Noah F. Greenwald

I agree, I think it makes sense to just switch. Everything else looks good.

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...

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...

This looks great! If we're already going to be looking into AnnData for post-clustering, seems like we should plan on using that for vitesse as well, at least until we...

Maybe tomorrow you, @camisowers, and @jranek can have a brief discussion about how to split up the tasks for AnnData conversion. Seems like 1 important thing to have is a...

I thought there was already the option to do this? Maybe it's not turned on by default in the notebook? Pretty sure @JLrumberger added this in.

Hi @jamesMo84, There's currently not a way baked into the notebook to rely on a local installation of Mesmer/Cellpose, mostly because it would significantly increase the complexity of the dependencies....

More concretely, we should come up with a core set of color maps that people really like. I think doing some user polling to see what Erin, YeEun, Meelad, Bryan,...

Hi @TerGla, The easiest would be the modify your segmentation masks to also exclude those same cells. That way, none of the downstream analysis needs to be modified. If you...