QIM Volume Explorer

The QIM Volume Explorer is a browser-based data exploration tool for 3D image analysis, developed by the QIM Center.

It is implemented on top of the vole-core library, made by the Allen Institute for Cell Science.

Features

• Volumetric 3D rendering — interactive volume rendering with adjustable opacity.
• 2D slice and ortho views — jump between X, Y, and Z slice views, three-way orthogonal views, and the 3D volume with a single control, and step through slices with a slider.
• Multiple data formats — load OME-Zarr, OME-NGff (.h5/.hdf5), and OME-Tiff data directly from a URL, or open local .tif/.tiff.
• Colormaps & histogram — pick from a set of scientific colormaps (viridis, plasma, inferno, magma, cividis, grayscale), invert them, and drive the intensity window by brushing directly on the intensity histogram.
• Area of interest cropping — crop X/Y/Z with dual sliders or numeric indices, and toggle draggable 3D crop handles right in the viewport. Copy the crop coordinates for reuse elsewhere.
• OME-Zarr scale level selection — automatically pick the most detailed level that fits in memory, or override it per dataset from the top bar.
• Pixel readout — hover over a 2D slice view to see the voxel coordinates and intensity value under the cursor.

Installation

Install globally to get the volume-explorer command on your PATH:

npm install -g @qim3d/volume-explorer
volume-explorer

You can also run it without a global install:

npx @qim3d/volume-explorer

To open a dataset directly:

volume-explorer https://public.qim.dk/escargot/escargot.zarr/

Usage

The explorer opens with a OME-Zarr public dataset by default. Paste any dataset URL into the top bar and press Load to switch.

Supported data types

• .zarr / .ome.zarr
• .h5 / .hdf5
• .ome.tif / .ome.tiff
• .tif / .tiff

URL parameters

The app URL accepts a few query parameters, which are preserved when sharing a view link:

| Parameter | Description | | --- | --- | | src | Dataset URL to load on start. | | colormap | Initial colormap name (e.g. viridis, plasma, inferno, magma, cividis, grayscale). | | hidden | true hides the UI panels, for embedded use. | | turntable | true enables auto-rotation of the camera (pauses while hovering). | | maxActiveRequests | Number of concurrent data fetches (useful on large datasets). |

Example:

https://viz.qim.dk/?src=https%3A%2F%2Fpublic.qim.dk%2Fescargot%2Fescargot.zarr%2F

Advanced

There is a hidden menu for advanced users, accessible by pressing Ctrl + Alt + 1 and Ctrl + Alt + 2. It exposes low-level rendering controls such as ray step size, camera focus/aperture, mask alpha, and per-channel isosurface values.

Development

git clone [email protected]:qim-center/volume-explorer.git
cd volume-explorer
npm install
npm run dev

For a production-style local run that uses the packaged CLI and built assets:

npm run build
npm start

• The library code lives in src/ and compiles to es/; the web app lives in public/ and is built to dist/app/.
• npm run checks runs lint, typecheck, and tests.