Vimo Sketches (Seung Lab fork for Codex)

React component for interactively sketching & searching for network motifs.

NB: This repo contains the source for VIMO as it is used in Codex. Contains Codex-specific modifications, as well as our particular build config. Not a general purpose fork.

Requirements

• npm (8.1.0 or later)
• "@testing-library/react": "^12.1.3
• "react": "^17.0.2"
• "react-dom": "^17.0.2"

Install Package

npm install @vimo-public/vimo-sketches

Getting Started

Basic Example

import {Sketch} from "@vimo-public/vimo-sketches";

function App() {
    const processRequest = async (motifJson, lim) => {
        console.log("This function is called upon clicking the search button.");
    };
    return (
        <div>
            <Sketch processRequest={processRequest}/>
        </div>
    );
}
export default App;

Node & Edge Attributes

If you want to add attributes to nodes or edges, please refer react-awesome-query-builder config fields. Also here's an example

import {Sketch} from "@vimo-public/vimo-sketches";

function App() {

    const attributes = {
        NodeFields: {
            node_attr_1: {
                label: "attr1_name",
                type: "text",
            },
            node_attr_2: {
                label: "attr2_name",
                type: "select",
                fieldSettings: {
                    showSearch: true,
                    listValues: [
                        "alpha",
                        "betha",
                        "theta",
                    ],
                },
                valueSources: ["value"],
                operators: ["select_equals", "select_not_equals"],
            },
        },
        EdgeFields: {
            edge_attr_1: {
                label: "attr1_name",
                type: "number",
                fieldSettings: {
                    min: 0,
                },
                valueSources: ["value"],
                preferWidgets: ["number"],
            },
            edge_attr_2: {
                label: "attr2_name",
                type: "number",
                operators: ["greater", "less", "equal"],
                valueSources: ["value"],
            },
        },
    }
    const processRequest = async (motifJson, lim) => {
        // this function is called when the user clicks the "Search" button
        console.log(motifJson);
        console.log(lim);
    };
    return (
        <div>
            <Sketch processRequest={processRequest} attributes={attributes}/>
        </div>
    );
}

export default App;

Searching Motifs in NeuPrint

We provide a direct interface to sketch & search for networks motifs in large connectome data sets hosted on Neuprint. Here's an example of how to use it.

import React, { useEffect, useState } from "react";
import {Sketch, NeuprintExecutor} from '@vimo-public/vimo-sketches';

function App() {
  const token = "ADD YOUR TOKEN HERE"; // copy token from here https://neuprint.janelia.org/account
  const data_server = "https://neuprint.janelia.org/";
  const data_version = "hemibrain:v1.2.1";
  const vimo_server = "http://127.0.0.1:4242"; // setup instructions https://github.com/VCG/vimo-server
  const ne = new NeuprintExecutor(
    data_server,
    data_version,
    token,
    vimo_server
  );

  const processRequest = async (motifJson, lim) => {
    const query = await ne.json2cypher(motifJson, lim);
    console.log(query);
    return query;
  };

  const [isQuerying, setIsQuerying] = useState(false);
  
  const [attributes, setAttributes] = useState({
    getMotifCount: ne.getMotifCount,
    getRelativeMotifCount: ne.getRelativeMotifCount,
    isQuerying: isQuerying,
  });
  
  useEffect(async () => {
    setAttributes({
      ...attributes,
      NodeFields: await ne.getNodeFields(),
      EdgeFields: await ne.getEdgeFields(),
    });
  }, []);

  return (
    <div>
      <Sketch processRequest={processRequest} attributes={attributes} />
    </div>
  );
}

export default App;

Sketch Component Props

Name	Sub-field	Description	Type
processRequest(query)	N/A	callback function for search button	Function
attributes	isQuerying	enable/disable search button	Boolean
	NodeFields	constraint fields for node	Object
	EdgeFields	constraint fields for edge	Object
	getMotifCount	get count of motif in network	Function
	getRelativeMotifCount	get relative count of motif in network	Function
	buttonText	text on button, default is "Search"	String
	nodeColors	color set for nodes in sketch, default is ["#9400D3", "#DAA520", "#97d0b5", "#76acf3", "#FF6347", "#4C56B3", "#D9C226", "#263DD9",]	Array

• Token can be found in here.

NeuprintExecutor Parameters

Name	Description	Type
token	neuPrint authentication token	String
data_server	url of database (e.g., 'https://neuprint.janelia.org/')	String
data_version	name and version of dataset (e.g., 'hemibrain:v1.2.1')	String
vimo_server	url of vimo_server (e.g., 'http://localhost:4242')	String

Output

This component turns motif sketch into JSON. This is an example of the JSON. This JSON can be converted to a Cypher query using the json2cypher method of the NeuprintExecutor class.

{
    nodes: [
      {
        label: "A",
        properties: null,
        index: 0,
        position: ["Point", 149.70313, 66.80469],
      },
      {
        label: "B",
        properties: null,
        index: 1,
        position: ["Point", 84.70313, 173.80469],
      },
      {
        label: "C",
        properties: null,
        index: 2,
        position: ["Point", 232.70313, 165.80469],
      },
    ],
    edges: [
      {
        label: "A -> B",
        properties: null,
        index: 0,
        indices: [0, 1],
        tree: null,
      },
      {
        label: "B -> C",
        properties: null,
        index: 1,
        indices: [1, 2],
        tree: null,
      },
      {
        label: "C -> A",
        properties: null,
        index: 2,
        indices: [2, 0],
        tree: null,
      },
    ],
    dimension: { width: 639.3984375, height: 232.796875 },
};

Citing

If you find our work helpful, please consider citing it.

@article {troidl2022vimo,
    title={Vimo: Visual Analysis of Neuronal Connectivity Motifs},
    author={Troidl, Jakob and Warchol, Simon and Choi, Jinhan and Matelsky, Jordan 
    and Dhanysai, Nagaraju and Wang, Xueying and Wester, Brock and Wei, Donglai 
    and Lichtman, Jeff W and Pfister, Hanspeter and Beyer, Johanna},
    year={2022},
    doi={10.1101/2022.12.09.519772},
    publisher={Cold Spring Harbor Laboratory},
    url={https://www.biorxiv.org/content/early/2022/12/11/2022.12.09.519772},
    journal={bioRxiv}
}