The objective of spatially aware QC

[boyiguo1]

@MicTott Do you have any vision or preferred definition of spatially-aware QC? For example, do you expect the QC happens at only the spot level, or as well as some micro-envrionment level (e.g. identify "hangnail" regions).

We don't have to them all depending on how challenging they are, but we could/should establish some priority that ouwld help us to define the tentative scope of the project.

Thanks

[MicTott]

@boyiguo1 Good question - my initial thought was being able to detect singular bad spots based on local neighborhood - but you're definitely right that there are likely technical artifacts or other that would result in bad areas composed of several spots, which something like outlier detection based on local neighborhood might do a poor job of detecting.

I think outliers based on local neighborhood is, in theory, fairly straightforward - so perhaps we focus on developing that and seeing how it performs? It might become clear at that point if additional methods to address these "hangnails" are needed.

[boyiguo1]

Sounds good. I agree that we should initially focus on singular bad spots. I figured we should align our expectation.

Also, just food for thought: in the future, if we want to address regional artifacts, e.g. "hangnails". We don't have to do it complete data driven way. I think if we could come up with some "computer-assisted" strategy/infrastructure to improve the whole manual process or provide reference for completely subjective annotation, that would be good too.