QuPath FastSlide Extension

A QuPath extension that reads whole-slide images using FastSlide.

Supports brightfield (RGB) and fluorescence/spectral (multi-channel) slides across all formats FastSlide handles: .svs, .tiff, .ome.tiff, .czi, .mrxs, .qptiff, .ndpi, .scn, .bif, .isyntax, .i2syntax.

Works on macOS (arm64/x86_64), Linux (x86_64/aarch64), and Windows (x86_64).

Install

Download qupath-extension-fastslide-fat-<version>.jar from the Releases page and drag it onto QuPath, or place it in QuPath's extensions directory.

Build

Prerequisites

• Java 21+ JDK

The FastSlide Java API and native libraries are not vendored in this repo. They are resolved from the FastSlide GitHub Releases as ordinary Gradle dependencies (dev.aifo:fastslide-java and dev.aifo:fastslide-native:<os>-<arch>) via an anonymous ivy/url repository declared in build.gradle.kts. No token is required.

Build the fat JAR

./gradlew fatJar

The output is at build/libs/qupath-extension-fastslide-fat-<version>.jar. This single JAR bundles the extension code, the FastSlide Java API, and the native libraries for every supported platform. Drop it into QuPath's extensions directory.

To target a different FastSlide release, bump fastslideVersion in build.gradle.kts.

Building against a local (unpublished) FastSlide

To test against FastSlide JARs you built yourself, stage a local release in the FastSlide repo and point Gradle at it -- no GitHub round-trip needed:

# In the FastSlide repo: build + stage a local file:// release.
python3 tools/build_java_artifacts.py --platform darwin_aarch64   # your host
python3 tools/publish_java_artifacts.py --dest local --out-dir /tmp/fastslide-release

# Back here: resolve from the local release instead of GitHub.
./gradlew fatJar -PfastslideRepoUrl=file:///tmp/fastslide-release

The -PfastslideRepoUrl override accepts any base URL laid out as <base>/<version>/<file>. See the FastSlide docs guide Java Packages and Releases for how releases are produced and published.

License

See LICENSE for details.