Using the converted data in Neuroglancer

The Neuroglancer info file

See the info JSON file specification from Neuroglancer.

Different conventions for coordinate transformations

Beware that Neuroglancer departs from the NIfTI convention in associating physical coordinates to voxels: Neuroglancer associates physical coordinates to the corner of a voxel, whereas NIfTI specifies that they refer to the centre of a voxel. Therefore, images will be offset by half a voxel relative to meshes if you do not compensate for this offset.

For standalone meshes, this offset can be compensated for by using the transform URL parameter. For pre-computed segmentation meshes however, there is no way of specifying a different transform for the image and the associated meshes: the offset must be applied to the vertex coordinates. This can be achieved by using the --coord-transform option.

Please note that if you want to display images correctly with respect to physical coordinates (e.g. stereotaxic coordinates), you have to use the transform parameter as well. The transform.json which is output by volume-to-precomputed does take the half-voxel shift into account.