Acknowledgement

This work is based mainly on openslide-rust library and openslide-python library

openslide-rs

Rust bindings to OpenSlide (https://openslide.org/).

This work has no affiliations with the official OpenSlide project.

openslide-rs is a rust interface to the OpenSlide library.

OpenSlide is a C library that provides a simple interface for reading whole-slide images, also known as virtual slides, which are high-resolution images used in digital pathology. These images can occupy tens of gigabytes when uncompressed, and so cannot be easily read using standard tools or libraries, which are designed for images that can be comfortably uncompressed into RAM. Whole-slide images are typically multi-resolution; OpenSlide allows reading a small amount of image data at the resolution closest to a desired zoom level.

OpenSlide can read virtual slides in several formats:

• Aperio (.svs, .tif)
• Hamamatsu (.ndpi, .vms, .vmu)
• Leica (.scn)
• MIRAX (.mrxs)
• Philips (.tiff)
• Sakura (.svslide)
• Trestle (.tif)
• Ventana (.bif, .tif)
• Generic tiled TIFF (.tif)

Requirements

• Rust ≥ 1.88
• OpenSlide build dependencies, required because of openslide-sys dependency

Installation

OpenSlide-rs requires OpenSlide.

You will find a Makefile to help you install all required dependencies for Ubuntu and MacOs. Below are the commands to run to build this crate.

Dependencies

To be able to build this crate you need to install OpenSlide

You will also find a Makefile to help you install all required dependencies for Ubuntu and MacOs

MacOs

brew update
brew install openslide

Ubuntu

apt-get update
apt-get install -y --no-install-recommends libopenslide-dev

Docker

Container build and usage instructions for the slide-info CLI are available in dockerfiles/README.md. Use Docker Buildx bake to build the image and run the binary against mounted slide files.

Usage

use openslide_rs::{Address, DeepZoomGenerator, DeepZoomOptions, OpenSlide, Region, Size};

let slide = OpenSlide::new("slide.svs")?;
println!("{} levels: {:?}", slide.level_count(), slide.all_level_dimensions());

// Read a region (address in level-0 coordinates) as an RGB image.
let image = slide.read_image_rgb(&Region {
    address: Address { x: 0, y: 0 },
    level: 0,
    size: Size { w: 512, h: 512 },
})?;

// Deep Zoom tiles, e.g. for a tile server.
let dz = DeepZoomGenerator::new(&slide, DeepZoomOptions::new(254).with_limit_bounds(true))?;
let tile = dz.tile_rgb(dz.level_count() - 1, Address { x: 0, y: 0 })?;

Features: image (RGB/RGBA images, thumbnails), deepzoom (default, implies image), openslide4 (tile cache, ICC color profiles; requires OpenSlide 4.x).

More Information

• API documentation
• Website
• GitHub
• Sample data