loki2

Loki2: A single-cell pathology foundation model for:

  1. cell type annotation, which infers cell type solely from morphological features;

  2. single-cell morphology-to-transcriptome retrieval, a cross-modality search engine that maps H&E-segmented cells to reference scRNA-seq atlases;

  3. morphological pseudotime inference, which leverages the continuous nature of the embedding space to infer dynamic developmental or pathological states;

  4. cell-level multiple instance learning (MIL), which aggregates individual cellular risk scores for patient-level prognostication;

  5. in silico staining, which generates virtual protein-level biomarker maps.

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