curated matches

package.json

@@ -1,13 +1,15 @@
 {
   "name": "neuronbridge",
-  "version": "3.4.0",
+  "version": "3.5.0",
   "private": true,
   "dependencies": {
     "@ant-design/icons": "^5.1.4",
     "@babel/eslint-parser": "^7.22.7",
     "@fortawesome/fontawesome-svg-core": "^6.4.0",
     "@fortawesome/free-brands-svg-icons": "^6.4.0",
+    "@fortawesome/free-solid-svg-icons": "^7.2.0",
     "@fortawesome/pro-regular-svg-icons": "^6.4.0",
+    "@fortawesome/pro-solid-svg-icons": "^6.7.1",
     "@fortawesome/react-fontawesome": "^0.2.0",
     "@testing-library/cypress": "^10.0.1",
     "@testing-library/jest-dom": "^5.16.5",

public/RELEASENOTES.md

@@ -1,3 +1,44 @@
+## VERSION 3.5.0 - 2026-04-17
+
+### Major Features
+
+  - **Curated Matches of Split-GAL4 Lines to Cell Types**: Search results now include a curated matches section that displays expert-annotated associations between Split-GAL4 lines and cell types
+    - Results are shown in a collapsible, paginated table with confidence level (Confident/Candidate), anatomical region, and source columns
+    - Curated matches appear above computed matches with a bookmark indicator when results are available
+    - See the [Curated Results section of the help page](/help#curated_results) for details on confidence levels and data sources.
+
+  - **Line Name Links**: Line names in search result metadata are now clickable links that navigate to a new search for that line
+
+### UI/UX Improvements
+
+  - **Updated Search Examples**: The example search terms have been refreshed to showcase curated matches functionality
+  - **Help Documentation**: Added a new help section explaining the curated matches feature
+
+---
+
+## VERSION 3.4.0 - 2026-04-17
+
+### Major Features
+
+  - **Aligned Volume Download for Custom Searches**: Custom search results now include a download link for the aligned volume, making it easier to retrieve aligned data for further analysis
+    - The "View in 3D" button is now available for custom uploads when an aligned volume exists
+
+  - **Searched Libraries Display**: The Color Depth Search step now shows which libraries were searched along with result counts, providing better visibility into search coverage
+
+### UI/UX Improvements
+
+  - **External Links Open in New Tabs**: All links to external sources now open in a new tab, preventing users from losing their place on the site
+
+### Bug Fixes & Improvements
+
+  - **Search & Navigation**:
+    - Improved search result filtering and duplicate removal logic
+    - Fixed external EM links to use id instead of library
+    - Fixed the "View" button to be clickable anywhere on the button area
+    - Updated search examples for accuracy
+
+---
+
 ## VERSION 3.3.1 - 2024-09-22
 
 ### Major Features

src/App.css

@@ -74,3 +74,11 @@ body {
   list-style: none;
   padding: 0;
 }
+
+/* hides the anchor offset on any page that needs it */
+.anchorOffset {
+  display: block;
+  position: relative;
+  top: -80px;
+  visibility: hidden;
+}

src/components/CuratedResults.jsx

@@ -0,0 +1,83 @@
+import PropTypes from "prop-types";
+import { Table, Typography } from "antd";
+import { Link } from "react-router-dom";
+
+const { Paragraph } = Typography;
+
+const columns = [
+  {
+    title: "Line Name",
+    dataIndex: "name",
+    key: "name",
+    render: (name) => <Link to={`/search?q=${name}`}>{name}</Link>,
+  },
+  {
+    title: "Confidence",
+    dataIndex: "confidence",
+    key: "confidence",
+  },
+  {
+    title: "Anatomical Region",
+    dataIndex: "anatomicalRegion",
+    key: "anatomicalRegion",
+  },
+  {
+    title: "Source",
+    dataIndex: "source",
+    key: "source",
+  },
+  {
+    title: "Cell Type / Neuron ID",
+    dataIndex: "matched",
+    key: "matched",
+    // if the match is a cell type, then we add a wildcard to the search
+    // to get all the sub cell types.
+    render: (matched, row) => <Link to={`/search?q=${matched}${row.addWildard}`}>{matched}</Link>,
+  },
+];
+
+export default function CuratedResults({ results, loadError }) {
+  // if we didn't find anything, then don't display anything.
+  if (results.length === 0) {
+    return null;
+  }
+
+  let pagination = {
+    position: ["bottomLeft"],
+    pageSizeOptions: ["2", "5", "10", "15", "20"],
+    defaultPageSize: 2,
+    showSizeChanger: true,
+    showQuickJumper: true
+  };
+
+  if (results.length < 3) {
+    pagination = false;
+  }
+
+  if (loadError) {
+    return (
+      <>
+        <Paragraph type="danger">
+          There was a problem retrieving the curated matches.
+        </Paragraph>
+        <Paragraph>Reloading the page may resolve the issue.</Paragraph>
+        <Paragraph>
+          If this problem persists, please contact us at{" "}
+          <a href="mailto:neuronbridge@janelia.hhmi.org">
+            neuronbridge@janelia.hhmi.org
+          </a>
+          . Please provide the search term used and any other relevant details.
+        </Paragraph>
+      </>
+    );
+  }
+
+  return (
+    <Table columns={columns} dataSource={results} pagination={pagination} />
+  );
+}
+
+CuratedResults.propTypes = {
+  results: PropTypes.arrayOf(PropTypes.object).isRequired,
+  loadError: PropTypes.bool.isRequired,
+};

src/components/Help/HelpButton.jsx

@@ -6,10 +6,17 @@ import { AppContext } from "../../containers/AppContext";
 export default function HelpButton({target, text, onClick}) {
   const { appState, setAppState } = useContext(AppContext);
 
-  const handleHelp = () => {
+  const handleHelp = (event) => {
+    // call the onClick callback if it is provided
     if (onClick) {
-      onClick();
+      onClick(event);
     }
+    // Toggle help if the button is clicked again
+    if (appState.helpTarget === target) {
+      setAppState({ ...appState, showHelp: !appState.showHelp });
+      return;
+    }
+    // Show help for the target
     setAppState({ ...appState, showHelp: true, helpTarget: target });
   }
 

src/components/Help/HelpContents.jsx

@@ -34,29 +34,24 @@ export default function HelpContents({ scroll }) {
     SearchInput: useRef(),
     UploadAlignment: useRef(),
     UploadSearch: useRef(),
+    CuratedResults: useRef(),
   };
 
   // use Effect to scroll to target set in the appState?
   useEffect(() => {
     if (scroll) {
-      if (refLookup[appState.helpTarget]) {
-        if (refLookup[appState.helpTarget].current) {
-          helpContentRef.current.parentElement.scrollTop =
-            refLookup[appState.helpTarget].current.offsetTop - 60;
-          refLookup[appState.helpTarget].current.classList.add("highlighted");
-          window.setTimeout(() => {
-            if (
-              refLookup[appState.helpTarget] &&
-              refLookup[appState.helpTarget].current
-            ) {
-              refLookup[appState.helpTarget].current.classList.remove(
-                "highlighted"
-              );
-            }
-          }, 3000);
+      const observer = new IntersectionObserver(([entry]) => {
+        if (entry.isIntersecting) {
+          refLookup[appState.helpTarget].current.scrollIntoView({ behavior: "instant" });
+          observer.disconnect();
         }
+      });
+      observer.observe(helpContentRef.current);
+      return () => {
+        observer.disconnect();
       }
     }
+    return () => {};
   }, [appState.helpTarget, refLookup, scroll]);
 
   const handleResultsPerLine = (count) => {
@@ -325,6 +320,33 @@ export default function HelpContents({ scroll }) {
         </p>
       </div>
       <Divider />
+      <a
+        ref={refLookup.CuratedResults}
+        className="anchorOffset"
+        id="curated_results"
+        href="#curated_results"
+      >
+        #curated_results
+      </a>
+      <Title level={3}>Curated Results</Title>
+      <p>
+      Curated results are based on human evaluations of EM cell types labeled in LM images of split-GAL4 lines. In general they should be more accurate than the average NeuronBridge image search hit. The name of the primary person evaluating the cell type is listed. 
+      </p>
+      <p>
+      Curated results come from two sources:
+      <ul>
+        <li>Annotations generated as part of split-GAL4 publications, and included with releases posted to <a href="https://splitgal4.janelia.org">https://splitgal4.janelia.org</a>.</li>
+        <li>Scoring of PatchPerPixMatch EM search results for a subset of the cell type lines published in <a href="https://doi.org/10.7554/elife.98405.3">Meissner et al., 2025</a>. These scores and additional details may be published in a forthcoming standalone paper or addendum to the above paper.</li>
+      </ul>
+
+      Results have one of three confidence levels: 
+      <ul>
+        <li>Confident: &gt;95% confidence, based on detailed examination of all potential associations, similar to criteria for publication.</li>
+        <li>Probable: 70-95% confidence, an association that seems correct but has not been as fully validated.</li>
+        <li>Candidate: 30-70% confidence, where more work is needed for validation and there are often multiple candidates.</li>
+      </ul>
+      </p>
+      <Divider />
       <a
         ref={refLookup.UploadAlignment}
         className="anchorOffset"

src/components/HelpPage.css

@@ -12,9 +12,4 @@
   }
 }
 
-.anchorOffset {
-  display: block;
-  position: relative;
-  top: -80px;
-  visibility: hidden;
-}
+

src/components/LineMeta.jsx

@@ -54,7 +54,7 @@ export default function LineMeta({ attributes, compact, fromSearch }) {
     return (
       <p>
         <b>Line Name: </b>
-        <span>{publishedName}</span>
+        <Link to={`/search?q=${publishedName}`}>{publishedName}</Link>
       </p>
     );
   }
@@ -64,7 +64,7 @@ export default function LineMeta({ attributes, compact, fromSearch }) {
       <Col md={24} lg={12}>
         <p>
           <b>Line Name: </b>
-          <span>{publishedName}</span>
+          <Link to={`/search?q=${publishedName}`}>{publishedName}</Link>
         </p>
         {attributes.normalizedScore ? (
           <p>

src/components/References.jsx

@@ -188,7 +188,7 @@ export default function References() {
 
       <dt>Raw (uncurated) Split-GAL4 Lines</dt>
       <dd>
-        <a href="https://doi.org/10.1101/2024.01.09.574419" target="_blank" rel="noopener noreferrer">Meissner et al., 2024 <FontAwesomeIcon icon={faExternalLink} size="xs" /></a>
+        <a href="https://doi.org/10.7554/elife.98405.3" target="_blank" rel="noopener noreferrer">Meissner et al., 2025 <FontAwesomeIcon icon={faExternalLink} size="xs" /></a>
       </dd>
 
       <dt>FlyWire</dt>

src/components/ScrollToTopOnMount.jsx

@@ -2,6 +2,14 @@ import { useEffect } from "react";
 
 function ScrollToTopOnMount() {
   useEffect(() => {
+    const { hash } = window.location;
+    if (hash) {
+      const element = document.getElementById(hash.slice(1));
+      if (element) {
+        element.scrollIntoView();
+        return;
+      }
+    }
     window.scrollTo(0, 0);
   }, []);
 

src/components/Search.jsx

@@ -24,14 +24,14 @@ function Search() {
       if (!searchTerm) {
         return;
       }
-      if (searchTerm.length < 3) {
+      if (searchTerm.length < 2) {
         message.error({
           duration: 0,
-          content: "Searches must have a minimum of 3 characters.",
+          content: "Searches must have a minimum of 2 characters.",
           key: "searchminimum",
           onClick: () => message.destroy("searchminimum"),
         });
-        setResults({ error: "Searches must have a minimum of 3 characters." });
+        setResults({ error: "Searches must have a minimum of 2 characters." });
         return;
       }
       if (searchTerm.match(/\*(\*|\.)\*/)) {