psudo

See our paper psudo: Exploring Multi-Channel Biomedical Image Data with Spatially and Perceptually Optimized Pseudocoloring for more information.

Publication

This package is developed following the research conducted by Simon Warchol, Jakob Troidl, Jeremy Muhlich, Robert Krueger, John Hoffer, Tica Lin, Johanna Beyer, Elena Glassman, Peter Sorger, and Hanspeter Pfister. For a detailed explanation of the methodologies and their applications, please refer to the original paper linked above.

Affiliations

• Harvard John A. Paulson School of Engineering and Applied Sciences
• Harvard Medical School
• New York University Tandon School of Engineering

Use this repository (web app + palette lab)

pnpm install
pnpm run wasm-build   # first time / after Rust changes (needs rustup + wasm-pack)
pnpm dev

Open the viewer at / or the WASM test UI at /lab.

Use as an npm package in another app

Install the published WASM package and import optimize (and related helpers) from JavaScript/TypeScript:

npm install psudo

import * as psudo from "psudo";
// or: import { optimize, calculate_palette_loss } from "psudo";

const optimized = await psudo.optimize(
  colors,           // Uint16Array — flat RGB 0–255 per channel
  locked,           // Uint16Array — 1 = locked, 0 = free
  intensities,      // Uint16Array — nRows × nChannels, column-major
  contrastLimits,   // Uint16Array — [min,max] per channel
  luminance,        // Uint16Array — [minL, maxL] in OKLab × 100
  excluded,         // string[] — C3 names to avoid (e.g. "grey", "white")
  colorNames,       // string[] — optional hint per channel, "" if none
  undefined,
  undefined,
  false             // include_spatial_channel_overlap (false = fast)
);
// optimized: Float32Array linear sRGB 0–1, length 3 × nChannels

Full API, Web Worker + Vite setup, React notes, and parameter tables: lib/README.md (also shipped on npm). Sync main-thread API: import from "psudo/sync".

WASM build prerequisites

wasm-pack must be on your PATH (cargo install wasm-pack or brew install wasm-pack).

Use rustup for the compiler (not Homebrew rustc alone). Homebrew Rust does not ship the wasm32-unknown-unknown target, which produces:

wasm32-unknown-unknown target not found in sysroot: "/opt/homebrew/Cellar/rust/..."

If both are installed, pnpm run wasm-build prepends rustup’s toolchain so the correct rustc is used. One-time setup:

rustup target add wasm32-unknown-unknown

CI / deploy

GitHub Actions (.github/workflows/deploy.yml) uses pnpm, Node 24, and wasm-pack to build dist/, then packages it into an nginx Docker image for ECR.

npm publish (.github/workflows/publish-npm.yml): on release or manual dispatch. Add repo secret NPM_TOKEN — a granular npm access token with publish permission (create at npmjs.com; do not commit tokens or CLI auth URLs).