Local neuroglancer - Shell interface

To run the app, simply type

nglocal

in your shell. It will open a neuroglancer window, and a shell-like interface:

             _              _
 _ __   __ _| |_ ___   ___ | |___
| '_ \ / _` | __/ _ \ / _ \| / __|
| | | | (_| | || (_) | (_) | \__ \
|_| |_|\__, |\__\___/ \___/|_|___/
       |___/

fileserver:   http://127.0.0.1:9123/
neuroglancer: http://127.0.0.1:9321/v/1/

Type help to list available commands, or help <command> for specific help.
Type Ctrl+C to interrupt the current command and Ctrl+D to exit the app.
[1]

Let's start with the list of commands

[1] help
usage: {help,load,unload,rename,...} ... [-h]

positional arguments:
  {help,load,unload,rename,...}
    help                Display help
    load                Load a file
    unload              Unload a file
    rename              Rename a file
    world_axes          Rename native axes
    rename_axes         Rename axes
    space               Cross-section orientation
    transform           Apply a transform
    channel_mode        Change the way a dimension is interpreted
    shader              Apply a shader
    display             Dimensions to display
    layout              Layout
    state               Return the viewer's state
    move (position)     Move cursor
    zoom                Zoom
    unzoom              Zoom
    zorder              Reorder layers
    cd                  Change directory
    ls                  List files
    ll                  List files (long form)
    pwd                 Path to working directory
    exit (quit)         Exit neuroglancer

options:
  -h, --help            show this help message and exit

We can load a bunch of files

[2] load /path/to/local_file.nii.gz
[3] load tiff:///path/to/file_without_extension
[4] load zarr://https://url.to/remote/zarr_asset --name my_image

change their colormaps

[5] shader blackred   --layer local_file.nii.gz
[6] shader blackgreen --layer file_without_extension
[7] shader blackblue  --layer my_image

and apply an affine transform

[8] transform /path/to/affine.lta --layer local_file.nii.gz

Note that even though we are using our own neuroglancer instance, its state can be transferred to a remote instance. Assuming that only remote files were loaded (or that the local fileserver is still running), states will be compatible, and the remote instance will display the exact same scene. The state can be obtained in JSON form, or in URL form (which is simply the quoted version of the JSON)

[10] state

{
    "dimensions": {
        "x": [
            0.001,
            "m"
        ],
        "y": [
            0.001,
            "m"
        ],
        "z": [
            0.001,
            "m"
        ]
    },
    "position": [
        2.5,
        1.5,
        22.5
    ],
    "crossSectionScale": 1,
    "projectionScale": 256,
    "layers": [
        {
            "type": "image",
            "source": "nifti://http://127.0.0.1:9123/root:///Users/yb947/Dropbox/data/niizarr/sub-control01_T1w.nii.gz",
            "tab": "source",
            "shaderControls": {
                "normalized": {
                    "range": [
                        0,
                        1140
                    ]
                }
            },
            "name": "sub-control01_T1w.nii.gz"
        }
    ],
    "layout": "4panel"
}

[11] state --url
https://neuroglancer-demo.appspot.com/#!%7B%22dimensions%22%3A%20%7B%22x%22%3A%20%5B0.001%2C%20%22m%22%5D%2C%20%22y%22%3A%20%5B0.001%2C%20%22m%22%5D%2C%20%22z%22%3A%20%5B0.001%2C%20%22m%22%5D%7D%2C%20%22displayDimensions%22%3A%20%5B%22x%22%2C%20%22y%22%2C%20%22z%22%5D%2C%20%22position%22%3A%20%5B2.5%2C%201.5%2C%2022.5%5D%2C%20%22crossSectionScale%22%3A%201%2C%20%22projectionScale%22%3A%20256%2C%20%22layers%22%3A%20%5B%7B%22type%22%3A%20%22image%22%2C%20%22source%22%3A%20%22nifti%3A//http%3A//127.0.0.1%3A9123/root%3A///Users/yb947/Dropbox/data/niizarr/sub-control01_T1w.nii.gz%22%2C%20%22tab%22%3A%20%22source%22%2C%20%22shaderControls%22%3A%20%7B%22normalized%22%3A%20%7B%22range%22%3A%20%5B0%2C%201140%5D%7D%7D%2C%20%22name%22%3A%20%22sub-control01_T1w.nii.gz%22%7D%5D%2C%20%22layout%22%3A%20%224panel%22%7D