Superimposing Local Files

siibra-explorer experimentally supports overlaying spatial features on top of existing atlas. They are never uploaded to any server, and are processed locally on your computer/browser.

Info

As the files never leave your browser, URL sharing will not include superimposed file.

Warning

Modern browser impose severe limitations on the amount of resources browser can request. As a result, loading local files may fail based on the spec of your machine (better spec, particularly RAM, reduces the likelihood of failure), size of the file (smaller file reduces the likelihood of failure), amidst other potential factors.

To start, navigate to the atlas/template/parcellation map o your choice, then drag and drop the file you would like to super impose.

NIFTI

siibra-explorer carries out a number of verification/normalization steps to ensure the volume is displayed correctly:

FLOAT64 is currently not supported by the underlying view engine, siibra-explorer will inform the user if the nifti uses FLOAT64 datatype
dim4, if set to > 1, indicates a time series. Since times series is not yet supported by the underlying view engine, siibra-explorer will inform the user
dim4, if set to 0, will be set to 1
xyzt_unit, if unset, will be set to mm, sec
the volume will be normalized between min and max
the affine of the volume is handled by the underlying view engine, neuroglancer

SWC

SWC files are plain text files encoding the structure of one (or more) neurons. One of the difficulty of overlaying SWC files on top of atlases is the lack of standardization of space (voxel vs physical, different MNI152 spaces etc).

Whilst siibra-explorer makes a best attempt at parsing the SWC file, it is likely that some SWC may still be parsed poorly. Feel free to contact us to have it rectified.

JSON (Pointclouds)

Pointclouds generated by the Nutil workflow in JSON format can be visualized in siibra-explorer. Pointcloud JSON file must be in CCF v3 (or, in Nutil parlance, ABA) space.