PrismToolBox

PrismToolBox is a comprehensive toolkit designed to streamline the process of working with digital pathology images. It provides a set of utilities and functionalities that simplify tasks such as reading slides, extracting patches, and embedding slides. It also provides useful functions to import/export data on QuPath.

The toolkit is still under development, and some features may not be fully implemented. If you encounter any issues or have suggestions for improvements, please open an issue or submit a pull request.

Features

• Slide Reading: Supports multiple backends for reading slides, including OpenSlide and TiffSlide.
• Patch Extraction: Extracts patches from slides at various magnification levels.
• Slide Embedding: Uses pre-trained models to generate embeddings from patches, facilitating downstream tasks like clustering or classification (in progress).
• Nuclei segmentation: Extracts nuclei using cellpose for H&E and SOP for IHC brighfield images.

Installation

To install PrismToolBox, run the following command in your terminal:

pip install prismtoolbox

To install PrismToolBox embedding and nuclei utilitaries, please run the following command:

pip install 'prismtoolbox[emb, seg]'

Usage

Here's a basic example of how to use PrismToolBox:

from prismtoolbox import WSI

# Initialize the reader
WSI_object = WSI(slide_path="path_to_your_slide", engine="openslide")

# Extract tissue contours
params_detect_tissue = {"seg_level": 4, "window_avg": 30, "window_eng": 5, "thresh": 90, "area_min": 1.5e3}

WSI_object.detect_tissue(**params_detect_tissue)

# Extract patches and save them as jpg images
params_patches = {"patch_size": 256, "patch_level": 0,"mode": "contours", "contours_mode": "four_pt_hard"}

WSI_object.extract_patches(**params_patches)
WSI_object.save_patches("path_to_folder", file_format="jpg")

For more detailed usage instructions and examples, please refer to the documentation.

Contributing

Contributions to PrismToolBox are welcome! Please open an issue or submit a pull request to propose changes or additions.

License

PrismToolBox is licensed under the BSD 3-Clause License. See LICENSE for more information.