• Info Panel

NeuroNLP.Hemibrain (beta) with Hemibrain release 1.2.

NeuroNLP with Hemibrain release 1.1 is available at this URL.

What is NeuroNLP?

NeuroNLP provides a modern web-based portal for navigating fruit fly brain circuit data. It enables in-depth exploration and investigation of brain structure, using intuitive plain English queries, such as

"show EPG neurons that have outputs in PB glomerulus L8 or PB glomerulus R2".

NeuroNLP can be accessed from any browser supporting WebGL. Remember to check it out on your smartphone!

Overview

Check out the Overview for a brief description of the layout and menus.

Open Overview!

Quick Query Reference

Check out the Quick Query Reference to be able to query data easily!

Open Query Reference!

News

Updates and announcements for NeuroNLP.Hemibrain.

See What's New!

Quick Demos

Want to get started? Go check out some real-time "Demos" for NLP queries and GUI usage!

Try Demos!

Sharing Query Results

Sharing query results is easy with the "Tags" feature. Create your own tags!

Try Tags!
  • Demos

  • Overview

What is NeuroNLP

NeuroNLP is a modern web-based portal for navigating fruit fly brain data. NLP stands for Natural Language Processing, which means the website allows user to use intuitive plain English queries for in-depth exploration and investigation of brain structure.

    The data currently provided are of the following kinds:
  • Neurons: 3D skeleton, neuron name, type, data source, neurotransmitter, transgenic lines, etc.
  • Synapses:presynaptic and postsynaptic neurons, number of synapses.

The NLP module allows for querying neurons and synaptic partners by a variety of attributes of the query targets (refer to Search Bar section below for examples).

NeuroNLP can be accessed from any browser supporting WebGL. Try it on your smartphone!

Layout Overview

    NeuroNLP site consists of mainly 4 sections
  • Header bar: provides operations such as hide neurons, create tags,etc.
  • 3D visualizer: 3D skeleton visualization of queried neurons and the underlying neuropils.
  • Information Panel: detailed information including synaptic partners of neuron pinned in the visualizer.
  • Search bar: natural language interface for query neurons.

Search Bar

The Search Bar is the central querying interface. It supports natural language queries of neurons, synaptic partners, etc. By combining various attributes of query targets, you can create some very powerful queries. Click on the info button to the left of the search bar.

Information Panel

Information panel is your major source of information regarding the individual neurons.

Visualization Panel

The visualization panel provides a interactive workspace of neuron skeletons in the context of relevant neuropils. It allows you to change view, select neurons, pin neurons, etc.
In addition the the neuron and neuropil mesh files, the visualization panel provides a list of useful buttons for ease of interaction. For more details regarding the visualization panel, click on the    button on the top right corner of the panel.

Pinning neuron of interest and removing all unpinned neuron by clicking the    button is a good way to clean up the workspace and keep only the neurons of your interest.

Graph View

    The graph view panel can be generated by clicking one of the graph view generation buttons in the visualization panel.
  • Graph View Generation Buttons: The buttons provide the capability to generate graphs from the currently queried data. These neurons can be at single-cell scale, or cell-type scale if supported by the dataset.
  • Graph View: The graph view provides a 2D graph visualizing all neurons and their connections in the current workspace. Nodes can be reordered by dragging them and hovering over nodes will highlight the corresponding neurons.
  • Quick Query Reference

Search Bar

The Search Bar is the central querying interface. It supports natural language queries of neurons, synaptic partners, etc. By combining various attributes of query targets, you can create some very powerful queries.

    Your queries should start with a verb; the verbs supported right now are:
  • show: clear workspace and then show the queried neurons,
  • add: add to the workspace the neurons queried,
  • remove/span>: remove from the workspace the queried neuron,
  • keep: keep in the workspace only the neurons that meet the criterion of the query,
  • hide: hide the neurons that meet the criterion of the query (this does not remove them from workspace, but reduce their visibility),
  • pin: pin the neurons that meet the criterion of the query. Pinned neurons are automatically highlighted, and cannot be removed by the "trash can" button on top of the NeuroNLP window.
  • unpin: unpin the neurons that meet the criterion of the query,
  • color: color the neurons that meet the criterion of the query with a user defined color (can be hex color code, e.g., FF0000 for red), or these predefined colors.
  • clear: clear up the workspace, removing all neurons and synapses.
    Other short-hands:
  • show /:referenceId:[5813014882, 912147912, 880875861]: Shows the neurons whose referenceId in the original dataset is in the list. It can be used similar to \$ \\$ and regular expression and combined with other types of criteria. Examples:

Coloring: if no criteria are specified, the color will be applied to the neurons added in the most recent query. For example, if you query: show A neurons, then add B neurons, color red will color B neurons red. color A neurons 0000FF will then color A neurons blue.

  • 3D GUI

Translation

Right-click and then drag the cursor to translate the entire 3D scene. On mobile and tablets, the scene can be translated by dragging with three fingers.

Rotation

Left-click and then drag the cursor to rotate the entire 3D scene. On mobile and tablets, touch and drag with one finger to rotate the scene.

Zoom

Scroll up or down to zoom in or out the entire 3D scene. On mobile and tablets, pinch out or in to zoom out or in respectively.

Select

Hover over a neuron and Left-Click to retrieve the detail information. On mobile and tablets, touch on the neuron with a single finger to select it.

Pin

Hover over a neuron and Double-Click to pin it in the scene. Pinned neurons will always be highlighted. After pinning neurons of interest, you can use the remove unpinned neurons icon (  ) to restrict the workspace to neurons you are interested in.

On mobile and tablets, select a neuron and then touch and hold on it for atleast 750ms to pin it.

  • Latest News