HistoAnnotator

Overview

HistoAnnotator is a cross-platform application for interactive annotation of histology and microscopy images. It supports browser-based use, standalone Desktop applications for Windows, Linux and macOS, and an Android tablet application for local or server-connected annotation workflows.

Desktop can run as an independent local HistoAnnotator server and display a QR code for quick Android pairing. Android can also work with supported local TIFF/images, allowing annotation workflows to continue without a continuous connection to a remote server.

Key features

• Standalone Desktop builds for Windows, Linux and macOS
• Android app with local image support and QR-based Desktop pairing
• OpenSlide-based whole-slide viewing with Deep Zoom / OpenSeadragon navigation
• Freehand, Brush, Polygon, Rectangle, Circle and Wand tools
• Multi-object selection with merge, intersection and subtraction operations
• Annotation classes, colors and undo / redo
• QuPath-compatible GeoJSON import, export and Android sharing
• Large generic TIFF preparation using bundled pyvips / libvips in Desktop builds
• Local-first annotation storage and offline-friendly image viewing

Multichannel fluorescence

Supported scientific fluorescence TIFF files can be visualized without flattening the source data to RGB first. Display controls are non-destructive and do not alter raw scientific pixel values.

• Independent channel visibility
• False-color assignment
• Automatic display-range estimation
• Per-channel minimum and maximum display values
• Gamma and brightness controls
• Persistent display settings per image

Typical use cases

• Manual annotation of histology and microscopy images
• Review and editing of QuPath-compatible annotations
• Tablet-based annotation workflows with local files or Desktop server pairing
• Standalone local annotation on Windows, Linux and macOS
• Exploration of multichannel fluorescence images

Project status

HistoAnnotator v1.2.0 is distributed as public research software. Windows, Linux and Android builds have been manually tested, while macOS Intel and Apple Silicon builds are generated and packaged self-tested through GitHub Actions. It is not clinically validated medical software and should be deployed according to institutional data-governance, security and ethics requirements.

Current scope

• Web, Windows, Linux, macOS and Android applications
• Whole-slide, raster and supported scientific TIFF annotation
• Independent Desktop server sessions with QR-based Android pairing
• QuPath interoperability through GeoJSON
• Offline-friendly local image and annotation workflows
• Research-oriented multichannel fluorescence visualization