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clemsgrs merged 1 commit into from
Jan 8, 2026
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improve readme #50

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37 changes: 33 additions & 4 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,37 @@
[![Docker Version](https://img.shields.io/docker/v/waticlems/slide2vec?sort=semver&label=docker&logo=docker&color=2496ED)](https://hub.docker.com/r/waticlems/slide2vec)


## Supported Models

### Tile-level models

| **Model** | **Architecture** | **Parameters** |
|:---------:|:----------------:|:--------------:|
| [CONCH](https://huggingface.co/MahmoodLab/conch) | ViT-B/16 | 86M |
| [H0-mini](https://huggingface.co/bioptimus/H0-mini) | ViT-B/16 | 86M |
| [Hibou-B](https://huggingface.co/histai/hibou-b) | ViT-B/16 | 86M |
| [Hibou-L](https://huggingface.co/histai/hibou-L) | ViT-L/16 | 307M |
| [MUSK](https://huggingface.co/xiangjx/musk) | ViT-L/16 | 307M |
| [Phikon-v2](https://huggingface.co/owkin/phikon-v2) | ViT-L/16 | 307M |
| [UNI](https://huggingface.co/MahmoodLab/UNI) | ViT-L/16 | 307M |
| [Virchow](https://huggingface.co/paige-ai/Virchow) | ViT-H/14 | 632M |
| [Virchow2](https://huggingface.co/paige-ai/Virchow2) | ViT-H/14 | 632M |
| [MidNight12k](https://huggingface.co/kaiko-ai/midnight) | ViT-G/14 | 1.1B |
| [UNI2](https://huggingface.co/MahmoodLab/UNI2-h) | ViT-G/14 | 1.1B |
| [Prov-GigaPath](https://huggingface.co/prov-gigapath/prov-gigapath) | ViT-G/14 | 1.1B |
| [H-optimus-0](https://huggingface.co/bioptimus/H-optimus-0) | ViT-G/14 | 1.1B |
| [H-optimus-1](https://huggingface.co/bioptimus/H-optimus-1) | ViT-G/14 | 1.1B |
| [Kaiko](https://github.com/kaiko-ai/towards_large_pathology_fms) | Various | 86M - 307M |

### Slide-level models

| **Model** | **Architecture** | **Parameters** |
|:---------:|:----------------:|:--------------:|
| [TITAN](https://huggingface.co/MahmoodLab/TITAN) | Transformer | 49M |
| [Prov-GigaPath](https://huggingface.co/prov-gigapath/prov-gigapath) | Transformer (LongNet) | 87M |
| [PRISM](https://huggingface.co/paige-ai/PRISM) | Perceiver Resampler | 99M |


## 🛠️ Installation

System requirements: Linux-based OS (e.g., Ubuntu 22.04) with Python 3.10+ and Docker installed.
Expand All @@ -23,7 +54,7 @@ Replace `/path/to/your/data` with your local data directory.
Alternatively, you can install `slide2vec` via pip:

```shell
pip install slide2vec
pip install slide2vechel
```

## 🚀 Extract features
Expand All @@ -43,9 +74,7 @@ pip install slide2vec
- for preprocessing options: `slide2vec/configs/default_tiling.yaml`
- for model options: `slide2vec/configs/default_model_.yaml`

We've also added default configuration files for each of the foundation models currently supported:
- tile-level: `uni`, `uni2`, `virchow`, `virchow2`, `prov-gigapath`, `h-optimus-0`, `h-optimus-1`, `h0-mini`, `conch`, `musk`, `phikonv2`, `hibou-b`, `hibou-L`, `MidNight12k`, [`kaiko`](https://github.com/kaiko-ai/towards_large_pathology_fms)
- slide-level: `prov-gigapath`, `titan`, `prism`
We've also added default configuration files for each of the foundation models currently supported (see above).


3. Kick off distributed feature extraction
Expand Down
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