Crate eozin 

Eozin: The dye-namic solution for digital pathology

Eozin is a pure-Rust decoder library for digital pathology. The library’s primary purpose is to provide efficient access to individual tiles within digital pathology images. It provides a native Rust API and bindings targeting Python, Web-based JavaScript, and Node.js. The name is derived from eosin, an essential dye solution used in pathological diagnosis.

Quickstart

This example demonstrates how to select the lowest resolution level from a digital pathology image in a native Rust environment, retrieve the central tile within that level, and save it as a JPEG file.

use eozin::std_io::DynamicDecoder;

let file = std::fs::File::open("/some/slide.svs").unwrap();
let reader = std::io::BufReader::new(file);
let mut decoder = DynamicDecoder::new(reader).unwrap();

let (width, height) = decoder.dimensions();

// Get the index of the lowest resolution level
let lowest_resolution_level = decoder.level_count() - 1;

// level_tile_ranges returns Vec<(horizontal_tiles, vertical_tiles)>
let lowres_tile_ranges = decoder.level_tile_ranges()[lowest_resolution_level];

// Retrieve the tile at the center of the level
let lowres_centered_tile = decoder.read_tile(
  lowest_resolution_level, 
  lowres_tile_ranges.0 / 2, 
  lowres_tile_ranges.1 / 2, 
).unwrap();

assert!(lowres_centered_tile.is_jpeg());
std::fs::write("tile.jpg", &lowres_centered_tile).unwrap();

Core Concept

Digital pathology images are captured using high-magnification microscopes, resulting in massive images that can reach hundreds of thousands of pixels in dimension. Because storing such large images in standard formats is impractical, they are designed as containers comprising small rectangular images called tiles.

Furthermore, since downscaling these images on the fly is computationally expensive, they typically store multiple lower-resolution versions, referred to as levels. Vendors have developed various proprietary formats, and libraries like OpenSlide and bioformats have been instrumental in handling them.

The motivation for Eozin is to provide lightweight and fast access to these tiles. Specifically, each tile is stored as a fragmented byte sequence; Eozin calculates the byte offset based on the requested level and coordinates, then appends the necessary headers so the buffer can be interpreted as a standard image format.

Pixel-level processing (such as intensity manipulation) is intentionally left to established libraries—such as the image crate in Rust, Pillow in Python, or Blob objects in JS/Web environments.

Since the I/O and decoding logic are completely decoupled, Eozin can be adapted to various environments. Client-side rendering in the browser achieves performant response times, and its efficiency is also ideal for high-throughput AI interpretation and analysis.

Notes

Vendor and file format names mentioned in this library are the property of their respective owners. This library is not certified for clinical use.

Modules

std_io

Decoder works with R: Read + Seek.

wasm

WebAssembly. This module is intended to be compiled with wasm-pack and called by JavaScript.

Structs

Tile

Contains the encoded tile byte sequence, dimensions, and image format information.

Enums

EozinError

Error type for this library

SlideFormat

File format for digital pathology.