Experimental data | Cell size metric | Standard [74] | Data format | Data analysis challenges | Orthogonal to sc/snRNA-seq |
---|---|---|---|---|---|
Label intensity | Gold | Image | Label performance; cell segmentation; image artifact removal [22, 28, 35, 40, 74] | Yes | |
IHQ/IHC [36] | Label intensity | Gold | Yes | ||
Expression/label intensity | Silver | Yes | |||
sc/snRNA-seq | mRNA spike-in expression | Silver | Gene expression counts | Embedding alignment, batch effects, dissociation biases, platform biases [26, 48, 81] | Yes |
sc/snRNA-seq | Housekeeping gene expression | Silver | No | ||
sc/snRNA-seq | Bronze | No | |||
sc/snRNA-seq | Bronze | No |