111 lines
3.7 KiB
YAML
111 lines
3.7 KiB
YAML
---
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title: "Provenance-backed spatial transcriptomics and imaging enrichment batch."
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task: ""
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lineage_type: import
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upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/7a064bf0/data/enrichment.spatial-imaging-v1.yml
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upstream_sha: 7a064bf0
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imported_at: 2026-08-08
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prompt_class: catalogue
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upstream_changes: accepted
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author: upstream
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validated: false
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---
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# Provenance-backed spatial transcriptomics and imaging enrichment batch.
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resources:
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aestetik:
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entities: [cell, gene, tissue]
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methods: [autoencoder]
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modalities: [histopathology, spatial-transcriptomics]
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tasks: [representation-learning]
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github: https://github.com/ratschlab/aestetik
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last_checked: 2026-08-08
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metadata_sources:
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- https://github.com/ratschlab/aestetik
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conch:
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entities: [tissue]
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methods: [contrastive-learning, transformer]
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modalities: [histopathology, imaging]
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tasks: [foundation-model-pretraining, representation-learning]
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github: https://github.com/mahmoodlab/CONCH
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last_checked: 2026-08-08
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metadata_sources:
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- https://github.com/mahmoodlab/CONCH
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deepspot:
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entities: [gene, tissue]
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modalities: [histopathology, spatial-transcriptomics]
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tasks: [regression]
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github: https://github.com/ratschlab/DeepSpot
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last_checked: 2026-08-08
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metadata_sources:
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- https://github.com/ratschlab/DeepSpot
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deepspot_m:
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entities: [gene, tissue]
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modalities: [histopathology, spatial-transcriptomics, transcriptomics]
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tasks: [foundation-model-pretraining, regression]
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github: https://github.com/ratschlab/DeepSpotM
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last_checked: 2026-08-08
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metadata_sources:
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- https://github.com/ratschlab/DeepSpotM
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deepspot2cell:
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entities: [cell, gene, tissue]
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modalities: [histopathology, spatial-transcriptomics]
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tasks: [regression]
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github: https://github.com/ratschlab/DeepSpot2Cell
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last_checked: 2026-08-08
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metadata_sources:
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- https://github.com/ratschlab/DeepSpot2Cell
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gigapath:
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entities: [tissue]
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methods: [self-supervised-learning, transformer]
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modalities: [histopathology, imaging]
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tasks: [foundation-model-pretraining, representation-learning]
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github: https://github.com/prov-gigapath/prov-gigapath
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last_checked: 2026-08-08
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metadata_sources:
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- https://github.com/prov-gigapath/prov-gigapath
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phikon:
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entities: [tissue]
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methods: [self-supervised-learning, transformer]
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modalities: [histopathology, imaging]
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tasks: [foundation-model-pretraining, representation-learning]
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documentation: https://huggingface.co/owkin/phikon
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last_checked: 2026-08-08
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metadata_sources:
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- https://huggingface.co/owkin/phikon
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plip:
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entities: [tissue]
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methods: [contrastive-learning]
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modalities: [histopathology, imaging]
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tasks: [classification, representation-learning]
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github: https://github.com/PathologyFoundation/plip
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last_checked: 2026-08-08
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metadata_sources:
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- https://github.com/PathologyFoundation/plip
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uni:
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entities: [tissue]
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methods: [self-supervised-learning, transformer]
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modalities: [histopathology, imaging]
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tasks: [foundation-model-pretraining, representation-learning]
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github: https://github.com/mahmoodlab/UNI
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last_checked: 2026-08-08
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metadata_sources:
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- https://github.com/mahmoodlab/UNI
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hest_xenium_virtual_spatial_transcriptomics:
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entities: [cell, gene, tissue]
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modalities: [histopathology, spatial-transcriptomics, transcriptomics]
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tasks: [regression]
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documentation: https://huggingface.co/datasets/ratschlab/HEST_Xenium_virtual_spatial_transcriptomics
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last_checked: 2026-08-08
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metadata_sources:
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- https://huggingface.co/datasets/ratschlab/HEST_Xenium_virtual_spatial_transcriptomics
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