HistoAnnotator v1.3.0-alpha.3

Pre-release checkpoint for the new annotation workflow, Tissue ROI analysis region, Artifact handling, and valid-tissue statistics.

Highlights

• Focus Mode with configurable keyboard shortcuts and compact class access.
• Review workflow with Draft / Reviewed / Approved lifecycle, review decisions, provenance, and batch workflow actions.
• Tissue ROI as a protected structural analysis region.
• Manual Tissue ROI drawing and server-side tissue detection.
• Non-destructive external Tissue ROI border exclusion with persistent base/effective ROI visualization.
• Built-in Artifact class:
  • always available;
  • normal drawing/editing/reclassification;
  • included in Review Mode and provenance;
  • reserved class name/configuration;
  • used as an exclusion mask for valid-tissue statistics.
• Valid Tissue statistics:
  • Tissue ROI or full image as analysis base;
  • optional external border exclusion;
  • Artifact union subtraction;
  • biological class areas reported against the remaining valid tissue.
• Fill unannotated tissue:
  • computes remaining valid tissue after existing annotations;
  • interactive preview;
  • choose the target class before creating a Polygon/MultiPolygon annotation.
• Annotation-file deletion with Default protection and local-first synchronization safeguards.
• UI refinements for compact annotation-file controls and non-blocking remaining-tissue preview.

Research-software status

This is a pre-release research/testing build. It is not clinically validated medical software.

HistoAnnotator v1.3.0-alpha.2 — Workflow & Provenance

Phase C release checkpoint.

Highlights:

• Draft / Reviewed / Approved lifecycle
• Correct / Maybe / Review Later decisions
• Annotation provenance and versioning
• Reviewer metadata
• Review invalidation after geometry or class edits
• Batch Workflow for selected annotations, current class, or current file
• Batch approval of Reviewed annotations
• Workflow summary after Review Mode
• Phase A reliability and Phase B Focus/shortcuts retained

HistoAnnotator v1.3.0-alpha.1 — Workflow & Interaction

HistoAnnotator v1.3.0-alpha.1

Pre-release checkpoint after Phase A and Phase B of the v1.3 workflow update.

Highlights

• Reliable local-first annotation persistence and sequential synchronization
• Protection against stale server responses and rapid annotation loss
• Downloaded images can refresh annotation-file catalogs without re-downloading the WSI
• Offline annotation-file caching and reconnect synchronization
• Improved class locking for newly drawn annotations
• Freehand tap-to-select interaction
• Area selection by geometric intersection
• Compact Settings menu
• Focus Mode for distraction-free annotation
• Collapsible, horizontally scrollable class selector for tablet use
• Configurable keyboard shortcuts
• Numeric shortcuts 1-8 follow the visual tool order
• Review shortcuts: Z Correct, X Maybe, C Review Later, V Delete
• Rectangle geometry information: X, Y, Width and Height

Status

Pre-release. Provenance/review lifecycle, Tissue ROI, Artifact masks and ROI-aware statistics are planned for the remaining v1.3 phases.

HistoAnnotator v1.2.0

HistoAnnotator v1.2.0

HistoAnnotator v1.2.0 expands the project from a Web + Android annotator into a
cross-platform research annotation environment with standalone Desktop builds,
Android local-image support and explicit Desktop-to-Android pairing.

Highlights

• Standalone HistoAnnotator Desktop for Windows, Linux and macOS.
• Independent Desktop image, annotation, cache, prepared-image and upload data.
• Desktop Start Server mode with explicit LAN URL and QR code.
• Android Scan QR pairing from Connection settings.
• Android runtime server switching with no deployment-specific IP embedded in
  the public APK.
• Native Android HTTP transport for API calls and image tiles.
• Android local TIFF/image workflow with persistent local-image access.
• Bundled pyvips/libvips preparation for large generic TIFF files.
• OpenSlide / Deep Zoom / OpenSeadragon image viewing.
• QuPath-compatible GeoJSON import/export and sharing.
• Review mode, annotation statistics and calibration.
• H&E, H-DAB and supported multichannel fluorescence display controls.

Downloads

• Windows x64: HistoAnnotator-v1.2.0-Windows-x64.zip
• Linux x64: HistoAnnotator-v1.2.0-Linux-x64.tar.gz
• macOS Apple Silicon: HistoAnnotator-v1.2.0-macOS-AppleSilicon.tar.gz
• macOS Intel: HistoAnnotator-v1.2.0-macOS-Intel.tar.gz
• Android: HistoAnnotator-v1.2.0-Android.apk
• Checksums: SHA256SUMS.txt

Extract the complete Desktop archive before starting HistoAnnotator. Do not
move only the executable from its packaged directory.

Desktop and pairing

Desktop runs an independent local backend. Select an image folder, work
locally, or press Start Server to make the session reachable on a trusted
LAN/VPN.

On Android use:

File → Connection settings → Scan QR

Large generic TIFF files that need preparation are converted into a tiled
pyramidal TIFF in the writable HistoAnnotator data directory. The source image
is not modified.

Android

The public APK is generic. Select a server at runtime by entering an HTTP/HTTPS
URL or scanning the Desktop QR. Deployment-specific institutional CA files are
not included in the public APK.

Android also supports supported local TIFF/images independently from a remote
server.

Validation

The v1.2.0 release candidate was manually tested on Windows x64, Linux x64 and
Android. macOS Intel and Apple Silicon artifacts are built and package-tested
in GitHub Actions but are currently unsigned.

The release workflow validates OpenSlide and pyvips/libvips, extracts each
Desktop archive and runs the packaged self-test before publication.

Research software

HistoAnnotator is research software. It is not clinically validated medical
software and does not currently provide individual user authentication, a
complete audit trail or regulatory controls.

Desktop server mode should be used only on a trusted LAN/VPN unless additional
security controls are deployed.

# HistoAnnotator v1.1.0 — Review, quantitative statistics and physical calibration

This pre-release expands HistoAnnotator's annotation workflow with a dedicated review system, quantitative annotation summaries, and physical image calibration support.

Highlights

• Review annotations by all classes or a selected class.
• Review decisions: Correct, Maybe, Review Later, and Delete.
• Correct annotations are skipped in later sessions.
• Maybe annotations receive a second pass.
• Review Later annotations receive a final pass after Maybe annotations; if deferred again, they remain for the next review session.
• Partial review sessions resume without repeating finalized annotations.
• Completed scopes can optionally be reset for a full re-review.
• Only the current annotation is shown during Review Mode to reduce visual ambiguity.
• Small annotations are initially framed with at least a 1024 × 1024 level-0 pixel field of view.
• Review Mode exits automatically 30 seconds after completion.
• Annotation Statistics reports per-class annotation count, geometric union area in px², and percentage of full image area.
• Physical calibration is read from OpenSlide, OME-TIFF, or TIFF resolution metadata when available.
• The viewer displays a physical scale bar and approximate digital magnification.
• Image Information shows one symmetric resolution value in µm/px.
• Manual per-image overrides are available for resolution and source magnification when the values are known but absent from the source image.

Calibration behavior

HistoAnnotator does not infer physical scale when metadata is absent. Manual calibration is explicitly labeled, stored locally per image/device, and does not modify the source image.

Android

The attached APK is a debug-signed research/testing build intended for the current HistoAnnotator deployment.

Research-use notice

HistoAnnotator is research software and is not clinically validated medical software.

HistoAnnotator v1.0.0 – First public pre-release

HistoAnnotator v1.0.0 — First public pre-release

This is the first public pre-release of HistoAnnotator, a research-oriented
web and Android application for histology and microscopy annotation.

Highlights

• Android tablet application built with Capacitor
• Local-first/offline annotation workflow
• QuPath-compatible GeoJSON import/export
• GeoJSON sharing from Android
• Freehand, Brush, Polygon, Rectangle, Circle and Wand tools
• Multi-object selection and geometry operations
• H&E and H-DAB display visualization
• Scientific multichannel fluorescence TIFF support
• Per-channel visibility, false color, Min/Max, gamma and brightness
• Persistent per-image fluorescence display settings

Android APK

The attached APK is a debug-signed research/testing build.
It is not clinically validated medical software.

Known limitations

• No individual authentication or complete audit trail
• Offline fluorescence currently caches rendered display variants rather than all raw scientific channels
• Some image-aware tools may require the backend while offline
• Complex T/Z/C scientific datasets are not fully supported yet

Citation

HistoAnnotator v1.0.0 is archived on Zenodo:

DOI: 10.5281/zenodo.21941344