Clarify the docs due to differences between Visium and Visium SPG processing pipeline steps

[lcolladotor]

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

[madhavitippani]

HI @boyiguo1 CAN YOU REMIND ME WHAT THESE FILES ARE, SORRY I FORGOT.

[boyiguo1]

@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.