Simple DeepZoom Whole Slide Image viewer

Based on OpenSlide and the DeepZoom protocol. Uses OpenSeaDragon as a frontend browser-based viewer. Written in Rust.

Why?

Most pathology slide viewers are desktop apps that read slides from the local filesystem. My slides usually reside on a research HPC cluster of some kind. As these slides are usually multi-GB files, it can be quite annoying to have to download a full slide whenever I have to inspect one. This tool spins up a webserver that can serve any OpenSlide-compatible slide using the DeepZoom protocol for quick browser-based inspections of slides.

Warning

The state of this project: its just a quick hack to solve a small problem. As the many TODO comments in the code suggest, this project is not what decent programmers would consider 'production quality'.

Building

Install the OpenSlide dependency

This tool uses forked code from these OpenSlide rust bindings: https://crates.io/crates/openslide.

See https://openslide.org/download/ for instructions on how to install OpenSlide 3.4.1.

On MacOS (ARM), do not forget to add OpenSlide to your LIBRARY_PATH.:

brew install openslide
export LIBRARY_PATH=$LIBRARY_PATH:/opt/homebrew/Cellar/openslide/3.4.1_7/lib

Build and run the example

We use the CMU-1 slide, which is one of the example tissue slides provided by Carnegie Mellon University (licensed CC0 1.0).

cargo run --release ./assets/CMU-1-Small-Region.svs

Then open 127.0.0.1:8080 in the browser.

Benchmarks

A single benchmark is provided for the get_tile() function. Run it using:

cargo bench

Profiling using flamegraph

Requires https://crates.io/crates/flamegraph.

Note that flamegraph requires sudo privileges to run on most machines.

Example command:

sudo cargo flamegraph --bench benchmarks

jjhbw / slidestream