Installation#

You can install wsidata with whatever package manager you prefer. The default installation only ship with tiffslide, please refer to next section on how to install different slide readers to support variety of file formats.

The default installation.

pip install wsidata

uv add wsidata

conda install conda-forge::wsidata

If you want to install the latest version from the GitHub repository, you can use the following command:

pip install git+https://github.com/rendeirolab/wsidata.git

Installation for slide readers#

TiffSlide is a cloud native openslide-python replacement based on tifffile.

TiffSlide is installed by default. You don’t need to install it manually.

pip install tiffslide

OpenSlide is a C library that provides a simple interface to read whole-slide images.

OpenSlide is installed by default from v0.3.0. You don’t need to install it manually.

You can easily install from PyPI

pip install openslide-python openslide-bin

In case that PyPI doesn’t work for you:

For Linux and OSX users, it’s suggested that you install openslide with conda or mamba:

conda install -c conda-forge openslide-python
# or
mamba install openslide-python

For Windows users, you need to download compiled openslide from GitHub Release. If you open the folder, you should find a bin folder.

Make sure you point the bin folder for python to locate the openslide binary. You need to run following code to import the openslide, it’s suggested to run this code before everything:

import os
with os.add_dll_directory("path/to/openslide/bin")):
    import openslide

FastSlide is a high-performance whole-slide image reader built on top of OpenSlide.

pip install fastslide

BioFormats is a standalone Java library for reading and writing life sciences image file formats.

scyjava is used to interact with the BioFormats library.

pip install scyjava

CuCIM is a GPU-accelerated image I/O library.

Please refer to the CuCIM GitHub.

pyisyntax a Python library for working with pathology images in the iSyntax file format, powered by libisyntax.

pip install pyisyntax

pylibCZIrw is the official Python binding to libCZI, maintained by Zeiss, for reading and writing Zeiss CZI whole-slide images. Unlike BioFormats, it decodes JPEG-XR natively on every platform it ships wheels for - including arm64 macOS, where BioFormats cannot load the ome:jxrlib native library. It is therefore the recommended backend for .czi files on Apple Silicon.

pip install pylibCZIrw

Wheels are published for Linux (x86_64 and aarch64), macOS (arm64), and Windows (x86_64) on CPython 3.9-3.13. There is no macOS x86_64 wheel, so Intel Macs will need to build from source or use BioFormats.