Installation

ASlide targets Linux and Python 3.10 or newer. The package bundles several native SDK libraries and uses optional Python extras for readers that are harder to install everywhere.

Prerequisites

• Linux, tested on Ubuntu 22.04/24.04, Red Hat 9.6, and similar distributions
• Python 3.10 or newer
• OpenSlide support through openslide-bin and openslide-python
• patchelf is recommended when reinstalling bundled SDPC libraries so runtime paths stay local to the package

The base install pins numpy<2 because several compiled scientific dependencies are still sensitive to NumPy ABI changes.

Install from GitHub

pip install git+https://github.com/MrPeterJin/ASlide.git

Source installation is also supported:

git clone https://github.com/MrPeterJin/ASlide.git
cd ASlide
python setup.py install

The install step copies bundled OpenCV, KFB, TRON, and SDPC shared libraries into the installed package and creates optional runtime helper scripts.

Optional Bio-Formats Support

Use the bioformats extra for readers that require Java-backed Bio-Formats, including VSI and the Bio-Formats CZI fallback path.

pip install 'git+https://github.com/MrPeterJin/ASlide.git#egg=Aslide[bioformats]'

Bio-Formats support requires:

• python-bioformats
• python-javabridge
• Java 11 or newer available on PATH, or exposed through JAVA_HOME

Example Java setup:

export JAVA_HOME=/path/to/your/jdk
export PATH="$JAVA_HOME/bin:$PATH"

Optional CZI Support

Use the czi extra when you need the lightweight Zeiss CZI path without forcing a full Java/Bio-Formats environment.

pip install 'git+https://github.com/MrPeterJin/ASlide.git#egg=Aslide[czi]'

For environments already pinned to numpy<2, install the CZI reader dependencies without letting pip re-resolve NumPy:

python -m pip install pylibCZIrw xmltodict --no-deps

Runtime Library Setup

Most bundled backends work after installation. If a backend still needs explicit runtime library hints, configure the process before opening slides.

Recommended Python setup:

from Aslide.bootstrap import setup_runtime_environment

setup_runtime_environment()
from Aslide import Slide

Manual shell setup:

ASLIDE_PATH=/path/to/site-packages/Aslide
export LD_LIBRARY_PATH=$ASLIDE_PATH/sdpc/lib:$ASLIDE_PATH/tron/lib:$LD_LIBRARY_PATH

Generated helper script:

source /path/to/site-packages/Aslide/setup_env.sh

Base Dependencies

The base package installs numpy<2, Pillow, h5py, openslide-bin, openslide-python, qptifffile, tifffile, readimc, imageio, pandas, pyisyntax, and olefile.