wli13/HistAgent-data

HistAgent tutorial and Agent Module data

This repository contains the public data used by the HistAgent tutorials and the configurable Agent Module.

Contents

HistAgent-data/
├── tutorials/              # tables and images loaded by the notebooks
├── rankridge_tutorial_packs/
│   ├── human__breast/
│   ├── human__kidney/
│   ├── human__stomach/
│   ├── mouse__lung/
│   ├── mouse__spleen/
│   └── rcc__human_kidney/
├── rankridge_pack_versions.csv
├── rankridge_validation.csv
├── chat/
│   ├── spots.jsonl         # 9,150 spatial transcriptomics spot records
│   ├── config.example.env  # Agent Module data-path configuration
│   └── slice_images/       # three RCC tissue images for the slice selector
└── manifest.json           # byte sizes and SHA-256 checksums

The tutorial files include benchmark summaries, spot examples, WSI panels, a pretrained ABMIL example and atlas retrieval examples. The RankRidge packs contain sparse reference rank features, reference expression targets, query rank features and fitted coefficients. The notebooks can refit or run the mapping without downloading the source H5AD collection.

The Agent Module JSONL contains ranked genes, cell-state summaries, pathways and spatial context for each public demo spot. The tissue images use public study accessions as filenames so the server can match them to their slices.

Download

from huggingface_hub import snapshot_download

root = snapshot_download(
    "wli13/HistAgent-data",
    repo_type="dataset",
)

Tutorial notebooks expect:

DATA_DIR = root / "tutorials"
RANKRIDGE_DIR = root / "rankridge_tutorial_packs"

The hosted notebooks download only the packs used on the current page. To use a local copy, set HISTAGENT_TUTORIAL_DATA and HISTAGENT_RANKRIDGE_PACKS.

For the Agent Module:

HISTAGENT_INPUT_JSONL=<root>/chat/spots.jsonl
HISTAGENT_ATLAS_SQLITE=
HISTAGENT_SLICE_IMAGE_DIRS=<root>/chat/slice_images

The public bundle does not require the optional full-atlas SQLite file. Natural-language retrieval uses the 9,150 rich spot records in spots.jsonl.

Provenance and use

The bundle contains derived research outputs and examples assembled from the public studies cited by the HistAgent manuscript. Source-study terms continue to apply to the underlying data.