Neuroglancer: Web-based volumetric data visualization

Neuroglancer is a WebGL-based viewer for volumetric data. It is capable of displaying arbitrary (non axis-aligned) cross-sectional views of volumetric data, as well as 3-D meshes and line-segment based models (skeletons).

Refer to the documentation website at https://neuroglancer-docs.web.app for more details.

This is not an official Google product.

Examples

A live demo is hosted at https://neuroglancer-demo.appspot.com. (The prior link opens the viewer without any preloaded dataset.) Use the viewer links below to open the viewer preloaded with an example dataset.

The four-pane view consists of 3 orthogonal cross-sectional views as well as a 3-D view (with independent orientation) that displays 3-D models (if available) for the selected objects. All four views maintain the same center position. The orientation of the 3 cross-sectional views can also be adjusted, although they maintain a fixed orientation relative to each other. (Try holding the shift key and either dragging with the left mouse button or pressing an arrow key.)

• FlyEM Hemibrain (8x8x8 cubic nanometer resolution). <a href="https://hemibrain-dot-neuroglancer-demo.appspot.com/#!gs://neuroglancer-janelia-flyem-hemibrain/v1.0/neuroglancer_demo_states/base.json" target="_blank">Open viewer</a>

• FAFB-FFN1 Full Adult Fly Brain Automated Segmentation (4x4x40 cubic nanometer resolution). <a href="https://neuroglancer-demo.appspot.com/fafb.html#!gs://fafb-ffn1/main_ng.json" target="_blank">Open viewer</a>

• Kasthuri et al., 2014. Mouse somatosensory cortex (6x6x30 cubic nanometer resolution). <a href="https://neuroglancer-demo.appspot.com/#!{'layers':{'original-image':{'type':'image'_'source':'precomputed://gs://neuroglancer-public-data/kasthuri2011/image'_'visible':false}_'corrected-image':{'type':'image'_'source':'precomputed://gs://neuroglancer-public-data/kasthuri2011/image_color_corrected'}_'ground_truth':{'type':'segmentation'_'source':'precomputed://gs://neuroglancer-public-data/kasthuri2011/ground_truth'_'selectedAlpha':0.63_'notSelectedAlpha':0.14_'segments':['3208'_'4901'_'13'_'4965'_'4651'_'2282'_'3189'_'3758'_'15'_'4027'_'3228'_'444'_'3207'_'3224'_'3710']}}_'navigation':{'pose':{'position':{'voxelSize':[6_6_30]_'voxelCoordinates':[5523.99072265625_8538.9384765625_1198.0423583984375]}}_'zoomFactor':22.573112129999547}_'perspectiveOrientation':[-0.004047565162181854_-0.9566211104393005_-0.2268827110528946_-0.1827099621295929]_'perspectiveZoom':340.35867907175077}" target="_blank">Open viewer.</a>

  This dataset was copied from https://neurodata.io/data/kasthuri15/ and is made available under the Open Data Common Attribution License. Paper: <a href="http://dx.doi.org/10.1016/j.cell.2015.06.054" target="_blank">Kasthuri, Narayanan, et al. "Saturated reconstruction of a volume of neocortex." Cell 162.3 (2015): 648-661.</a>

• Janelia FlyEM FIB-25. 7-column Drosophila medulla (8x8x8 cubic nanometer resolution). <a href="https://neuroglancer-demo.appspot.com/#!{'layers':{'image':{'type':'image'_'source':'precomputed://gs://neuroglancer-public-data/flyem_fib-25/image'}_'ground-truth':{'type':'segmentation'_'source':'precomputed://gs://neuroglancer-public-data/flyem_fib-25/ground_truth'_'segments':['21894'_'22060'_'158571'_'24436'_'2515']}}_'navigation':{'pose':{'position':{'voxelSize':[8_8_8]_'voxelCoordinates':[2914.500732421875_3088.243408203125_4045]}}_'zoomFactor':30.09748283999932}_'perspectiveOrientation':[0.3143535554409027_0.8142156600952148_0.4843369424343109_-0.06040262430906296]_'perspectiveZoom':443.63404517712684_'showSlices':false}" target="_blank">Open viewer.</a>

  This dataset was copied from https://www.janelia.org/project-team/flyem/data-and-software-release, and is made available under the Open Data Common Attribution License. Paper: <a href="http://dx.doi.org/10.1073/pnas.1509820112" target="_blank">Takemura, Shin-ya et al. "Synaptic Circuits and Their Variations within Different Columns in the Visual System of Drosophila." Proceedings of the National Academy of Sciences of the United States of America 112.44 (2015): 13711-13716.</a>

• Example of viewing 2D microscopy (coronal section of rat brain at 325 nanometer resolution). <a href="https://neuroglancer-demo.appspot.com/#!%7B%22dimensions%22:%7B%22x%22:%5B1e-9%2C%22m%22%5D%2C%22y%22:%5B1e-9%2C%22m%22%5D%7D%2C%22position%22:%5B10387071%2C5347131%5D%2C%22crossSectionScale%22:263.74955563693914%2C%22projectionScale%22:65536%2C%22layers%22:%5B%7B%22type%22:%22image%22%2C%22source%22:%7B%22url%22:%22deepzoom://https://data-proxy.ebrains.eu/api/v1/buckets/localizoom/14122_mPPC_BDA_s186.tif/14122_mPPC_BDA_s186.dzi%22%2C%22transform%22:%7B%22outputDimensions%22:%7B%22x%22:%5B1e-9%2C%22m%22%5D%2C%22y%22:%5B1e-9%2C%22m%22%5D%2C%22c%5E%22:%5B1%2C%22%22%5D%7D%2C%22inputDimensions%22:%7B%22x%22:%5B3.25e-7%2C%22m%22%5D%2C%22y%22:%5B3.25e-7%2C%22m%22%5D%2C%22c%5E%22:%5B1%2C%22%22%5D%7D%7D%7D%2C%22tab%22:%22rendering%22%2C%22shader%22:%22void%20main%28%29%7BemitRGB%28vec3%28toNormalized%28getDataValue%280%29%29%2CtoNormalized%28getDataValue%281%29%29%2CtoNormalized%28getDataValue%282%29%29%29%29%3B%7D%22%2C%22channelDimensions%22:%7B%22c%5E%22:%5B1%2C%22%22%5D%7D%2C%22name%22:%2214122_mPPC_BDA_s186.dzi%22%7D%5D%2C%22selectedLayer%22:%7B%22layer%22:%2214122_mPPC_BDA_s186.dzi%22%7D%2C%22layout%22:%22xy%22%7D" target="_blank">Open viewer.</a> (Use <kbd>Ctrl</kbd>+<kbd>MouseWheel</kbd> to zoom out)

  This image is part of: Olsen et al., 2020. Anterogradely labeled axonal projections from the posterior parietal cortex in rat [Data set]. EBRAINS. https://doi.org/10.25493/FKM4-ZCC

Supported data sources

Neuroglancer itself is purely a client-side program, but it depends on data being accessible via HTTP in a suitable format. It is designed to easily support many different data sources, and there is existing support for the following data APIs/formats:

• Neuroglancer precomputed format
• N5
• Zarr v2/v3 and OME-Zarr 0.4/0.5
• Python in-memory volumes (with automatic mesh generation)
• BOSS https://bossdb.org/
• DVID https://github.com/janelia-flyem/dvid
• Render https://github.com/saalfeldlab/render
• Single NIfTI files https://www.nitrc.org/projects/nifti
• Deep Zoom images

Supported browsers

• Chrome >= 51
• Firefox >= 46
• Safari >= 15.0

Keyboard and mouse bindings

For the complete set of bindings, see src/ui/default_input_event_bindings.ts, or within Neuroglancer, press h or click on the button labeled ? in the upper right corner.

• Click on a layer name to toggle its visibility.

• Double-click on a layer name to edit its properties.

• Hover over a segmentation layer name to see the current list of objects shown and to access the opacity sliders.

• Hover over an image layer name to access the opacity slider and the text editor for modifying the rendering code.

Troubleshooting

• Neuroglancer doesn't appear to load properly.

  Neuroglancer requires WebGL (2.0) and the EXT_color_buffer_float extension.

  To troubleshoot, check the developer console, which is accessed by the keyboard shortcut control-shift-i in Firefox and Chrome. If there is a message regarding failure to initialize WebGL, you can take the following steps:

  • Chrome

    Check chrome://gpu to see if your GPU is blacklisted. There may be a flag you can enable to make it work.

  • Firefox

    Check about:support. There may be webgl-related properties in about:config that you can change to make it work. Possible settings:

    • webgl.disable-fail-if-major-performance-caveat = true
    • webgl.force-enabled = true
    • webgl.msaa-force = true

• Failure to access a data source.

  As a security measure, browsers will in many cases prevent a webpage from accessing the true error code associated with a failed HTTP request. It is therefore often necessary to check the developer tools to see the true cause of any HTTP request error.

  There are several likely causes:

  • Cross-origin resource sharing (CORS)

    Neuroglancer relies on cross-origin requests to retrieve data from third-party servers. As a security measure, if an appropriate Access-Control-Allow-Origin response header is not sent by the server, browsers prevent webpages from accessing any information about the response from a cross-origin request. In order to make the data accessible to Neuroglancer, you may need to change the cross-origin request sharing (CORS) configuration of the HTTP server.

  • Accessing an http:// resource from a Neuroglancer client hosted at an https:// URL

    As a security measure, recent versions of Chrome and Firefox prohibit webpages hosted at https:// URLs from issuing requests to http:// URLs. As a workaround, you can use a Neuroglancer client hosted at a http:// URL, e.g. the demo client running at http://neuroglancer-demo.appspot.com, or one running on localhost. Alternatively, you can start Chrome with the --disable-web-security flag, but that should be done only with extreme caution. (Make sure to use a separate profile, and do not access a