Open lcolladotor opened 1 year ago
HI @boyiguo1 CAN YOU REMIND ME WHAT THESE FILES ARE, SORRY I FORGOT.
@madhavitippani This is relevant to the improvement that you and @Ukaipa9 worked on recently to allow counting for different protein channels of Visium SPG.
And the two types of .mat
refers to the outcomes of splitSlide
and refineVNS
. If you feed splitSlide .mat
outcome
to countNuclei, there are still results instead of a warning.
Hi,
From today's spatial meeting, it sounds like there's a need to clarify the two types of
.mat
files in Visium and Visium Spatial Proteogenomics (Visium-SPG) processing pipelines, to avoid this confusion in the future. Otherwise you get a silent error: you get numbers but they are not the right ones.This could be an excellent opportunity for Uma @Ukaipa9 / Boyi @boyiguo1 to learn / practice sending pull requests. Request a DSgs with Nick @Nick-Eagles if you need to learn more about pull requests.
Thanks! Leo