slide2vec

slide2vec encodes whole-slide images with publicly available pathology foundation models. It uses hs2p for tissue detection and tiling, and handles batching, multi-GPU execution, and embedding storage.

Install

Python 3.10 or newer is required:

pip install slide2vec

Many models need additional dependencies available through pip install "slide2vec[fm]". See the model installation guide for model-specific extras, separate environments, and upstream packages.

For gated models such as Virchow2, request access on the model’s Hugging Face page and authenticate with hf auth login or an HF_TOKEN environment variable.

Embed a slide

from slide2vec import Model, PreprocessingConfig

model = Model.from_preset("virchow2")
preprocessing = PreprocessingConfig(requested_spacing_um=0.5)
embedded = model.embed_slide("/path/to/slide.svs", preprocessing=preprocessing)

tile_embeddings = embedded.tile_embeddings  # (N, 2560)
x, y = embedded.x, embedded.y               # level-0 tile coordinates

The preset supplies tile size and…