Metadata-Version: 2.4
Name: prism_embedder
Version: 1.1.0
Summary: Embedding of whole slide images with PRISM
Home-page: https://github.com/clemsgrs/prism-embedder
Author: Clément Grisi
Author-email: clement.grisi@radboudumc.nl
Project-URL: Bug Tracker, https://github.com/clemsgrs/prism-embedder/issues
Platform: unix
Platform: linux
Platform: osx
Platform: cygwin
Platform: win32
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: omegaconf
Requires-Dist: huggingface-hub
Requires-Dist: numpy<2
Requires-Dist: pandas
Requires-Dist: pillow
Requires-Dist: tqdm
Requires-Dist: numba
Requires-Dist: torchvision
Requires-Dist: opencv-python
Requires-Dist: matplotlib
Requires-Dist: wholeslidedata<0.0.16
Requires-Dist: timm
Requires-Dist: torch
Requires-Dist: transformers
Requires-Dist: environs
Requires-Dist: sacremoses
Requires-Dist: einops
Requires-Dist: einops-exts
Requires-Dist: xformers
Provides-Extra: testing
Requires-Dist: pytest>=6.0; extra == "testing"
Requires-Dist: pytest-cov>=2.0; extra == "testing"
Requires-Dist: mypy>=0.910; extra == "testing"
Requires-Dist: flake8>=3.9; extra == "testing"
Requires-Dist: tox>=3.24; extra == "testing"
Dynamic: author-email
Dynamic: description
Dynamic: description-content-type
Dynamic: home-page
Dynamic: license-file
Dynamic: project-url

# prism-embedder

[![PyPI version](https://img.shields.io/pypi/v/prism-embedder?label=pypi&logo=pypi&color=3776AB)](https://pypi.org/project/prism-embedder/)
[![Docker Version](https://img.shields.io/docker/v/waticlems/prism_embedder?sort=semver&label=docker&logo=docker&color=2496ED)](https://hub.docker.com/r/waticlems/prism_embedder)


## 🛠️ Installation

System requirements: Linux-based OS (e.g., Ubuntu 22.04) with Python 3.10+ and Docker installed.

We recommend running the script inside a container using the latest `prism_embedder` image from Docker Hub:

```shell
docker pull waticlems/prism_embedder:latest
docker run --rm -it \
    -v /path/to/your/slide.tif:/input/images/whole-slide-image/slide.tif \
    -v /path/to/your/mask.tif:/input/images/tissue-mask/mask.tif \
    waticlems/prism_embedder:latest
```

Update the command with the path pointing to your slide & tissue mask.

Alternatively, you can install `prism-embedder` via pip:

```shell
pip install prism-embedder
```

## TODO

- [] save feature in `.json` compatible with GC interface
- [] update interface slug based on new interface request (whole-slide image and whole-slide tiling visualization)
- [] plot tSNE for a few slides to debug implementation
