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Yoshihiro OKUMURA 2022-05-11 18:50:27 +09:00
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# See https://help.github.com/articles/ignoring-files/ for more about ignoring files.
# dependencies
/node_modules
/.pnp
.pnp.js
# testing
/coverage
# production
/build
# misc
.DS_Store
.env.local
.env.development.local
.env.test.local
.env.production.local
.eslintcache
npm-debug.log*
yarn-debug.log*
yarn-error.log*

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This project was bootstrapped with [Create React App](https://github.com/facebook/create-react-app).
## Available Scripts
In the project directory, you can run:
### `npm start`
Runs the app in the development mode.<br>
Open [http://localhost:3000](http://localhost:3000) to view it in the browser.
The page will reload if you make edits.<br>
You will also see any lint errors in the console.
### `npm test`
Launches the test runner in the interactive watch mode.<br>
See the section about [running tests](https://facebook.github.io/create-react-app/docs/running-tests) for more information.
### `npm run build`
Builds the app for production to the `build` folder.<br>
It correctly bundles React in production mode and optimizes the build for the best performance.
The build is minified and the filenames include the hashes.<br>
Your app is ready to be deployed!
See the section about [deployment](https://facebook.github.io/create-react-app/docs/deployment) for more information.
### `npm run eject`
**Note: this is a one-way operation. Once you `eject`, you can’t go back!**
If you aren’t satisfied with the build tool and configuration choices, you can `eject` at any time. This command will remove the single build dependency from your project.
Instead, it will copy all the configuration files and the transitive dependencies (Webpack, Babel, ESLint, etc) right into your project so you have full control over them. All of the commands except `eject` will still work, but they will point to the copied scripts so you can tweak them. At this point you’re on your own.
You don’t have to ever use `eject`. The curated feature set is suitable for small and middle deployments, and you shouldn’t feel obligated to use this feature. However we understand that this tool wouldn’t be useful if you couldn’t customize it when you are ready for it.
## Learn More
You can learn more in the [Create React App documentation](https://facebook.github.io/create-react-app/docs/getting-started).
To learn React, check out the [React documentation](https://reactjs.org/).

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{
"name": "celloc3d",
"version": "2.0.0",
"private": true,
"dependencies": {
"@reduxjs/toolkit": "^1.8.1",
"@testing-library/jest-dom": "^5.16.4",
"@testing-library/react": "^13.2.0",
"@testing-library/user-event": "^14.1.1",
"@types/node": "^17.0.32",
"@types/react": "^18.0.9",
"@types/react-dom": "^18.0.3",
"@types/react-redux": "^7.1.24",
"@types/react-router-dom": "^5.3.3",
"@types/three": "^0.140.0",
"axios": "^0.27.2",
"react": "^18.1.0",
"react-app-polyfill": "^3.0.0",
"react-dom": "^18.1.0",
"react-helmet-async": "^1.3.0",
"react-nl2br": "^1.0.4",
"react-redux": "^8.0.1",
"react-router-dom": "^6.3.0",
"react-scripts": "^5.0.1",
"redux": "^4.2.0",
"three": "^0.140.2",
"typescript": "^4.6.4"
},
"resolutions": {
"@svgr/webpack": "^6.2.1"
},
"scripts": {
"start": "react-scripts start",
"build": "react-scripts build",
"test": "react-scripts test",
"eject": "react-scripts eject"
},
"eslintConfig": {
"extends": "react-app"
},
"browserslist": {
"production": [
">0.2%",
"not dead",
"not op_mini all",
"ie 11"
],
"development": [
"last 1 chrome version",
"last 1 firefox version",
"last 1 safari version",
"ie 11"
]
}
}

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RewriteEngine on
RewriteBase /
RewriteRule ^DB/TE/(.+\.dat) /data/$1? [R=301,L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d [OR]
RewriteCond %{REQUEST_FILENAME} -d
RewriteCond %{REQUEST_FILENAME}index.html !-f
RewriteRule . /index.html [L]

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{
"title": "3D arrangements of glutamatergic\/excitatory, GABAergic\/inhibitory and astrocytes in the layer 2\/3 of mouse visual cortex.",
"author": "Ebina, T., Sohya, K., Imayoshi, I., Yin, S.T., Kimura, R., Yanagawa, Y., Kameda, H., Hioki, H., Kaneko, T., and Tsumoto, T.",
"figure": {
"file": "\/data\/TE0001.png",
"caption": "3D Arrangemtns of cells in TE0001"
},
"download": "\/data\/TE0001.dat",
"view": "\/data\/TE0001\/viewer",
"mouseLine": "VGAT-Venus transgenic mouse",
"imagingArea": "Layer 2\/3, Primary Visual Cortex",
"cellType": [
"Glutamatergic\/Excitatory neurons",
"GABAergic\/Inhibitory neurons",
"Astrocytes"
],
"postnatalDays": 67,
"imagingVolumeSize": "317 x 317 x 90 um",
"imagingDepth": "from 120 to 210 um",
"journal": "submitted",
"summary": "3D arrangements of three types of cells in the layer 2\/3 of mouse visual cortex were observed by <em>in vivo<\/em> two-photon functional Ca<sup>2+<\/sup> imaging method. Only the location of visually responsive cells were provided in this dataset.",
"releaseDate": "Nov. 1, 2014"
}

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{
"title": "3D arrangements of glutamatergic\/excitatory, GABAergic=\/inhibitory and astrocytes in the layer 2\/3 of mouse visual cortex.",
"author": "Ebina, T., Sohya, K., Imayoshi, I., Yin, S.T., Kimura, R., Yanagawa, Y., Kameda, H., Hioki, H., Kaneko, T., and Tsumoto, T.",
"figure": {
"file": "\/data\/TE0002.png",
"caption": "3D Arrangemtns of cells in TE0002"
},
"download": "\/data\/TE0002.dat",
"view": "\/data\/TE0002\/viewer",
"mouseLine": "VGAT-Venus transgenic mouse",
"imagingArea": "Layer 2\/3, Primary Visual Cortex",
"cellType": [
"Glutamatergic\/Excitatory neurons",
"GABAergic\/Inhibitory neurons",
"Astrocytes"
],
"postnatalDays": 78,
"imagingVolumeSize": "317 x 317 x 90 um",
"imagingDepth": "from 130 to 220 um",
"journal": "submitted",
"summary": "3D arrangements of three types of cells in the layer 2\/3 of mouse visual cortex were observed by <em>in vivo<\/em> two-photon functional Ca<sup>2+<\/sup> imaging method. Only the location of visually responsive cells were provided in this dataset.",
"releaseDate": "Nov. 1, 2014"
}

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{
"title": "3D arrangements of glutamatergic\/excitatory, GABAergic\/inhibitory and astrocytes in the layer 2\/3 of mouse visual cortex.",
"author": "Ebina, T., Sohya, K., Imayoshi, I., Yin, S.T., Kimura, R., Yanagawa, Y., Kameda, H., Hioki, H., Kaneko, T., and Tsumoto, T.",
"figure": {
"file": "\/data\/TE0003.png",
"caption": "3D Arrangemtns of cells in TE0003"
},
"download": "\/data\/TE0003.dat",
"view": "\/data\/TE0003\/viewer",
"mouseLine": "VGAT-Venus transgenic mouse",
"imagingArea": "Layer 2\/3, Primary Visual Cortex",
"cellType": [
"Glutamatergic\/Excitatory neurons",
"GABAergic\/Inhibitory neurons",
"Astrocytes"
],
"postnatalDays": 70,
"imagingVolumeSize": "317 x 317 x 90 um",
"imagingDepth": "from 120 to 225 um",
"journal": "submitted",
"summary": "3D arrangements of three types of cells in the layer 2\/3 of mouse visual cortex were observed by <em>in vivo<\/em> two-photon functional Ca<sup>2+<\/sup> imaging method. Only the location of visually responsive cells were provided in this dataset.",
"releaseDate": "Nov. 1, 2014"
}

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{
"title": "3D arrangements of glutamatergic\/excitatory, GABAergic\/inhibitory and astrocytes in the layer 2\/3 of mouse visual cortex.",
"author": "Ebina, T., Sohya, K., Imayoshi, I., Yin, S.T., Kimura, R., Yanagawa, Y., Kameda, H., Hioki, H., Kaneko, T., and Tsumoto, T.",
"figure": {
"file": "\/data\/TE0004.png",
"caption": "3D Arrangemtns of cells in TE0004"
},
"download": "\/data\/TE0004.dat",
"view": "\/data\/TE0004\/viewer",
"mouseLine": "VGAT-Venus transgenic mouse",
"imagingArea": "Layer 2\/3, Primary Visual Cortex",
"cellType": [
"Glutamatergic\/Excitatory neurons",
"GABAergic\/Inhibitory neurons",
"Astrocytes"
],
"postnatalDays": 90,
"imagingVolumeSize": "317 x 317 x 90 um",
"imagingDepth": "from 110 to 200 um",
"journal": "submitted",
"summary": "3D arrangements of three types of cells in the layer 2\/3 of mouse visual cortex were observed by <em>in vivo<\/em> two-photon functional Ca<sup>2+<\/sup> imaging method. Only the location of visually responsive cells were provided in this dataset.",
"releaseDate": "Nov. 1, 2014"
}

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{
"title": "3D arrangements of glutamatergic\/excitatory, GABAergic\/inhibitory and astrocytes in the layer 2\/3 of mouse visual cortex.",
"author": "Ebina, T., Sohya, K., Imayoshi, I., Yin, S.T., Kimura, R., Yanagawa, Y., Kameda, H., Hioki, H., Kaneko, T., and Tsumoto, T.",
"figure": {
"file": "\/data\/TE0005.png",
"caption": "3D Arrangemtns of cells in TE0005"
},
"download": "\/data\/TE0005.dat",
"view": "\/data\/TE0005\/viewer",
"mouseLine": "VGAT-Venus transgenic mouse",
"imagingArea": "Layer 2\/3, Primary Visual Cortex",
"cellType": [
"Glutamatergic\/Excitatory neurons",
"GABAergic\/Inhibitory neurons",
"Astrocytes"
],
"postnatalDays": 75,
"imagingVolumeSize": "317 x 317 x 90 um",
"imagingDepth": "from 125 to 230 um",
"journal": "submitted",
"summary": "3D arrangements of three types of cells in the layer 2\/3 of mouse visual cortex were observed by <em>in vivo<\/em> two-photon functional Ca<sup>2+<\/sup> imaging method. Only the location of visually responsive cells were provided in this dataset.",
"releaseDate": "Nov. 1, 2014"
}

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{
"title": "3D arrangements of PV neurons, SOM neurons, astrocytes and putative excitatory neurons in the layer 2\/3 of mouse visual cortex.",
"author": "Ebina, T., Sohya, K., Imayoshi, I., Yin, S.T., Kimura, R., Yanagawa, Y., Kameda, H., Hioki, H., Kaneko, T., and Tsumoto, T.",
"figure": {
"file": "\/data\/TE0006.png",
"caption": "3D Arrangemtns of cells in TE0006"
},
"download": "\/data\/TE0006.dat",
"view": "\/data\/TE0006\/viewer",
"mouseLine": "PV\/myrGFP-LDLRct transgenic mouse",
"imagingArea": "Layer 2\/3, Primary Visual Cortex",
"cellType": [
"PV-positive neurons",
"SOM-positive neurons",
"Putative excitatory neurons",
"Astrocytes"
],
"postnatalDays": 77,
"imagingVolumeSize": "317 x 317 x 105 um",
"imagingDepth": "from 110 to 215 um",
"journal": "submitted",
"summary": "3D arrangements of four types of cells in the layer 2\/3 of mouse visual cortex were observed by <em>in vivo<\/em> two-photon functional Ca<sup>2+<\/sup> imaging method. SOM-positive neurons were identified by immunohistochemistry. Only the location of visually responsive cells were provided in this dataset.",
"releaseDate": "Nov. 1, 2014"
}

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{
"title": "3D arrangements of PV neurons, SOM neurons, astrocytes and putative excitatory neurons in the layer 2/3 of mouse visual cortex.",
"author": "Ebina, T., Sohya, K., Imayoshi, I., Yin, S.T., Kimura, R., Yanagawa, Y., Kameda, H., Hioki, H., Kaneko, T., and Tsumoto, T.",
"figure": {
"file": "\/data\/TE0007.png",
"caption": "3D Arrangemtns of cells in TE0007"
},
"download": "\/data\/TE0007.dat",
"view": "\/data\/TE0007\/viewer",
"mouseLine": "PV/myrGFP-LDLRct transgenic mouse",
"imagingArea": "Layer 2\/3, Primary Visual Cortex",
"cellType": [
"PV-positive neurons",
"SOM-positive neurons",
"Putative excitatory neurons",
"Astrocytes"
],
"postnatalDays": 73,
"imagingVolumeSize": "317 x 317 x 105 um",
"imagingDepth": "from 110 to 215 um",
"journal": "submitted",
"summary": "3D arrangements of four types of cells in the layer 2\/3 of mouse visual cortex were observed by <em>in vivo<\/em> two-photon functional Ca<sup>2+<\/sup> imaging method. SOM-positive neurons were identified by immunohistochemistry. Only the location of visually responsive cells were provided in this dataset.",
"releaseDate": "Nov. 1, 2014"
}

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{
"title": "3D arrangements of PV neurons, SOM neurons, astrocytes and putative excitatory neurons in the layer 2\/3 of mouse visual cortex.",
"author": "Ebina, T., Sohya, K., Imayoshi, I., Yin, S.T., Kimura, R., Yanagawa, Y., Kameda, H., Hioki, H., Kaneko, T., and Tsumoto, T.",
"figure": {
"file": "\/data\/TE0008.png",
"caption": "3D Arrangemtns of cells in TE0008"
},
"download": "\/data\/TE0008.dat",
"view": "\/data\/TE0008\/viewer",
"mouseLine": "PV/myrGFP-LDLRct transgenic mouse",
"imagingArea": "Layer 2\/3, Primary Visual Cortex",
"cellType": [
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"SOM-positive neurons",
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"Astrocytes"
],
"postnatalDays": 70,
"imagingVolumeSize": "317 x 317 x 105 um",
"imagingDepth": "from 110 to 215 um",
"journal": "submitted",
"summary": "3D arrangements of four types of cells in the layer 2\/3 of mouse visual cortex were observed by <em>in vivo<\/em> two-photon functional Ca<sup>2+</sup> imaging method. SOM-positive neurons were identified by immunohistochemistry. Only the location of visually responsive cells were provided in this dataset.",
"releaseDate": "Nov. 1, 2014"
}

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{
"title": "3D arrangements of GABAergic/inhibitory neurons in the layer 2/3 of mouse visual cortex.",
"author": "Ebina, T., Sohya, K., Imayoshi, I., Yin, S.T., Kimura, R., Yanagawa, Y., Kameda, H., Hioki, H., Kaneko, T., and Tsumoto, T.",
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},
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"journal": "submitted",
"summary": "3D arrangements of GABAergic\/inhibitory neurons in the layer 2\/3 of mouse visual cortex were observed by <em>in vivo<\/em> two-photon functional Ca<sup>2+<\/sup> imaging method. Only the location of visually responsive cells were provided in this dataset.",
"releaseDate": "Nov. 1, 2014"
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{
"title": "3D arrangements of GABAergic\/inhibitory neurons in the layer 2\/3 of mouse visual cortex.",
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"releaseDate": "Nov. 1, 2014"
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21
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{
"title": "3D arrangements of GABAergic\/inhibitory neurons in the layer 2\/3 of mouse visual cortex.",
"author": "Ebina, T., Sohya, K., Imayoshi, I., Yin, S.T., Kimura, R., Yanagawa, Y., Kameda, H., Hioki, H., Kaneko, T., and Tsumoto, T.",
"figure": {
"file": "\/data\/TE0015.png",
"caption": "3D Arrangemtns of cells in TE0015"
},
"download": "\/data\/TE0015.dat",
"view": "\/data\/TE0015\/viewer",
"mouseLine": "Dlx5\/6-GCaMP3 mouse (Crossing Dlx5\/6-Flpe and R26-CAG-FRT-GCaMP3 transgenic mice)",
"imagingArea": "Layer 2\/3, Primary Visual Cortex",
"cellType": [
"GABAergic\/inhibitory neurons"
],
"postnatalDays": 92,
"imagingVolumeSize": "512 x 512 x 110 um",
"imagingDepth": "from 90 to 200 um",
"journal": "submitted",
"summary": "3D arrangements of GABAergic\/inhibitory neurons in the layer 2\/3 of mouse visual cortex were observed by <em>in vivo<\/em> two-photon functional Ca<sup>2+<\/sup> imaging method. Only the location of visually responsive cells were provided in this dataset.",
"releaseDate": "Nov. 1, 2014"
}

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21
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{
"title": "3D arrangements of GABAergic\/inhibitory neurons in the layer 2\/3 of mouse visual cortex.",
"author": "Ebina, T., Sohya, K., Imayoshi, I., Yin, S.T., Kimura, R., Yanagawa, Y., Kameda, H., Hioki, H., Kaneko, T., and Tsumoto, T.",
"figure": {
"file": "\/data\/TE0016.png",
"caption": "3D Arrangemtns of cells in TE0016"
},
"download": "\/data\/TE0016.dat",
"view": "\/data\/TE0016\/viewer",
"mouseLine": "Dlx5\/6-GCaMP3 mouse (Crossing Dlx5\/6-Flpe and R26-CAG-FRT-GCaMP3 transgenic mice)",
"imagingArea": "Layer 2\/3, Primary Visual Cortex",
"cellType": [
"GABAergic\/inhibitory neurons"
],
"postnatalDays": 47,
"imagingVolumeSize": "512 x 512 x 110 um",
"imagingDepth": "from 90 to 200 um",
"journal": "submitted",
"summary": "3D arrangements of GABAergic\/inhibitory neurons in the layer 2\/3 of mouse visual cortex were observed by <em>in vivo<\/em> two-photon functional Ca<sup>2+<\/sup> imaging method. Only the location of visually responsive cells were provided in this dataset.",
"releaseDate": "Nov. 1, 2014"
}

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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8" />
<link rel="icon" href="%PUBLIC_URL%/favicon.ico" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name="theme-color" content="#000000" />
<meta
name="description"
content="CelLoc-3D is a database of the 3D arrangement of neocortical cells (gultamatargic/excitatory, GABAergic/inhibitory and/or astrocytes) identified in vivo in layer 2/3 of the primary visual cortex of the mouse by two-photon imaging."
/>
<link rel="manifest" href="%PUBLIC_URL%/manifest.json" />
<title>CelLoc3D Server</title>
</head>
<body>
<noscript>You need to enable JavaScript to run this app.</noscript>
<div id="root"></div>
</body>
</html>

15
public/manifest.json Normal file
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{
"short_name": "CelLoc3D Server",
"name": "CelLoc3D Server",
"icons": [
{
"src": "favicon.ico",
"sizes": "32x32",
"type": "image/x-icon"
}
],
"start_url": ".",
"display": "standalone",
"theme_color": "#000000",
"background_color": "#ffffff"
}

3
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# https://www.robotstxt.org/robotstxt.html
User-agent: *
Disallow:

49
src/App.module.css Normal file
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.container {
width: 480px;
padding: 10px 10px 0 10px;
margin: 0 auto;
margin-bottom: 5px;
}
.main {
width: 100%;
min-height: 330px;
height: auto !important;
border: thin solid #bb3300;
text-align: left;
border-radius: 20px;
padding: 10px 0;
}
.header {
width: 100%;
height: 150px;
text-align: left;
margin-bottom: 0px;
padding-top: 10px;
padding-bottom: 5px;
background-image: url("./assets/images/logo.jpg");
background-repeat: no-repeat;
background-position: center center;
}
.header ul {
position: absolute;
top: 120px;
padding: 0;
}
.header ul li {
display: inline-block;
float: left;
}
.header ul li a {
display: block;
padding: 0 15px;
outline: none;
text-decoration: none;
line-height: 20px;
}
.footer {
font-size: 90%;
width: 100%;
clear: both;
text-align: center;
margin: 10px 0;
}

15
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import { render } from "@testing-library/react";
import React from "react";
import { Provider } from "react-redux";
import App from "./App";
import { store } from "./app/store";
test("renders learn react link", () => {
const { getByText } = render(
<Provider store={store}>
<App />
</Provider>
);
expect(getByText(/learn/i)).toBeInTheDocument();
});

49
src/App.tsx Normal file
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import React from "react";
import { BrowserRouter, NavLink, Route, Routes } from "react-router-dom";
import styles from "./App.module.css";
import CompatRedirect from "./features/compat-redirect/CompatRedirect";
import Contact from "./features/contact/Contact";
import Data from "./features/data/Data";
import Help from "./features/help/Help";
import News from "./features/news/News";
import PageTitle from "./features/page-title/PageTitle";
import Search from "./features/search/Search";
const App: React.FC = () => {
return (
<BrowserRouter>
<div className={styles.container}>
<div className={styles.header}>
<ul>
<li>
<NavLink to="/">Home</NavLink>
</li>
<li>
<NavLink to="/search">Search</NavLink>
</li>
<li>
<NavLink to="/help">Help</NavLink>
</li>
<li>
<NavLink to="/contact">Contact</NavLink>
</li>
</ul>
</div>
<PageTitle />
<div className={styles.main}>
<Routes>
<Route index element={<News />} />
<Route path="search/*" element={<Search />} />
<Route path="data/:name/*" element={<Data />} />
<Route path="help/*" element={<Help />} />
<Route path="contact" element={<Contact />} />
<Route path="*" element={<CompatRedirect />} />
</Routes>
</div>
<div className={styles.footer}>&copy;2014 Laboratory for cortical circuit plasticity, RIKEN BSI.</div>
</div>
</BrowserRouter>
);
};
export default App;

6
src/app/hooks.ts Normal file
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import { TypedUseSelectorHook, useDispatch, useSelector } from "react-redux";
import type { AppDispatch, RootState } from "./store";
// Use throughout your app instead of plain `useDispatch` and `useSelector`
export const useAppDispatch = () => useDispatch<AppDispatch>();
export const useAppSelector: TypedUseSelectorHook<RootState> = useSelector;

14
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import { Action, configureStore, ThunkAction } from "@reduxjs/toolkit";
import pageTitleReducer from "../features/page-title/pageTitleSlice";
import searchResultsReducer from "../features/search-results/searchResultsSlice";
export const store = configureStore({
reducer: {
pageTitle: pageTitleReducer,
searchResults: searchResultsReducer,
},
});
export type AppDispatch = typeof store.dispatch;
export type RootState = ReturnType<typeof store.getState>;
export type AppThunk<ReturnType = void> = ThunkAction<ReturnType, RootState, unknown, Action<string>>;

306
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{
"TE0001": {
"pd": 67,
"recordingVolume": {
"width": 317,
"height": 317,
"depth": 90
},
"imagingDepth": {
"from": 120,
"to": 210
},
"cellType": ["E", "I", "G"],
"area": "L2\/3, V1",
"cellNum": 422,
"expDate": "Jun. 23 2009",
"releaseDate": "141101",
"geneType": "VGAT-Venus",
"remark": "3D arrangements of excitatory neurons, inhibitory neurons and astrocytes in the V1 layer 2\/3 of VGAT-Venus transgenic mouse at PD67."
},
"TE0002": {
"pd": 78,
"recordingVolume": {
"width": 317,
"height": 317,
"depth": 90
},
"imagingDepth": {
"from": 130,
"to": 220
},
"cellType": ["E", "I", "G"],
"area": "L2\/3, V1",
"cellNum": 348,
"expDate": "Dec. 17 2009",
"releaseDate": "141101",
"geneType": "VGAT-Venus",
"remark": "3D arrangements of excitatory neurons, inhibitory neurons and astrocytes in the V1 layer 2\/3 of VGAT-Venus transgenic mouse at PD78."
},
"TE0003": {
"pd": 70,
"recordingVolume": {
"width": 317,
"height": 317,
"depth": 105
},
"imagingDepth": {
"from": 120,
"to": 225
},
"cellType": ["E", "I", "G"],
"area": "L2\/3, V1",
"cellNum": 631,
"expDate": "Jan. 27 2010",
"releaseDate": "141101",
"geneType": "VGAT-Venus",
"remark": "3D arrangements of excitatory neurons, inhibitory neurons and astrocytes in the V1 layer 2\/3 of VGAT-Venus transgenic mouse at PD70."
},
"TE0004": {
"pd": 90,
"recordingVolume": {
"width": 317,
"height": 317,
"depth": 90
},
"imagingDepth": {
"from": 110,
"to": 200
},
"cellType": ["E", "I", "G"],
"area": "L2\/3, V1",
"cellNum": 759,
"expDate": "Dec. 5 2011",
"releaseDate": "141101",
"geneType": "VGAT-Venus",
"remark": "3D arrangements of excitatory neurons, inhibitory neurons and astrocytes in the V1 layer 2\/3 of VGAT-Venus transgenic mouse at PD90."
},
"TE0005": {
"pd": 75,
"recordingVolume": {
"width": 317,
"height": 317,
"depth": 105
},
"imagingDepth": {
"from": 125,
"to": 230
},
"cellType": ["E", "I", "G"],
"area": "L2\/3, V1",
"cellNum": 710,
"expDate": "May. 28 2012",
"releaseDate": "141101",
"geneType": "VGAT-Venus",
"remark": "3D arrangements of excitatory neurons, inhibitory neurons and astrocytes in the V1 layer 2\/3 of VGAT-Venus transgenic mouse at PD75."
},
"TE0006": {
"pd": 77,
"recordingVolume": {
"width": 317,
"height": 317,
"depth": 105
},
"imagingDepth": {
"from": 110,
"to": 215
},
"cellType": ["E", "P", "S", "G"],
"area": "L2\/3, V1",
"cellNum": 382,
"expDate": "Feb. 22 2011",
"releaseDate": "141101",
"geneType": "PV\/myrGFP-LDLRct",
"remark": "3D arrangements of PV neurons, SOM neurons, astrocytes and putative excitatory neurons in the V1 layer 2\/3 of PV\/myrGFP-LDLRct transgenic mouse at PD77."
},
"TE0007": {
"pd": 73,
"recordingVolume": {
"width": 317,
"height": 317,
"depth": 105
},
"imagingDepth": {
"from": 110,
"to": 215
},
"cellType": ["E", "P", "S", "G"],
"area": "L2\/3, V1",
"cellNum": 774,
"expDate": "Mar. 24 2011",
"releaseDate": "141101",
"geneType": "PV\/myrGFP-LDLRct",
"remark": "3D arrangements of PV neurons, SOM neurons, astrocytes and putative excitatory neurons in the V1 layer 2\/3 of PV\/myrGFP-LDLRct transgenic mouse at PD73."
},
"TE0008": {
"pd": 70,
"recordingVolume": {
"width": 317,
"height": 317,
"depth": 105
},
"imagingDepth": {
"from": 110,
"to": 215
},
"cellType": ["E", "P", "S", "G"],
"area": "L2\/3, V1",
"cellNum": 536,
"expDate": "Jun. 23 2011",
"releaseDate": "141101",
"geneType": "PV\/myrGFP-LDLRct",
"remark": "3D arrangements of PV neurons, SOM neurons, astrocytes and putative excitatory neurons in the V1 layer 2\/3 of PV\/myrGFP-LDLRct transgenic mouse at PD70."
},
"TE0009": {
"pd": 53,
"recordingVolume": {
"width": 317,
"height": 317,
"depth": 110
},
"imagingDepth": {
"from": 100,
"to": 210
},
"cellType": ["I"],
"area": "L2\/3, V1",
"cellNum": 42,
"expDate": "Oct. 10 2013",
"releaseDate": "141101",
"geneType": "Dlx5\/6-GCaMP3",
"remark": "3D arrangement of GABAergic\/inhibitory neurons in the V1 layer 2\/3 of Dlx5\/6-GCaMP3 transgenic mouse at PD53."
},
"TE0010": {
"pd": 100,
"recordingVolume": {
"width": 512,
"height": 512,
"depth": 110
},
"imagingDepth": {
"from": 90,
"to": 200
},
"cellType": ["I"],
"area": "L2\/3, V1",
"cellNum": 177,
"expDate": "Nov. 7 2013",
"releaseDate": "141101",
"geneType": "Dlx5\/6-GCaMP3",
"remark": "3D arrangement of GABAergic\/inhibitory neurons in the V1 layer 2\/3 of Dlx5\/6-GCaMP3 transgenic mouse at PD100."
},
"TE0011": {
"pd": 70,
"recordingVolume": {
"width": 512,
"height": 512,
"depth": 100
},
"imagingDepth": {
"from": 90,
"to": 200
},
"cellType": ["I"],
"area": "L2\/3, V1",
"cellNum": 194,
"expDate": "Nov. 25 2013",
"releaseDate": "141101",
"geneType": "Dlx5\/6-GCaMP3",
"remark": "3D arrangement of GABAergic\/inhibitory neurons in the V1 layer 2\/3 of Dlx5\/6-GCaMP3 transgenic mouse at PD70."
},
"TE0012": {
"pd": 78,
"recordingVolume": {
"width": 512,
"height": 512,
"depth": 110
},
"imagingDepth": {
"from": 90,
"to": 200
},
"cellType": ["I"],
"area": "L2\/3, V1",
"cellNum": 179,
"expDate": "Dec. 3 2013",
"releaseDate": "141101",
"geneType": "Dlx5\/6-GCaMP3",
"remark": "3D arrangement of GABAergic\/inhibitory neurons in the V1 layer 2\/3 of Dlx5\/6-GCaMP3 transgenic mouse at PD78."
},
"TE0013": {
"pd": 69,
"recordingVolume": {
"width": 512,
"height": 512,
"depth": 110
},
"imagingDepth": {
"from": 90,
"to": 200
},
"cellType": ["I"],
"area": "L2\/3, V1",
"cellNum": 144,
"expDate": "Dec. 19 2013",
"releaseDate": "141101",
"geneType": "Dlx5\/6-GCaMP3",
"remark": "3D arrangement of GABAergic\/inhibitory neurons in the V1 layer 2\/3 of Dlx5\/6-GCaMP3 transgenic mouse at PD69."
},
"TE0014": {
"pd": 44,
"recordingVolume": {
"width": 317,
"height": 317,
"depth": 110
},
"imagingDepth": {
"from": 90,
"to": 200
},
"cellType": ["I"],
"area": "L2\/3, V1",
"cellNum": 40,
"expDate": "Jul. 23 2014",
"releaseDate": "141101",
"geneType": "Dlx5\/6-GCaMP3",
"remark": "3D arrangement of GABAergic\/inhibitory neurons in the V1 layer 2\/3 of Dlx5\/6-GCaMP3 transgenic mouse at PD44."
},
"TE0015": {
"pd": 92,
"recordingVolume": {
"width": 512,
"height": 512,
"depth": 100
},
"imagingDepth": {
"from": 90,
"to": 200
},
"cellType": ["I"],
"area": "L2\/3, V1",
"cellNum": 125,
"expDate": "Jul. 30 2014",
"releaseDate": "141101",
"geneType": "Dlx5\/6-GCaMP3",
"remark": "3D arrangement of GABAergic\/inhibitory neurons in the V1 layer 2\/3 of Dlx5\/6-GCaMP3 transgenic mouse at PD92."
},
"TE0016": {
"pd": 47,
"recordingVolume": {
"width": 512,
"height": 512,
"depth": 100
},
"imagingDepth": {
"from": 90,
"to": 200
},
"cellType": ["I"],
"area": "L2\/3, V1",
"cellNum": 100,
"expDate": "Aug. 1 2014",
"releaseDate": "141101",
"geneType": "Dlx5\/6-GCaMP3",
"remark": "3D arrangement of GABAergic\/inhibitory neurons in the V1 layer 2\/3 of Dlx5\/6-GCaMP3 transgenic mouse at PD47."
}
}

BIN
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[
{
"date": "Nov. 1, 2014",
"desc": "16 datasets have been added to CelLoc-3D\nProvided by Ebina et al.\n(Lab. for Cortical Circuit Plasticity, RIKEN BSI)"
},
{
"date": "Nov. 1, 2014",
"desc": "CelLoc-3D becomes available online"
}
]

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import React from "react";
import { Navigate, useLocation } from "react-router-dom";
import NotFound from "../not-found/NotFound";
const CompatRedirect: React.FC = () => {
const { pathname } = useLocation();
switch (pathname) {
case "/index.html":
return <Navigate to="/" />;
case "/Search.html":
return <Navigate to="/search" />;
case "/Help.html":
return <Navigate to="/help" />;
case "/Help_S1.html":
return <Navigate to="/help/search/1" />;
case "/Help_S2.html":
return <Navigate to="/help/search/2" />;
case "/Help_S3.html":
return <Navigate to="/help/search/3" />;
case "/Help_S4.html":
return <Navigate to="/help/search/4" />;
case "/Help_S5.html":
return <Navigate to="/help/search/5" />;
case "/Help_Dataset.html":
return <Navigate to="/help/dataset" />;
case "/Help_Viewer.html":
return <Navigate to="/help/viewer" />;
case "/Contact.html":
return <Navigate to="/help/contact" />;
case "/cgi-bin/SearchResult.cgi":
return <Navigate to="/search/results" />;
default:
const match = pathname.match(/^\/DB\/TE\/(3D-)?(.+)\.html$/);
if (match !== null) {
const url = "/data/" + match[2] + (typeof match[1] !== "undefined" ? "/viewer" : "");
return <Navigate to={url} />;
}
break;
}
return <NotFound />;
};
export default CompatRedirect;

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.contact {
margin: 20px;
}
.contact h4 {
margin: 5px 0 10px 0;
}
.contact p {
margin: 5px 0 15px 15px;
}
.notice {
margin: 10px 0 20px;
color: #ff0000;
}
.note {
margin-left: 15px;
font-style: italic;
}

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import React, { useEffect } from "react";
import { useAppDispatch } from "../../app/hooks";
import { setTitle } from "../page-title/pageTitleSlice";
import styles from "./Contact.module.css";
const Contact: React.FC = () => {
const dispatch = useAppDispatch();
useEffect(() => {
dispatch(setTitle("Contact Information"));
}, [dispatch]);
return (
<div className={styles.contact}>
<section className={styles.notice}>Notice: This site has been archived since May 2019 and is no longer updated.</section>
<h4>CelLoc-3D is managed by Teppei Ebina and Tadaharu Tsumoto</h4>
<p>
Laboratory for cortical circuit plasticity
<br />
Brain Science Institute, RIKEN
<br />
2-1, Hirosawa, Wako, Saitama, 351-0198 Japan
</p>
<h4>E-mail:</h4>
<p>
teppei-ebina (at) brain.riken.jp
<br />
<span className={styles.note}>or</span>
<br />
tsumoto (at) brain.riken.jp
<br />
<span className={styles.note}>(change (at) to @)</span>
</p>
</div>
);
};
export default Contact;

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.detail {
margin: 10px 10px 20px 10px;
}
.title,
.author,
.detail figure,
.detail dl {
margin: 5px 0 10px 0;
}
.detail figure {
text-align: center;
}
.detail figure img {
width: 80%;
}
.detail dl dt {
font-weight: bold;
}
.detail dl dd {
margin-left: 30px;
}

156
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import axios from "axios";
import React, { Component } from "react";
import { Link } from "react-router-dom";
import { useAppDispatch } from "../../app/hooks";
import DataUtils from "../data/DataUtils";
import Loading from "../loading/Loading";
import NotFound from "../not-found/NotFound";
import { setTitle } from "../page-title/pageTitleSlice";
import styles from "./DataDetail.module.css";
interface DetailDataJson {
title: string;
author: string;
figure: {
file: string;
caption: string;
};
download: string;
view: string;
mouseLine: string;
imagingArea: string;
cellType: string[];
postnatalDays: number;
imagingVolumeSize: string;
imagingDepth: string;
journal: string;
summary: string;
releaseDate: string;
}
interface PropsFC {
name: string;
}
interface Props extends PropsFC {
dispatch: any;
}
interface State {
name: string;
data: DetailDataJson | null;
}
class DataDetail extends Component<Props, State> {
isActive = false;
constructor(props: Props) {
super(props);
this.state = {
name: props.name,
data: null,
};
}
componentDidMount() {
const { name } = this.state;
this.isActive = true;
if (!DataUtils.exists(name)) {
if (name !== "") {
this.setState({ name: "" });
}
return;
}
axios
.get(`/data/${name}.json`, { responseType: "json" })
.then((response) => {
if (this.isActive) {
this.props.dispatch(setTitle(`DS: ${name}`));
this.setState({ data: response.data as DetailDataJson });
}
})
.catch((error) => {
if (this.isActive) {
this.setState({ name: "" });
}
});
}
componentWillUnmount() {
this.isActive = false;
}
render() {
const { name, data } = this.state;
if (name === "") {
return <NotFound />;
}
if (!data) {
return <Loading />;
}
return (
<section className={styles.detail}>
<h4 className={styles.title}>{data.title}</h4>
<div className={styles.author}>{data.author}</div>
<figure>
<img src={data.figure.file} alt={data.figure.caption} />
<figcaption>{data.figure.caption}</figcaption>
</figure>
<dl>
<dt>Download &amp; View</dt>
<dd>
<a href={data.download}>Text download</a>
</dd>
<dd>
<Link to={data.view}>View 3D structure</Link>
</dd>
</dl>
<dl>
<dt>Mouse line</dt>
<dd>{data.mouseLine}</dd>
</dl>
<dl>
<dt>Imaging area</dt>
<dd>{data.imagingArea}</dd>
</dl>
<dl>
<dt>Cell type</dt>
{data.cellType.map((value, key) => {
return <dd key={key}>{value}</dd>;
})}
</dl>
<dl>
<dt>Postnatal days</dt>
<dd>{data.postnatalDays}</dd>
</dl>
<dl>
<dt>Imaging volume size</dt>
<dd>{data.imagingVolumeSize}</dd>
</dl>
<dl>
<dt>Imaging depth</dt>
<dd>{data.imagingDepth}</dd>
</dl>
<dl>
<dt>Journal</dt>
<dd>{data.journal}</dd>
</dl>
<dl>
<dt>Summary</dt>
<dd dangerouslySetInnerHTML={{ __html: data.summary }}></dd>
</dl>
<dl>
<dt>Release date</dt>
<dd>{data.releaseDate}</dd>
</dl>
</section>
);
}
}
const DataDetailFC: React.FC<PropsFC> = (props) => {
const dispatch = useAppDispatch();
return <DataDetail dispatch={dispatch} name={props.name} />;
};
export default DataDetailFC;

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.no_webgl {
margin: 10px auto;
text-align: center;
}
.back {
margin-bottom: 10px;
text-align: center;
}
.viewer {
width: 100%;
height: 400px;
}

207
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import axios from "axios";
import React, { Component } from "react";
import { Link } from "react-router-dom";
import * as THREE from "three";
import { TrackballControls } from "three/examples/jsm/controls/TrackballControls";
import { useAppDispatch } from "../../app/hooks";
import DataUtils from "../data/DataUtils";
import Loading from "../loading/Loading";
import NotFound from "../not-found/NotFound";
import { setTitle } from "../page-title/pageTitleSlice";
import styles from "./DataViewer.module.css";
class Viewer3D {
private mount: HTMLDivElement;
private frameId: number | null = null;
private scene: THREE.Scene | null = null;
private camera: THREE.PerspectiveCamera | null = null;
private controls: TrackballControls | null = null;
private renderer: THREE.WebGLRenderer | null = null;
constructor(mount: HTMLDivElement) {
this.mount = mount;
this.start = this.start.bind(this);
this.stop = this.stop.bind(this);
this.animate = this.animate.bind(this);
}
init(data: string) {
const lines = data.split("\n");
const head = lines
.shift()
?.trim()
.split("\t")
.map((line, k) => {
return parseInt(line.replace(/^#/g, ""), 10) || 0;
});
if (typeof head === "undefined" || head.length !== 3 || head.includes(0)) {
return false;
}
const width = this.mount.clientWidth;
const height = this.mount.clientHeight;
const fov = 7.5 + (head[0] * 2.5) / 100.0;
this.camera = new THREE.PerspectiveCamera(fov, width / height, 1, 10000);
this.camera.position.x = 1300;
this.camera.position.y = 1300;
this.camera.position.z = 1100;
this.camera.up.set(0, 0, 1);
this.controls = new TrackballControls(this.camera, this.mount);
const obj3d = new THREE.Object3D();
this.scene = new THREE.Scene();
this.scene.add(obj3d);
const DrawCube = (width: number, height: number, depth: number) => {
const mesh = new THREE.Mesh(new THREE.BoxGeometry(width, height, depth * 2), new THREE.MeshBasicMaterial());
const cube = new THREE.BoxHelper(mesh, 0x000000);
return cube;
};
obj3d.add(DrawCube(head[0], head[1], head[2]));
const material = {
e: new THREE.MeshBasicMaterial({ color: 0x0000ff }),
i: new THREE.MeshBasicMaterial({ color: 0xff0000 }),
g: new THREE.MeshBasicMaterial({ color: 0x00ff00 }),
p: new THREE.MeshBasicMaterial({ color: 0xffff00 }),
s: new THREE.MeshBasicMaterial({ color: 0xff00ff }),
ps: new THREE.MeshBasicMaterial({ color: 0x00ffff }),
};
const geometory = new THREE.SphereGeometry(4, 10, 10);
lines.forEach((line) => {
const point = line.trim().split("\t");
if (point.length === 4 && material.hasOwnProperty(point[0])) {
const particle = new THREE.Mesh(geometory, material[point[0] as "e" | "i" | "g" | "p" | "s" | "ps"]);
particle.position.x = parseFloat(point[1]) - head[0] / 2.0;
particle.position.y = parseFloat(point[2]) - head[1] / 2.0;
particle.position.z = head[2] - parseFloat(point[3]) * 2.0;
obj3d.add(particle);
}
});
try {
this.renderer = new THREE.WebGLRenderer({ antialias: true });
this.renderer.setSize(width, height);
this.renderer.setClearColor(0xffffff);
this.mount.appendChild(this.renderer.domElement);
} catch (error) {
return false;
}
return true;
}
start() {
this.frameId = requestAnimationFrame(this.animate);
}
stop() {
this.frameId && cancelAnimationFrame(this.frameId);
this.renderer && this.mount.removeChild(this.renderer.domElement);
}
animate() {
this.controls && this.controls.update();
this.renderer && this.renderer.clear();
this.renderer && this.scene && this.camera && this.renderer.render(this.scene, this.camera);
this.frameId = requestAnimationFrame(this.animate);
}
}
interface PropsFC {
name: string;
}
interface Props extends PropsFC {
dispatch: any;
}
interface State {
name: string;
data: string;
}
class DataViewer extends Component<Props, State> {
private isActive = false;
private mount: HTMLDivElement | null = null;
private viewer: Viewer3D | null = null;
constructor(props: Props) {
super(props);
this.state = {
name: this.props.name,
data: "",
};
}
componentDidMount() {
const { name } = this.state;
this.isActive = true;
if (!DataUtils.exists(name)) {
if (name !== "") {
this.setState({ name: "" });
}
return;
}
axios
.get(`/data/${name}.dat`, { responseType: "text" })
.then((response) => {
if (this.isActive) {
this.props.dispatch(setTitle(`View 3D: ${name}`));
this.setState({ data: response.data });
}
})
.catch((error) => {
if (this.isActive) {
this.setState({ name: "" });
}
});
}
componentDidUpdate(prevProps: Props, prevState: State) {
if (this.mount && this.state.data !== "" && !this.viewer) {
const viewer = new Viewer3D(this.mount);
if (viewer.init(this.state.data)) {
this.viewer = viewer;
this.viewer.start();
} else {
this.setState({ name: "@@NOWEBGL@@" });
}
}
}
componentWillUnmount() {
this.isActive = false;
if (this.viewer) {
this.viewer.stop();
this.viewer = null;
}
}
render() {
const { name, data } = this.state;
switch (name) {
case "":
return <NotFound />;
case "@@NOWEBGL@@":
return <div className={styles.no_webgl}>It does not appear your computer supports WebGL.</div>;
}
if (data === "") {
return <Loading />;
}
return (
<section>
<div className={styles.back}>
<Link to={`/data/${name}`}>Back to {name}</Link>
</div>
<div
className={styles.viewer}
ref={(mount) => {
this.mount = mount;
}}
/>
</section>
);
}
}
const DataViewerFC: React.FC<PropsFC> = (props) => {
const dispatch = useAppDispatch();
return <DataViewer dispatch={dispatch} name={props.name} />;
};
export default DataViewerFC;

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.data {
margin: 10px;
}

25
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import React from "react";
import { Route, Routes, useParams } from "react-router-dom";
import DataDetail from "../data-detail/DataDetail";
import DataViewer from "../data-viewer/DataViewer";
import NotFound from "../not-found/NotFound";
import styles from "./Data.module.css";
import DataUtils from "./DataUtils";
const Data: React.FC = () => {
const { name } = useParams<"name">();
if (typeof name === "undefined" || !DataUtils.exists(name)) {
return <NotFound />;
}
return (
<div className={styles.data}>
<Routes>
<Route index element={<DataDetail name={name} />} />
<Route path="viewer" element={<DataViewer name={name} />} />
<Route path="*" element={<NotFound />} />
</Routes>
</div>
);
};
export default Data;

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import JsonData_ from "../../assets/data.json";
const cellTypes = ["E", "I", "G", "P", "S"] as const;
type TCellType = typeof cellTypes[number];
interface JsonDataItem {
pd: number;
recordingVolume: {
width: number;
height: number;
depth: number;
};
imagingDepth: {
from: number;
to: number;
};
cellType: string[]; // TCellType[] or ("E"|"I"|"G"|"P"|"S")[];
area: string;
cellNum: number;
expDate: string;
releaseDate: string;
geneType: string;
remark: string;
}
interface JsonData {
[name: string]: JsonDataItem;
}
export interface SearchParams {
pdStart: number;
pdEnd: number;
widthMin: number;
widthMax: number;
depthMin: number;
depthMax: number;
cellType: string;
area: string;
geneType: string;
keyword: string;
}
interface SearchResult {
name: string;
item: JsonDataItem;
}
export type SearchResults = SearchResult[];
const jsonData: JsonData = JsonData_;
class DataUtils {
static exists(name: string): boolean {
return jsonData.hasOwnProperty(name);
}
static search(params: SearchParams): SearchResults {
const results: SearchResults = [];
for (let name in jsonData) {
const item = jsonData[name];
if (item.pd < params.pdStart || params.pdEnd < item.pd) {
continue;
}
if (item.recordingVolume.width < params.widthMin || params.widthMax < item.recordingVolume.width) {
continue;
}
if (item.imagingDepth.from < params.depthMin || params.depthMax < item.imagingDepth.to) {
continue;
}
if (params.cellType !== "any") {
if (!item.cellType.includes(params.cellType as TCellType)) {
continue;
}
}
if (params.area !== "all" && item.area !== params.area) {
continue;
}
if (params.geneType !== "all" && item.geneType !== params.geneType) {
continue;
}
if (params.keyword.length !== 0 && !item.remark.includes(params.keyword)) {
continue;
}
results.push({ name, item });
}
return results;
}
}
export default DataUtils;

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.help {
margin: 10px;
}
.help p {
margin: 5px 15px 5px 15px;
}
.index {
margin: 0 0 16px 0;
padding-left: 30px;
}
.index li {
margin-bottom: 15px;
}
.search_links {
margin: 0 10px;
font-size: 75%;
text-align: right;
}
.search_links:after {
content: ".";
display: block;
height: 0;
font-size: 0;
clear: both;
visibility: hidden;
}
.search_links li {
display: inline-block;
}
.search_links li a {
display: block;
padding: 0 10px;
outline: none;
text-decoration: none;
}
.title {
font-weight: bold;
font-size: 100%;
margin: 5px;
}
.legend {
font-weight: bold;
margin-right: 5px;
}
.figure {
width: 100%;
margin: 15px 0;
text-align: center;
}
.figure img {
width: 320px;
}

210
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import React, { useEffect } from "react";
import { Link, Route, Routes } from "react-router-dom";
import { useAppDispatch } from "../../app/hooks";
import NotFound from "../not-found/NotFound";
import { setTitle } from "../page-title/pageTitleSlice";
import styles from "./Help.module.css";
const HelpIndex = () => {
const title = "Help";
const dispatch = useAppDispatch();
useEffect(() => {
dispatch(setTitle(title));
}, [dispatch, title]);
return (
<ul className={styles.index}>
<li>
<Link to="/help/search/1">Search datasets on your browser</Link>
</li>
<li>
<Link to="/help/dataset">Downloadable dataset format</Link>
</li>
<li>
<Link to="/help/viewer">3D Viewer Mannual</Link>
</li>
</ul>
);
};
const HelpSearchLinks = (
<div className={styles.search_links}>
<ul>
<li>
<Link to="/help/search/1">Step 1</Link>
</li>
<li>
<Link to="/help/search/2">Step 2</Link>
</li>
<li>
<Link to="/help/search/3">Step 3</Link>
</li>
<li>
<Link to="/help/search/4">Step 4</Link>
</li>
<li>
<Link to="/help/search/5">Step 5</Link>
</li>
</ul>
</div>
);
const HelpSearch1 = () => {
const title = "Help - Search dataset - Step 1";
const dispatch = useAppDispatch();
useEffect(() => {
dispatch(setTitle(title));
}, [dispatch, title]);
return (
<div>
{HelpSearchLinks}
<div className={styles.title}>Step 1</div>
<p>Click the "Search" link above.</p>
<div className={styles.figure}>
<img src="/images/help-search1.jpg" alt={title} />
</div>
</div>
);
};
const HelpSearch2 = () => {
const title = "Help - Search dataset - Step 2";
const dispatch = useAppDispatch();
useEffect(() => {
dispatch(setTitle(title));
}, [dispatch, title]);
return (
<div>
{HelpSearchLinks}
<div className={styles.title}>Step 2</div>
<p>Set parameter value and/or chose options.</p>
<div className={styles.figure}>
<img src="/images/help-search2.jpg" alt={title} />
</div>
</div>
);
};
const HelpSearch3 = () => {
const title = "Help - Search dataset - Step 3";
const dispatch = useAppDispatch();
useEffect(() => {
dispatch(setTitle(title));
}, [dispatch, title]);
return (
<div>
{HelpSearchLinks}
<div className={styles.title}>Step 3</div>
<p>Click the "Search" button.</p>
<div className={styles.figure}>
<img src="/images/help-search3.jpg" alt={title} />
</div>
</div>
);
};
const HelpSearch4 = () => {
const title = "Help - Search dataset - Step 4";
const dispatch = useAppDispatch();
useEffect(() => {
dispatch(setTitle(title));
}, [dispatch, title]);
return (
<div>
{HelpSearchLinks}
<div className={styles.title}>Step 4</div>
<p>Chose datasets that you want to download. Click dataset ID.</p>
<div className={styles.figure}>
<img src="/images/help-search4.jpg" alt={title} />
</div>
</div>
);
};
const HelpSearch5 = () => {
const title = "Help - Search dataset - Step 5";
const dispatch = useAppDispatch();
useEffect(() => {
dispatch(setTitle(title));
}, [dispatch, title]);
return (
<div>
{HelpSearchLinks}
<div className={styles.title}>Step 5</div>
<p>
The result page consists of details of the dataset.
<br />
Click the links in the "Download &amp; View" section to download the dataset and/or view 3D model on your browser.{" "}
</p>
<div className={styles.figure}>
<img src="/images/help-search5.jpg" alt={title} />
</div>
</div>
);
};
const HelpDataset = () => {
const title = "Help - Downloadable dataset format";
const dispatch = useAppDispatch();
useEffect(() => {
dispatch(setTitle(title));
}, [dispatch, title]);
return (
<section>
<div className={styles.title}>Dataset Format</div>
<div className={styles.figure}>
<img src="/images/help-dataset.jpg" alt={title} />
</div>
<p>
<span className={styles.legend}>First row:</span> The first row of the data file indicates the size of the imaging volume. The first, second and third column represent the width, height and depth of the volume, respectively.
</p>
<p>
<span className={styles.legend}>Other rows:</span> Each row consists of the type (first column) and the position (second to fourth columns for x, y and z position) of the cell.
</p>
</section>
);
};
const HelpViewer = () => {
const title = "Help - 3D Viewer Manual";
const dispatch = useAppDispatch();
useEffect(() => {
dispatch(setTitle(title));
}, [dispatch, title]);
return (
<section>
<div className={styles.title}>3D Viewer Manual</div>
<div className={styles.figure}>
<img src="/images/help-viewer.jpg" alt={title} />
</div>
<p>
<span className={styles.legend}>Rotate:</span> Left click and drag.
</p>
<p>
<span className={styles.legend}>Move:</span> Right click and drag.
</p>
<p>
<span className={styles.legend}>Zoom In/Out:</span> Use mouse wheel.
</p>
</section>
);
};
const Help: React.FC = () => {
return (
<div className={styles.help}>
<Routes>
<Route index element={<HelpIndex />} />
<Route path="search/1" element={<HelpSearch1 />} />
<Route path="search/2" element={<HelpSearch2 />} />
<Route path="search/3" element={<HelpSearch3 />} />
<Route path="search/4" element={<HelpSearch4 />} />
<Route path="search/5" element={<HelpSearch5 />} />
<Route path="dataset" element={<HelpDataset />} />
<Route path="viewer" element={<HelpViewer />} />
<Route path="*" element={<NotFound />} />
</Routes>
</div>
);
};
export default Help;

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.loading {
margin: 120px 0;
text-align: center;
}

15
src/features/loading/Loading.tsx Normal file
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import React, { useEffect } from "react";
import { useAppDispatch } from "../../app/hooks";
import { setTitle } from "../page-title/pageTitleSlice";
import styles from "./Loading.module.css";
const Loading: React.FC = () => {
const dispatch = useAppDispatch();
useEffect(() => {
dispatch(setTitle("Loading now..."));
}, [dispatch]);
return <div className={styles.loading}>Loading now...</div>;
};
export default Loading;

24
src/features/news/News.module.css Normal file
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.news {
margin: 10px;
}
.item {
margin: 0 10px 10px 10px;
}
.item:after {
content: ".";
display: block;
height: 0;
font-size: 0;
clear: both;
visibility: hidden;
}
.date {
width: 25%;
float: left;
text-align: left;
}
.desc {
width: 70%;
float: right;
text-align: left;
}

37
src/features/news/News.tsx Normal file
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import React, { useEffect } from "react";
import { useAppDispatch } from "../../app/hooks";
import JsonNews_ from "../../assets/news.json";
import { setTitle } from "../page-title/pageTitleSlice";
import styles from "./News.module.css";
const nl2br = require("react-nl2br");
interface IJsonNewsItem {
date: string;
desc: string;
}
type IJsonNews = IJsonNewsItem[];
const JsonNews: IJsonNews = JsonNews_;
const News: React.FC = () => {
const dispatch = useAppDispatch();
useEffect(() => {
dispatch(setTitle("What's new"));
}, [dispatch]);
return (
<div className={styles.news}>
{JsonNews.map((item, key) => {
return (
<div className={styles.item} key={key}>
<div className={styles.date}>{item.date}</div>
<div className={styles.desc}>{nl2br(item.desc)}</div>
</div>
);
})}
</div>
);
};
export default News;

4
src/features/not-found/NotFound.module.css Normal file
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.notFound {
margin: 120px 0;
text-align: center;
}

15
src/features/not-found/NotFound.tsx Normal file
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import React, { useEffect } from "react";
import { useAppDispatch } from "../../app/hooks";
import { setTitle } from "../page-title/pageTitleSlice";
import styles from "./NotFound.module.css";
const NotFound: React.FC = () => {
const dispatch = useAppDispatch();
useEffect(() => {
dispatch(setTitle("Page Not Found"));
}, [dispatch]);
return <div className={styles.notFound}>Page not found.</div>;
};
export default NotFound;

6
src/features/page-title/PageTitle.module.css Normal file
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.pageTitle {
width: 100%;
height: 30px;
font-size: 150%;
margin-bottom: 10px;
}

19
src/features/page-title/PageTitle.tsx Normal file
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import React from "react";
import { Helmet } from "react-helmet-async";
import { useAppSelector } from "../../app/hooks";
import styles from "./PageTitle.module.css";
import { selectPageTitle } from "./pageTitleSlice";
const PageTitle: React.FC = () => {
const title = useAppSelector(selectPageTitle);
return (
<>
<Helmet>
<title>{title} - CelLoc3D Server</title>
</Helmet>
<div className={styles.pageTitle}>{title}</div>
</>
);
};
export default PageTitle;

25
src/features/page-title/pageTitleSlice.ts Normal file
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import { createSlice, PayloadAction } from "@reduxjs/toolkit";
import { RootState } from "../../app/store";
export interface PageTitleState {
value: string;
}
const initialState: PageTitleState = {
value: "",
};
const pageTitleSlice = createSlice({
name: "pageTitle",
initialState,
reducers: {
setTitle: (state, action: PayloadAction<string>) => {
state.value = action.payload;
},
},
});
export const { setTitle } = pageTitleSlice.actions;
export const selectPageTitle = (state: RootState) => state.pageTitle.value;
export default pageTitleSlice.reducer;

41
src/features/search-form/SearchForm.module.css Normal file
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.formGroup {
margin: 0 10px;
height: 40px;
}
.formGroup:after {
content: ".";
display: block;
height: 0;
font-size: 0;
clear: both;
visibility: hidden;
}
.formGroup label {
width: 55%;
float: left;
}
.value {
float: right;
text-align: right;
}
.range {
margin: 0 10px;
}
.txtParam {
width: 50px;
}
.txtParamStr {
width: 100px;
}
.txtKeyword {
width: 150px;
}
.selParam {
width: 150px;
}
.submit {
text-align: center;
}
.submit input {
padding: 5px 15px;
}

198
src/features/search-form/SearchForm.tsx Normal file
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import React, { Component } from "react";
import { useNavigate } from "react-router-dom";
import { useAppDispatch } from "../../app/hooks";
import DataUtils, { SearchResults } from "../data/DataUtils";
import { setTitle } from "../page-title/pageTitleSlice";
import { setResults } from "../search-results/searchResultsSlice";
import styles from "./SearchForm.module.css";
interface FCProps {}
interface Props extends FCProps {
navigate: any;
dispatch: any;
}
interface State {
pdStart: string;
pdEnd: string;
widthMin: string;
widthMax: string;
depthMin: string;
depthMax: string;
cellType: string;
area: string;
geneType: string;
keyword: string;
}
class SearchForm extends Component<Props, State> {
constructor(props: Props) {
super(props);
this.state = {
pdStart: "44",
pdEnd: "100",
widthMin: "317",
widthMax: "512",
depthMin: "90",
depthMax: "230",
cellType: "any",
area: "all",
geneType: "all",
keyword: "",
};
this.handleInputChange = this.handleInputChange.bind(this);
this.handleSelectChange = this.handleSelectChange.bind(this);
this.handleSubmit = this.handleSubmit.bind(this);
}
componentDidMount() {
this.props.dispatch(setTitle("Database Search"));
}
doSearch(): SearchResults {
const toNumber = (v: string): number => parseInt(v.trim(), 10);
const params = {
pdStart: toNumber(this.state.pdStart),
pdEnd: toNumber(this.state.pdEnd),
widthMin: toNumber(this.state.widthMin),
widthMax: toNumber(this.state.widthMax),
depthMin: toNumber(this.state.depthMin),
depthMax: toNumber(this.state.depthMax),
cellType: this.state.cellType.trim(),
area: this.state.area.trim(),
geneType: this.state.geneType.trim(),
keyword: this.state.keyword.trim(),
};
return DataUtils.search(params);
}
handleInputChange: React.ChangeEventHandler<HTMLInputElement> = (event: React.ChangeEvent<HTMLInputElement>) => {
const target = event.target;
const value = target.value;
const name = target.name;
switch (name) {
case "pdStart":
this.setState({ pdStart: value });
break;
case "pdEnd":
this.setState({ pdStart: value });
break;
case "widthMin":
this.setState({ widthMin: value });
break;
case "widthMax":
this.setState({ widthMax: value });
break;
case "depthMin":
this.setState({ depthMin: value });
break;
case "depthMax":
this.setState({ depthMax: value });
break;
case "cellType":
this.setState({ cellType: value });
break;
case "keyword":
this.setState({ keyword: value });
break;
}
};
handleSelectChange: React.ChangeEventHandler<HTMLSelectElement> = (event: React.ChangeEvent<HTMLSelectElement>) => {
const target = event.target;
const value = target.value;
const name = target.name;
switch (name) {
case "area":
this.setState({ area: value });
break;
case "geneType":
this.setState({ geneType: value });
break;
}
};
handleSubmit: React.FormEventHandler<HTMLFormElement> = (event: React.FormEvent) => {
event.preventDefault();
const results = this.doSearch();
this.props.dispatch(setResults(results));
this.props.navigate("/search/results");
};
render() {
return (
<form onSubmit={this.handleSubmit}>
<div className={styles.formGroup}>
<label htmlFor="pdStart">Postnatal Days</label>
<div className={styles.value}>
<input type="number" name="pdStart" className={styles.txtParam} value={this.state.pdStart} onChange={this.handleInputChange} />
<span className={styles.range}>-</span>
<input type="number" name="pdEnd" className={styles.txtParam} value={this.state.pdEnd} onChange={this.handleInputChange} />
</div>
</div>
<div className={styles.formGroup}>
<label htmlFor="widthMin">Recording volume width (height)</label>
<div className={styles.value}>
<input type="number" name="widthMin" className={styles.txtParam} value={this.state.widthMin} onChange={this.handleInputChange} />
<span className={styles.range}>-</span>
<input type="number" name="widthMax" className={styles.txtParam} value={this.state.widthMax} onChange={this.handleInputChange} />
</div>
</div>
<div className={styles.formGroup}>
<label htmlFor="depthMin">Recording volume depth</label>
<div className={styles.value}>
<input type="number" name="depthMin" className={styles.txtParam} value={this.state.depthMin} onChange={this.handleInputChange} />
<span className={styles.range}>-</span>
<input type="number" name="depthMax" className={styles.txtParam} value={this.state.depthMax} onChange={this.handleInputChange} />
</div>
</div>
<div className={styles.formGroup}>
<label htmlFor="cellType">Cell type (E, I, G, P, S, or "any")</label>
<div className={styles.value}>
<input type="text" name="cellType" className={styles.txtParamStr} value={this.state.cellType} onChange={this.handleInputChange} />
</div>
</div>
<div className={styles.formGroup}>
<label htmlFor="area">Target area</label>
<div className={styles.value}>
<select name="area" className={styles.selParam} value={this.state.area} onChange={this.handleSelectChange}>
<option value="all">All</option>
<option value="L2/3, V1">L2/3 in the visual cortex</option>
</select>
</div>
</div>
<div className={styles.formGroup}>
<label htmlFor="geneType">Mouse line</label>
<div className={styles.value}>
<select name="geneType" className={styles.selParam} value={this.state.geneType} onChange={this.handleSelectChange}>
<option value="all">All</option>
<option value="VGAT-Venus">VGAT-Venus</option>
<option value="PV/myrGFP-LDLRct">PV/myrGFP-LDLRct</option>
<option value="Dlx5/6-GCaMP3">Dlx5/6-GCaMP3</option>
</select>
</div>
</div>
<div className={styles.formGroup}>
<label htmlFor="keyword">Keyword Search</label>
<div className={styles.value}>
<input type="text" name="keyword" className={styles.txtKeyword} value={this.state.keyword} onChange={this.handleInputChange} />
</div>
</div>
<div className={styles.formGroup}>
<div className={styles.submit}>
<input type="submit" value="Search" />
</div>
</div>
</form>
);
}
}
const SearchFormFC: React.FC<FCProps> = (props: FCProps) => {
const navigate = useNavigate();
const dispatch = useAppDispatch();
return <SearchForm navigate={navigate} dispatch={dispatch} />;
};
export default SearchFormFC;

17
src/features/search-results/SearchResults.module.css Normal file
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.empty,
.error {
margin: 120px 0;
text-align: center;
}
.error {
color: red;
}
.result {
margin: 10px 10px 20px 10px;
}
.title {
font-size: 105%;
}
.remark {
margin: 5px 5px 0 10px;
}

37
src/features/search-results/SearchResults.tsx Normal file
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import React, { useEffect } from "react";
import { Link } from "react-router-dom";
import { useAppDispatch, useAppSelector } from "../../app/hooks";
import { setTitle } from "../page-title/pageTitleSlice";
import styles from "./SearchResults.module.css";
import { selectSearchResults } from "./searchResultsSlice";
const SearchResults: React.FC = () => {
const results = useAppSelector(selectSearchResults);
const dispatch = useAppDispatch();
useEffect(() => {
dispatch(setTitle("Search Results"));
}, [dispatch]);
return (
<div>
{results.length === 0 ? (
<div className={styles.empty}>No search results found.</div>
) : (
results.map((result, key) => {
return (
<div className={styles.result} key={key}>
<div className={styles.title}>
<Link to={`/data/${result.name}`}>
{key + 1}. {result.name}
</Link>
</div>
<div className={styles.remark}>{result.item.remark}</div>
</div>
);
})
)}
</div>
);
};
export default SearchResults;

26
src/features/search-results/searchResultsSlice.ts Normal file
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import { createSlice, PayloadAction } from "@reduxjs/toolkit";
import { RootState } from "../../app/store";
import { SearchResults } from "../data/DataUtils";
export interface SearchResultsState {
value: SearchResults;
}
const initialState: SearchResultsState = {
value: [],
};
const searchResultsSlice = createSlice({
name: "searchResults",
initialState,
reducers: {
setResults: (state, action: PayloadAction<SearchResults>) => {
state.value = action.payload;
},
},
});
export const { setResults } = searchResultsSlice.actions;
export const selectSearchResults = (state: RootState) => state.searchResults.value;
export default searchResultsSlice.reducer;

3
src/features/search/Search.module.css Normal file
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.search {
margin: 10px;
}

20
src/features/search/Search.tsx Normal file
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import React from "react";
import { Route, Routes } from "react-router-dom";
import NotFound from "../not-found/NotFound";
import SearchForm from "../search-form/SearchForm";
import SearchResults from "../search-results/SearchResults";
import styles from "./Search.module.css";
const Search: React.FC = () => {
return (
<div className={styles.search}>
<Routes>
<Route index element={<SearchForm />} />
<Route path="results" element={<SearchResults />} />
<Route path="*" element={<NotFound />} />
</Routes>
</div>
);
};
export default Search;

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src/index.css Normal file
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@import-normalize;
body {
margin: 0;
padding: 0;
font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", "Roboto", "Oxygen", "Ubuntu", "Cantarell", "Fira Sans", "Droid Sans", "Helvetica Neue", sans-serif;
-webkit-font-smoothing: antialiased;
-moz-osx-font-smoothing: grayscale;
}
code {
font-family: source-code-pro, Menlo, Monaco, Consolas, "Courier New", monospace;
}

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