Bio Spatial Transcriptomics High Resolution Binning

Reconstructs single cells from sub-cellular spatial capture units (Visium HD 2um bins, Stereo-seq DNB spots, Slide-seqV2 beads) by aggregating bins UP into cells rather than deconvolving a mixture DOWN. Use when choosing a bin size and recognizing the sparsity-vs-mixture dilemma (2um bins are too sparse to cluster, but binning to 8/16um re-creates the multi-cell mixture deconvolution was meant to escape); deciding between morphology-driven cell reconstruction (Bin2cell -- StarDist/Cellpose nuclei on a registered H&E/DAPI image, then assign 2um bins to nuclei) and fixed-bin aggregation by whether a co-registered cell image exists; recognizing this as the INVERSE of deconvo…