Garnett on VISIUM

[Justine Seow]

Dear Garnett team,

Thank you for generating Garnett. I have used it in multiple occasions to solve questions!

May I know if this model can be used to predict cell types on VISIUM dataset which might have multiple cell types each pixel?

Best,
Justine

[hpl...@gmail.com]

Hi Justine,

I haven't tried to run Garnett on Visium data. On an engineering level you should be able to use the package so long as you can generate a cell_data_set object (i.e. the code should work), however unless your tissue is very pure and you expect spots to each only have one cell type, I would guess that the classification will not work very well because of the mixing. Hope this helps!

Best,

Hannah