prism-embedder 1.1.0

Embedding of whole slide images with PRISM

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:

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:

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