loki2
=====

.. py:module:: loki2

.. autoapi-nested-parse::

   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.



Subpackages
-----------

.. toctree::
   :maxdepth: 1

   /autoapi/loki2/cl/index
   /autoapi/loki2/config/index
   /autoapi/loki2/data/index
   /autoapi/loki2/inference/index
   /autoapi/loki2/mil/index
   /autoapi/loki2/models/index
   /autoapi/loki2/utils/index


Submodules
----------

.. toctree::
   :maxdepth: 1

   /autoapi/loki2/detect_cells/index
   /autoapi/loki2/encode_trans/index
   /autoapi/loki2/immstain/index
   /autoapi/loki2/plot/index
   /autoapi/loki2/preprocess/index
   /autoapi/loki2/psdtime/index
   /autoapi/loki2/retrieve/index
   /autoapi/loki2/retrieve_from_sc/index