GRAPHY
GRAPHY Lab

Guides and plugins

How to use GRAPHY, and how to extend it.

GRAPHY-Next how-to ↗ In progress

From installing the desktop and web editions through 2D, MPR, 3D and plugins.

Installation guide (PDF)

Installing and launching GRAPHY-Next, with screenshots of the first-launch warnings on Windows and Mac.

GRAPHY classic how-to ↗

Basic operation and each of the viewers (the user manual).

Plugin development guide ↗

The plugin mechanism, the host API, releasing, installing and signing. With three working demos.
Build a plugin

Build a plugin

GRAPHY-Next keeps its core small and lets you add capability from the outside. There are three working examples, ordered from easiest to hardest. Any one of their READMEs takes you all the way from writing a plugin to releasing, installing and signing it.

  1. Hello GRAPHY \u2197 UI only, no build step

    Adds a menu item that prints "Hello, I'm GRAPHY-Next." — nothing more.

    What it teaches: The smallest possible plugin (plugin.json and ui.js), where it goes, and how to load it.

  2. Mean filter \u2197 UI only, no build step

    Applies a mean filter to the series open in the 2D viewer and shows before and after side by side.

    What it teaches: Finding the open series, calling the backend REST API, building your own dialog, and pixel processing.

  3. Gemini findings editor \u2197 UI + Java (desktop edition only)

    Sends your own rough findings and the image to Gemini and has it polish the wording. This is not diagnostic support.

    What it teaches: The backend side (a Java JAR), calling an external API under CSP, handling API keys, and signed releases.

Browse the plugin demos ↗

The hub repository. It gathers the mechanism, every field of plugin.json, the host API, distribution through GitHub Releases, the differences between the desktop and web editions, and signing with minisign (TOFU) — all on one page.

Plugins

Plugins

Official plugins we can show with screenshots and documents. The full list is on the GRAPHY-Next page.

Exclusive In development 3D T1 MRI

Brain atrophy Z-score

From a single 3D T1-weighted MRI series, it computes a voxel-wise Z-score (positive for gray-matter atrophy) against a healthy reference (373 healthy subjects aged 20 to 84 from the public IXI dataset), and produces a Z map, hippocampal volumes, differential reference indices and a two-page A4 report. The pipeline is HD-BET brain extraction, N4 bias correction, ANTs (Affine + SyN) registration to a standard brain, Atropos tissue segmentation, modulated gray matter, then voxel-wise regression Z. Hippocampal volumes come from HippoDeep.

Everything runs on this PC; no images leave it. You can check each stage (brain extraction, registration, segmentation, the Z map) in three planes before saving the report as HTML or PDF.

Development version 0.1.0, not yet distributed. It is research and educational software, not a medical device. The output is a reference value showing the difference from a healthy reference and does not replace a physician's judgment based on the images and clinical information. Sensitivity in Alzheimer's disease cases has not been evaluated. The screens below show one healthy subject from the public IXI dataset; the patient name, ID and birth date are fictitious.

Screenshots

A sagittal T1-weighted head image in the GRAPHY-Next 2D viewer
The imported T1-weighted series in the GRAPHY-Next 2D viewer. The plugin starts from the analysis menu here.
The plugin result window listing the metrics
Results: whole-brain Z-score metrics, hippocampal Z, Z after global normalization, whole-brain white matter (reference) and differential reference indices.
Stage images shown in axial, coronal and sagittal planes
Stage check: each stage from input to the Z score can be inspected in three planes.
The two A4 report pages side by side
The report (two A4 pages): processing steps, Z-score tables, the Z map on the standard brain, maximum-intensity projections, hippocampus, VOIs and limitations.

Technical note: Method and evaluation of the gray-matter atrophy Z-score plugin for T1-weighted MRI (PDF, Japanese, 22 pages)

The processing pipeline, the reference database, pre-registered evaluation results, comparison with VSRAD, limitations and reproducibility.

Public: free, available on GitHub. Exclusive: provided only to site-support (enterprise plan) customers. Apply for site support →

See all official plugins