NGLui

NGLui is a library for programmatically generating shareable Neuroglancer states in order to explore and visualize large, 3d image datasets. It is designed to be used in conjunction with the Neuroglancer web viewer and the CAVE analysis ecosystem. It aims to separate the rules you want to use to generate states from the data you want to visualize, allowing you make reusable code to generate states from different datasets and analyses.

Installation

NGLui is available on PyPI and can be installed with pip:

pip install nglui

If you want to clone the repository and develop on NGLui, note that it uses Hatch for development and packaging.

Quick Usage

Note

Using the CAVEclient with the MICrONs dataset is required for the following examples.

Here's a quick example of how to use NGLui to generate a Neuroglancer state from the Microns cortical dataset.

import caveclient
from nglui import statebuilder

client = caveclient.CAVEclient('minnie65_public')

# Get a root id of a specific neuron
root_id = client.materialize.query_table(
    'nucleus_detection_v0',
    filter_equal_dict={'id': 255258}
)['pt_root_id']

statebuilder.helpers.make_neuron_neuroglancer_link(
    client,
    root_id,
    show_inputs=True,
    show_outputs=True,
    ngl_url='https://spelunker.cave-explorer.org',
)

This code will generate a link to produce a Neuroglancer state showing a neuron and its synapses.