing CD31, then when you go to annotate cell clusters, those inaccuracies will propagate downstream. If you want to QC the results, the important thing is that you have representative images of the important regions. If random sampling will do the trick, you could do that, or a guided approach where you select specific regions |
Hi @ngreenwald, thanks a lot for the suggestions!!
For another thing, what kind of QC steps will you suggest? Could you give me some examples? Thank you very much!! Looking forward to your reply! |
Whatever decisions you make at the pixel level will impact your cell clustering. If you have a pixel cluster that expresses GFAP and CD20, but you think the CD20 is artifactual/unimportant, then labeling that cluster GFAP makes sense. However, if you think the GFAP/CD44 co-expression represents actual signal that is expressed by both, and you label it GFAP only, then when you do cell clustering, you won't be able to separate GFAP+CD44- from GFAP+CD44+. It all depends on how you want to do cell clustering, if this is a problem or not. For QC, we use Mantis viewer currently. The notebook/README explains how we use it. |
Noted with thanks! |
Hi, thanks a lot for the great work and congratulations!!
I wish to apply this wonderful method on my codex dataset to reduce manual work! However, I found that some cells are misclassified after the pixel and cell cluster annotation. I felt lost when I looked back and want to optimize the annotations. May I have some insights from you? Thanks a lot!
Like the image above shows the cells with label "endothelial cell". However, some of them do not express CD31 (the marker we select at all), and some of the cells with high CD31 expression are not labeled as endothelial cells. Would you please give me some suggestions under these circumstance?
Thank you very much and looking forward to you reply!!
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