Software

Software produced and maintained by our lab:

Marsilea

Declarative creation of composable visualizations

Marsilea is a Python library for creating composable visualizations in a declarative way. It is built on top of Matplotlib and provides a high-level API for you to assemble a visualization based on composable parts.

Github: https://github.com/Marsilea-viz/marsilea
Docs: https://marsilea.readthedocs.io/

LazySlide

Modular and scalable whole slide image analysis

LasySlide is a Python library for processing whole slide images (WSI) analysis. It provides a simple interface to perform robust preprocessing and advanced analysis for WSIs.

Github: https://github.com/RendeiroLab/LazySlide
Docs: https://lazyslide.readthedocs.io/

WSIData

Efficient data structures and IO operations for whole slide images analysis

WSIData is a data structure for manipulating whole slide images (WSI) and storing its analysis results in Python. It can read a variety of WSI formats and it inherits directly from SpatialData, making it interoperable with the scverse ecosystem. wsidata is designed to used with LazySlide.

Github: https://github.com/RendeiroLab/WSIData
Docs: https://wsidata.readthedocs.io/

wsi

Python library for processing whole slide images (WSI)

A simple Python library for processing whole slide images (WSI) with an object-oriented interface. It has the goal of doing basic processing of WSIs with reasonable defaults, but high customizability. It is a fork of the "CLAM" repository from the Mahmood lab.

Github: https://github.com/RendeiroLab/wsi
Docs: https://wsi.readthedocs.io/

cytomine-utils

Python package for high-level interaction with a Cytomine instance

Github: https://github.com/RendeiroLab/cytomine-utils
Docs: https://cytomine-utils.readthedocs.io/en/latest

Rendeiro group