---
title: "Provenance-backed spatial transcriptomics and imaging enrichment batch."
task: ""
lineage_type: import
upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/7a064bf0/data/enrichment.spatial-imaging-v1.yml
upstream_sha: 7a064bf0
imported_at: 2026-08-08
prompt_class: catalogue
upstream_changes: accepted
author: upstream
validated: false
---

# Provenance-backed spatial transcriptomics and imaging enrichment batch.
resources:
  aestetik:
    entities: [cell, gene, tissue]
    methods: [autoencoder]
    modalities: [histopathology, spatial-transcriptomics]
    tasks: [representation-learning]
    github: https://github.com/ratschlab/aestetik
    last_checked: 2026-08-08
    metadata_sources:
      - https://github.com/ratschlab/aestetik

  conch:
    entities: [tissue]
    methods: [contrastive-learning, transformer]
    modalities: [histopathology, imaging]
    tasks: [foundation-model-pretraining, representation-learning]
    github: https://github.com/mahmoodlab/CONCH
    last_checked: 2026-08-08
    metadata_sources:
      - https://github.com/mahmoodlab/CONCH

  deepspot:
    entities: [gene, tissue]
    modalities: [histopathology, spatial-transcriptomics]
    tasks: [regression]
    github: https://github.com/ratschlab/DeepSpot
    last_checked: 2026-08-08
    metadata_sources:
      - https://github.com/ratschlab/DeepSpot

  deepspot_m:
    entities: [gene, tissue]
    modalities: [histopathology, spatial-transcriptomics, transcriptomics]
    tasks: [foundation-model-pretraining, regression]
    github: https://github.com/ratschlab/DeepSpotM
    last_checked: 2026-08-08
    metadata_sources:
      - https://github.com/ratschlab/DeepSpotM

  deepspot2cell:
    entities: [cell, gene, tissue]
    modalities: [histopathology, spatial-transcriptomics]
    tasks: [regression]
    github: https://github.com/ratschlab/DeepSpot2Cell
    last_checked: 2026-08-08
    metadata_sources:
      - https://github.com/ratschlab/DeepSpot2Cell

  gigapath:
    entities: [tissue]
    methods: [self-supervised-learning, transformer]
    modalities: [histopathology, imaging]
    tasks: [foundation-model-pretraining, representation-learning]
    github: https://github.com/prov-gigapath/prov-gigapath
    last_checked: 2026-08-08
    metadata_sources:
      - https://github.com/prov-gigapath/prov-gigapath

  phikon:
    entities: [tissue]
    methods: [self-supervised-learning, transformer]
    modalities: [histopathology, imaging]
    tasks: [foundation-model-pretraining, representation-learning]
    documentation: https://huggingface.co/owkin/phikon
    last_checked: 2026-08-08
    metadata_sources:
      - https://huggingface.co/owkin/phikon

  plip:
    entities: [tissue]
    methods: [contrastive-learning]
    modalities: [histopathology, imaging]
    tasks: [classification, representation-learning]
    github: https://github.com/PathologyFoundation/plip
    last_checked: 2026-08-08
    metadata_sources:
      - https://github.com/PathologyFoundation/plip

  uni:
    entities: [tissue]
    methods: [self-supervised-learning, transformer]
    modalities: [histopathology, imaging]
    tasks: [foundation-model-pretraining, representation-learning]
    github: https://github.com/mahmoodlab/UNI
    last_checked: 2026-08-08
    metadata_sources:
      - https://github.com/mahmoodlab/UNI

  hest_xenium_virtual_spatial_transcriptomics:
    entities: [cell, gene, tissue]
    modalities: [histopathology, spatial-transcriptomics, transcriptomics]
    tasks: [regression]
    documentation: https://huggingface.co/datasets/ratschlab/HEST_Xenium_virtual_spatial_transcriptomics
    last_checked: 2026-08-08
    metadata_sources:
      - https://huggingface.co/datasets/ratschlab/HEST_Xenium_virtual_spatial_transcriptomics