Volumetric data rendering with Neuroglancer

Introduction

Main Features:

• Voxel-based rendering: Efficiently visualize large 3D datasets by streaming the data directly into the browser.
• Support for multiple data formats: Neuroglancer works with a variety of formats like ZARR and OME-ZARR for volumetric images, as well as annotation formats.
• Interactive, shareable views: Customize and share views by copying the URL directly from the Neuroglancer interface.

Available datasets

Popular datasets using Neuroglancer

• MICrONS Explorer: A large-scale dataset from the MICrONS Project, providing high-resolution volumetric reconstructions of a mouse brain.
• FlyEM Hemibrain: This dataset offers a detailed 3D reconstruction of the Drosophila melanogaster brain at nanometer resolution.
• “H01” Dataset: 1.4 Petabyte for one cubic millimeter of the human brain, released by the Harvard University and the Connectomics at Google team.

Available datasets

Helmholtz Imaging collaboration use case

Dataset requirements

Supported Data Types

• Neuroglancer precomputed format
• N5
• Zarr v2/v3 (including OME-ZARR)
• Python in-memory volumes (with automatic mesh generation)
• BOSS , DVID, Render, Single NIfTI files, Deep Zoom images

Data preparation

Volumetric images

Conversion Steps:

• Step 1: Convert the TIFF slices into ZARR format, which supports chunked, compressed storage.
• Step 2: Convert the ZARR files into OME-ZARR format, which includes metadata for biological imaging data and supports better integration with visualization tools like Neuroglancer.

Notebook: TIFF slices to multiscale OME-ZARR

Data preparation

Annotations

Conversion Steps:

• Step 1: Prepare a list of points or annotations that describe features in your dataset (e.g., 3D coordinates for cell locations).
• Step 2: Convert the list of points into CloudVolume annotations.

Notebook: JSON point locations to Neuroglancer Precomputed annotations

Streaming data locally

With Python:

• Step 1: Use Python’s built-in HTTP server to serve the data directory:

  python3 -m http.server
  

• Step 2: Open the Neuroglancer demo page and enter the local URL of your data (e.g., zarr://http://localhost:8000/my-dataset.ome.zarr).

Sharing views

Example of JSON in URL:

• Copy the URL from your browser, and you’ll notice that it contains encoded parameters for layers, views, and more.
• The JSON configuration embedded in the URL can be customized to adjust the view programmatically.

{
  "dimensions": {...},
  "position": [
    3744.089599609375,
    4562.4326171875,
    837.0703125
  ],
  "layers": [
    {
      "type": "image",
      "source": "zarr://https://hifis-storage.desy.de:2443/Helmholtz/HIP/collaborations/2405_MDC_Treier/public/G5111-S4/647nm_cFOS",
      "tab": "rendering",
      "shaderControls": {
        "normalized": {
          "range": [
            0,
            500
          ]
        }
      },
      "crossSectionRenderScale": 0.47742080195520836,
      "name": "cFOS"
    }
    {
      "type": "annotation",
      "source": "precomputed://https://hifis-storage.desy.de:2443/Helmholtz/HIP/collaborations/2405_MDC_Treier/public/G5111-S4/cells",
      "tab": "source",
      "name": "Cells"
    }
  ],
  "selectedLayer": {
    "visible": true,
    "layer": "cFOS"
  }
}

Programmatically generate URL

Link to the full notebook showing how to generate a Neuroglancer URL programmatically:

Data hosting for Neuroglancer

• Local Hosting: Serve data from your own machine or institution’s servers.
• AWS S3 or Google Cloud Storage: Store large datasets and stream them to Neuroglancer from the cloud.
• Scientific Data Services: e.g. BioImage Archive
• Do you know other compatible hosting places? Let us know!

Data hosting for Neuroglancer

Helmholtz storage compatible to Neuroglancer

Collaboration between Helmholtz Imaging and HIFIS at DESY, with the support of the Jülich Cluster.

• dCache / InfiniteSpace: Secure, scalable storage solution for Helmholtz researchers to host and stream datasets. The data hosted on the storage can be shared publicly.

Steps:

1. Authenticate yourself to access the storage using AAI.
2. Upload the data, i.e. using rclone command line tool or the Rclone Browser GUI

Data hosting for Neuroglancer

Helmholtz Neuroglancer Instance

• Helmholtz Imaging Neuroglancer instance: A dedicated Neuroglancer instance for the Helmholtz community.

Steps:

1. In https://hifis-storage.desy.de, right click on the dataset you want to stream and click “Get WebDAV link”
2. Replace the 2880 port with 2443
3. Open https://neuroglancer.helmholtz-imaging.de
4. Add your dataset using the modified URL