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Local neuroglancer - Python interface

The shell example can be run entirely from python.

Let us first instantiate a local viewer and open it in the browser:

from ngtools.local.viewer import LocalNeuroglancer
import webbrowser

viewer = LocalNeuroglancer()
print('fileserver:  ', viewer.get_fileserver_url())
print('neuroglancer:', neuroglancer.get_viewer_url())

webbrowser.open(viewer.get_viewer_url())

We may then apply the same set of commands as before:

viewer.load("/path/to/local_file.nii.gz")
viewer.load("tiff:///path/to/file_without_extension")
viewer.load({"my_image": "zarr://https://url.to/remote/zarr_asset"})
viewer.shader("blackred", layer="local_file.nii.gz")
viewer.shader("blackgreen", layer="file_without_extension")
viewer.shader("blackblue", layer="my_image")
viewer.transform("/path/to/affine.lta", layer="local_file.nii.gz")

Note that the viewer gets refreshed after each command is called. Alternatively, one may group such commands so that they are applied to the viewer in a single step:

with viewer.scene() as scene:
    scene.load("/path/to/local_file.nii.gz")
    scene.load("tiff:///path/to/file_without_extension")
    scene.load({"my_image": "zarr://https://url.to/remote/zarr_asset"})
    scene.shader("blackred", layer="local_file.nii.gz")
    scene.shader("blackgreen", layer="file_without_extension")
    scene.shader("blackblue", layer="my_image")
    scene.transform("/path/to/affine.lta", layer="local_file.nii.gz")

While these two procedures (through the viewer or through the scene) should in most cases yield equivalent results, it is not assured, as the neuroglancer instance may discard some of the requested changes, or add changes of its own in-between calls.

If the scene is compatible with a remote instance of neuroglancer (i.e., it does not contain local data, and does not use ngtools extended features such as new file formats), a url to a remote neuroglancer scene can be generated:

webbrowser.open(viewer.state(url=True))

Or, the JSON state can be printed and pasted into a neuroglancer window:

viewer.state(print=True)