Cytario

An open-core, web-based Image Management System (IMS) and scientific bioimaging viewer for digital pathology and spatial biology. Cytario is engineered to eliminate vendor lock-in, proprietary format silos, and cloud egress bottlenecks by managing petabytes of whole-slide images (WSI) and multi-channel multiplexed datasets using open standards (OME-TIFF, OME-Zarr, GeoTIFF, Apache Parquet, Apache Arrow) streaming directly from S3-compatible object storage.

Source Repository: cytario/cytario-web — AGPL-3.0
Official Platform Portal: cytario.com
Plugin API Specification: @cytario/plugin-api (packages/plugin-api)
Design System: @cytario/design

Core Capabilities & Pathology Workflows

1. Multiplex Immunofluorescence (mIF), IHC, and H&E in One Viewer

Built specifically for datasets that overwhelm conventional web viewers:

16-bit High-Plex Imaging: Handles multi-channel mIF and spatial biology datasets (spanning hundreds of gigabytes per slide) alongside standard brightfield H&E and immunohistochemistry (IHC).
Interactive Channel Windowing & True Intensity Readouts: Real-time channel contrast stretching on true image histograms, dynamic false-color assignment, and cursor-hover readouts of physical pixel intensity values.
Million-Cell Overlays: High-performance hardware-accelerated rendering of cell segmentation masks, centroids, and phenotypic classifications streamed directly from downstream machine-learning pipelines (e.g. [[HoVer-NeXt]], QuPath, Cellpose) or CSV/Parquet files.

2. Standards-First Interoperability

Replaces closed, vendor-proprietary archives with established open imaging standards: OME-TIFF, OME-Zarr, GeoTIFF, and GeoParquet.
Enables multi-vendor hospital and research networks where disparate slide scanners, laboratory information systems (LIS), and computational pathology AI algorithms interoperate without format conversion friction.

3. Petabyte-Scale Cloud-Native Storage Architecture

Direct-to-S3 Client-Side Streaming: Eliminates intermediate rasterization tile servers, heavy file downloads, and local hard drive shuttling. Slides stream directly into the browser from S3-compatible object stores (AWS S3, MinIO, RustFS) via range requests.
Short-Lived Credential Federation: Authenticates S3 requests using AWS Security Token Service (STS) temporary credentials, ensuring data governance and zero exposure of static storage keys.

Technical Architecture & Engineering Stack

Layer

Technology

Function

Frontend Framework

React Router v7 (SSR), React 19, Vite 6

Server-side rendering, fast hydration, and type-safe routing

Language

TypeScript (strict mode)

Strict end-to-end typing across host and plugin interfaces

Visualization & Rendering

Viv, deck.gl

GPU-accelerated multiscale visualization of high-resolution multiplexed bioimaging (developed by Harvard Medical School HIDIVE Lab)

In-Browser Analytics

DuckDB-WASM, Apache Arrow

In-memory columnar processing and spatial queries on Parquet cell tables directly in WebAssembly

Styling & UI

Tailwind CSS, @cytario/design

Modern component library and responsive pathology UI

Authentication & IAM

Keycloak 26.6 (Organizations)

Multi-tenant boundary isolation, scoped role-based access control (/admins, user groups)

State Management

Zustand (with DevTools)

Lightweight, predictable client state

Session Caching

Valkey / Redis (TLS enforced)

OAuth token caching and session lifecycle management

Application Database

PostgreSQL + Prisma ORM

Relational schema, tenant settings, and asset metadata

Cloud & Object Storage

AWS S3 / MinIO / RustFS

S3-compatible storage accessed via client-side SigV4 signedFetch

Deployment Runtime

Google Distroless Node.js 24

Hardened container runtime (gcr.io/distroless/nodejs24-debian12), Helm charts, Podman/Kubernetes

Extensibility & Plugin Model

Cytario Web features a modular plugin architecture based on @cytario/plugin-api. Format loaders for specialized or proprietary microscopy formats can be compiled into the application at build time without modifying core application code:

import type { CytarioPlugin } from "@cytario/plugin-api";

const vendorPlugin: CytarioPlugin = {
  name: "@vendor/wsi-loader",
  apiVersion: "^1.0.0",
  register(ctx) {
    ctx.formats.register(["wsi", "svs"], {
      load: async (url, opts) => {
        const res = await opts.signedFetch(url, { signal: opts.signal });
        return { data: res, metadata: { /* image metadata */ } };
      },
      fileTypeMeta: { label: "Vendor WSI", icon: "Microscope" },
    });
  },
};

export default vendorPlugin;

Security & Compatibility Gates

S3 SigV4 Security Boundary: All object storage requests execute through the host's signedFetch. Outgoing headers pass through a strict allowlist (Range, If-None-Match, Accept, Cache-Control) while sensitive authentication headers (Authorization, Cookie, x-amz-*) are strictly protected against plugin smuggling.
Strict Semver Gating: The host validates each plugin's apiVersion against the bundled @cytario/plugin-api version on bootstrap, skipping incompatible modules without crashing the host.

Licensing & Enterprise Model

Open Core (AGPL-3.0): The web viewer and core IMS (@cytario/web, @cytario/plugin-api) are freely available under AGPL-3.0 for self-hosting on on-premise, cloud, or hybrid infrastructure.
Cytario Enterprise Edition: Proprietary format loaders, white-label deployment bundles, commercial dual-licensing (exempting consumers from AGPL-3.0 source-disclosure requirements), and fully managed cloud operations are offered through cytario.com.

Relationship to the Digital Pathology Ecosystem

[[Cytomine]]: While Cytomine provides an established Java/Grails and PostGIS microservice suite for collaborative annotation and algorithm execution, Cytario focuses on a modern cloud-native TypeScript/React 19 stack, serverless S3 client-side streaming via Viv and deck.gl, and in-browser analytics with DuckDB-WASM.
[[Celldega]]: Celldega emphasizes exploratory spatial transcriptomics and interactive clustering (AnnData/Squidpy/ParquetWASM); Cytario functions as an enterprise-wide Image Management System (IMS) connecting clinical scanners, multi-tenant Keycloak IAM, and diagnostic pathology workflows.
[[QuPath]]: QuPath serves as the gold standard desktop workstation for tissue analysis; Cytario serves as the scalable web platform to host, view, and organize whole-slide libraries and visualize QuPath-generated cellular measurements at institutional scale.
[[HoVer-NeXt]] & [[WSInfer]]: Deep learning segmentation models output cell coordinates and class labels that can be exported directly into Cytario as GeoParquet or CSV layers for web exploration.

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Last updated 17 days ago