From 8408b6a869857073042db98cd01d92b03e52124a Mon Sep 17 00:00:00 2001 From: Jody Clements Date: Thu, 18 Dec 2025 09:17:32 -0500 Subject: [PATCH 1/2] feat: All links to external sources now open in a new tab. --- src/components/About.jsx | 10 +- src/components/Admin.jsx | 2 +- src/components/DevSiteBanner.jsx | 2 +- src/components/ExternalLink.jsx | 8 +- src/components/Help/HelpContents.jsx | 14 +-- src/components/HelpPage.jsx | 10 +- src/components/ImageCollections.jsx | 2 +- src/components/Landing.jsx | 24 ++--- src/components/MatchModal/Citations.jsx | 2 +- src/components/MatchModal/Download3D.jsx | 6 +- src/components/NoSearch.jsx | 6 +- src/components/References.jsx | 120 +++++++++++------------ 12 files changed, 104 insertions(+), 102 deletions(-) diff --git a/src/components/About.jsx b/src/components/About.jsx index c9c762a4..7290d6ae 100644 --- a/src/components/About.jsx +++ b/src/components/About.jsx @@ -16,8 +16,8 @@ export default function About() { quick to look up by identifier. You can also upload your own data and match it against these public data sets. - More information about the software infrastructure is available in our published paper and {" "} - AWS blog post. + More information about the software infrastructure is available in our published paper and {" "} + AWS blog post. @@ -69,7 +69,7 @@ export default function About() { Release Notes @@ -86,13 +86,13 @@ export default function About() { Site Feedback Survey Please take a moment to fill out our{" "} - site feedback survey. + site feedback survey. Source Code You can find all of the code for this website and the supporting infrastructure in our{" "} - GitHub repositories. + GitHub repositories. diff --git a/src/components/Admin.jsx b/src/components/Admin.jsx index efaef05a..8b23ff51 100644 --- a/src/components/Admin.jsx +++ b/src/components/Admin.jsx @@ -34,7 +34,7 @@ export default function Admin() { return ( <>

Admin Page

- + Custom search admin site

Bearer token:

diff --git a/src/components/DevSiteBanner.jsx b/src/components/DevSiteBanner.jsx index fce4f198..0dc5390c 100644 --- a/src/components/DevSiteBanner.jsx +++ b/src/components/DevSiteBanner.jsx @@ -14,7 +14,7 @@ export default function DevSiteBanner() {

This is the development server. For the public release, please go to{" "} - prod | {" "} + prod | {" "} { appState.isAdmin ? ( /, name)}> + /, name)} target="_blank" rel="noopener noreferrer"> Virtual Fly Brain{" "} @@ -35,6 +35,8 @@ function FlyWireLink({ tag }) { href={flyWireUrl .replace(//, id) .replace(//, version.replace(/^v/, ""))} + target="_blank" + rel="noopener noreferrer" > FlyWire{" "} @@ -61,7 +63,7 @@ export default function ExternalLink({ id, isLM, library, publishedName }) { return ( <> - /, id)}> + /, id)} target="_blank" rel="noopener noreferrer"> {extName}{" "} @@ -137,7 +139,7 @@ export default function ExternalLink({ id, isLM, library, publishedName }) { <> { !library.match(/flywire_fafb/i) ? ( <> - + NeuPrint{" "}
) : ""} diff --git a/src/components/Help/HelpContents.jsx b/src/components/Help/HelpContents.jsx index af9c9672..24b74f52 100644 --- a/src/components/Help/HelpContents.jsx +++ b/src/components/Help/HelpContents.jsx @@ -179,7 +179,7 @@ export default function HelpContents({ scroll }) { Raw light microscopy (LM) data collected by FlyLight is transformed in several ways prior to matching using color depth MIP search ( - Otsuna et al., 2018). + Otsuna et al., 2018). To improve matches for denser MCFO data, the color depth MIP approach was extended in several ways (Otsuna, et al., in preparation). The data generation pipeline for LM images is shown @@ -188,7 +188,7 @@ export default function HelpContents({ scroll }) {

After images are aligned to a common template, we used direction selective local thresholding (DSLT;{" "} - + Kawase, et al., 2015 ) to generate a 3D segmentation and create a separate color depth @@ -204,7 +204,7 @@ export default function HelpContents({ scroll }) {

More details are available in the {" "} - + NeuronBridge paper . @@ -224,7 +224,7 @@ export default function HelpContents({ scroll }) {

The EM data sets were imaged and reconstructed by the FlyEM Project ( - + Scheffer, et al., 2020 ). After the imagery was registered to the JRC2018 template, we @@ -336,7 +336,7 @@ export default function HelpContents({ scroll }) { automatically registered to a standard color depth search alignment template. Currently, these are JRC2018_Unisex_20x_HR (Brain) and JRC2018_VNC_Unisex_40x_DS (VNC) both of which are derived from the{" "} - + JRC 2018 templates . @@ -351,7 +351,7 @@ export default function HelpContents({ scroll }) { The aligner provides an alignment score and a link to a verification movie. The verification movie allows you to visualize the aligned stack against the template. The alignment score is calculated as a{" "} - + Zero Mean Normalized Cross-Correlation (ZNCC) . @@ -424,7 +424,7 @@ export default function HelpContents({ scroll }) { This is unrecoverable in our system. You will need to use an alternative method to register your data. Once you have an aligned image stack, use the{" "} - + Color MIP Mask Search Fiji plugin {" "} to generate the aligned color depth MIPs and upload those for custom diff --git a/src/components/HelpPage.jsx b/src/components/HelpPage.jsx index 413679d8..8296274e 100644 --- a/src/components/HelpPage.jsx +++ b/src/components/HelpPage.jsx @@ -50,7 +50,7 @@ export default function HelpPage() { Downloading the data

You can download the{" "} - + Color-Depth MIPs {" "} for your own research. @@ -61,23 +61,23 @@ export default function HelpPage() { Programmatic API access

Access the images programmatically{" "} - + using the S3 API {" "} on AWS Open Data. The matches are also available on S3, in a{" "} - different bucket. + different bucket.

- You can also use Python API to access the matches and images using Python. + You can also use Python API to access the matches and images using Python.

#tools Third-party tools - neuronbridger - R + neuronbridger - R library for interacting with the NeuronBridge. diff --git a/src/components/ImageCollections.jsx b/src/components/ImageCollections.jsx index 0b33057b..6e36cae7 100644 --- a/src/components/ImageCollections.jsx +++ b/src/components/ImageCollections.jsx @@ -168,7 +168,7 @@ export default function ImageCollections() { const { id, refName } = doi; return ( - {refName} + {refName} {index < doisList.length - 1 ? ', ' : ''} ); diff --git a/src/components/Landing.jsx b/src/components/Landing.jsx index 1547ebc7..3b712e3c 100644 --- a/src/components/Landing.jsx +++ b/src/components/Landing.jsx @@ -41,13 +41,13 @@ function Landing(props) { Search light and electron microscopy data sets of the Drosophila nervous system provided by the{" "} - + FlyLight {" "} - and FlyEM{" "} + and FlyEM{" "} projects at{" "} - Janelia Research Campus, as well - as other public connectomic data sets. + Janelia Research Campus, as well + as other public connectomic data sets. You can find similar neurons based on shape regardless of data set. @@ -67,16 +67,16 @@ function Landing(props) { Light Microscopy
- FlyLight Generation 1 MCFO
- FlyLight Split-GAL4
- FlyLight Split-GAL4 Omnibus Broad
+ FlyLight Generation 1 MCFO
+ FlyLight Split-GAL4
+ FlyLight Split-GAL4 Omnibus Broad
Electron Microscopy
- FlyEM Male CNS
- FlyEM Hemibrain
- FlyEM MANC
- FlyWire Brain
+ FlyEM Male CNS
+ FlyEM Hemibrain
+ FlyEM MANC
+ FlyWire Brain
 @@ -85,7 +85,7 @@ function Landing(props) { search algorithms across image collections. You can also upload your own image to run a custom Color Depth MIP search (see About page). For NBLAST searching, try{" "} - Virtual Fly Brain. + Virtual Fly Brain. diff --git a/src/components/MatchModal/Citations.jsx b/src/components/MatchModal/Citations.jsx index 72d66adc..6a44a11e 100644 --- a/src/components/MatchModal/Citations.jsx +++ b/src/components/MatchModal/Citations.jsx @@ -40,7 +40,7 @@ export default function Citations({ match, mask, matchRank, matchesTotal }) {

Cite NeuronBridge

  • - + Clements et al., 2024
    • diff --git a/src/components/MatchModal/Download3D.jsx b/src/components/MatchModal/Download3D.jsx index 6be35ff6..9718e978 100644 --- a/src/components/MatchModal/Download3D.jsx +++ b/src/components/MatchModal/Download3D.jsx @@ -83,7 +83,7 @@ export default function Download3D(props) { )}

    For a 3D comparison with more features, use the{" "} - VVDViewer + VVDViewer desktop application.

    @@ -100,13 +100,13 @@ export default function Download3D(props) {
    1. Download the latest release of VVDViewer from{" "} - + https://github.com/JaneliaSciComp/VVDViewer/releases
    2. Usage instructions for VVDViewer can be found{" "} - here. + here.
    diff --git a/src/components/NoSearch.jsx b/src/components/NoSearch.jsx index 8b8693af..06071fb7 100644 --- a/src/components/NoSearch.jsx +++ b/src/components/NoSearch.jsx @@ -17,15 +17,15 @@ export default function NoSearch({ filters }) { Not sure what to search for? You can search for line names on the{" "} - Split-GAL4 or{" "} - + Split-GAL4 or{" "} + Generation 1 MCFO {" "} websites. Explore neurons on the{" "} - neuPrint website. + neuPrint website. Search Help

    diff --git a/src/components/References.jsx b/src/components/References.jsx index cab41c31..67a408b9 100644 --- a/src/components/References.jsx +++ b/src/components/References.jsx @@ -7,199 +7,199 @@ export default function References() {

    NeuronBridge
    - Clements et al., 2024 + Clements et al., 2024
    Neuron matching algorithms
    - Otsuna et al., 2018 + Otsuna et al., 2018
    - Hirsch et al., 2020 + Hirsch et al., 2020
    - Mais et al., 2021 + Mais et al., 2021
    Gen1 MCFO collection
    - Meissner et al., 2023 + Meissner et al., 2023
    EM Hemibrain
    - Scheffer et al., 2020 + Scheffer et al., 2020
    Gen1 GAL4 collections
    - Jenett et al., 2012; for Janelia Gen1 GAL4 + Jenett et al., 2012; for Janelia Gen1 GAL4
    - Tirian and Dickson, 2017; for VT Gen1 GAL4 + Tirian and Dickson, 2017; for VT Gen1 GAL4
    - Dionne et al., 2018; for Janelia hemidrivers + Dionne et al., 2018; for Janelia hemidrivers
    - Tirian and Dickson, 2017; for VT hemidrivers + Tirian and Dickson, 2017; for VT hemidrivers
    EM-LM unification template
    - Bogovic et al., 2020 + Bogovic et al., 2020
    Split-GAL4 Lines
    - Tuthill et al., 2013 + Tuthill et al., 2013
    - Aso et al., 2014 + Aso et al., 2014
    - Wu et al., 2016 + Wu et al., 2016
    - Hampel et al., 2015 + Hampel et al., 2015
    - Aso & Rubin, 2016 + Aso & Rubin, 2016
    - Robie et al., 2017 + Robie et al., 2017
    - Klapoetke et al., 2017 + Klapoetke et al., 2017
    - Namiki et al., 2018 + Namiki et al., 2018
    - Wolff & Rubin 2018 + Wolff & Rubin 2018
    - Dolan et al., 2019 + Dolan et al., 2019
    - Gao et al., 2019 + Gao et al., 2019
    - Wang et al., 2020 -
    + Wang et al., 2020 +
    - Morimoto et al., 2020 + Morimoto et al., 2020
    - Davis et al., 2020 + Davis et al., 2020
    - Wang et al., 2020 + Wang et al., 2020
    - Turner-Evans et al., 2020 + Turner-Evans et al., 2020
    - Wang et al., 2020 + Wang et al., 2020
    - Schretter et al., 2020 + Schretter et al., 2020
    - Feng et al., 2020 + Feng et al., 2020
    - Bogovic et al., 2020 + Bogovic et al., 2020
    - Mais et al., 2021 + Mais et al., 2021
    - Sterne et al., 2021 + Sterne et al., 2021
    - Namiki et al., 2022 + Namiki et al., 2022
    - Kind et al., 2021 + Kind et al., 2021
    - Hulse et al., 2021 + Hulse et al., 2021
    - Longden et al., 2021 + Longden et al., 2021
    - Klapoetke et al., 2022 + Klapoetke et al., 2022
    - Baker et al., 2022 + Baker et al., 2022
    - Cheong et al., 2023 + Cheong et al., 2023
    - Cheong et al., 2023 + Cheong et al., 2023
    - Ehrhardt et al., 2023 + Ehrhardt et al., 2023
    - Rubin & Aso, 2023 + Rubin & Aso, 2023
    - Minegishi, Ryo et al., 2023 + Minegishi, Ryo et al., 2023
    - Vijayan et al., 2023 + Vijayan et al., 2023
    - Yoo et al., 2023 + Yoo et al., 2023
    - Isaacson et al., 2023 + Isaacson et al., 2023
    - Lillvis et al., 2022 + Lillvis et al., 2022
    - Lillvis et al., 2023 + Lillvis et al., 2023
    - Meissner et al., 2024 + Meissner et al., 2024
    - Schretter et al., 2024 + Schretter et al., 2024
    - Gorko et al., 2024 + Gorko et al., 2024
    - Nern et al., 2024 + Nern et al., 2024
    - Wolff et al., 2024 + Wolff et al., 2024
    - Zung et al., 2025 + Zung et al., 2025
    Raw (uncurated) Split-GAL4 Lines
    - Meissner et al., 2024 + Meissner et al., 2024
    FlyWire
    - Dorkenwald et al., 2023 + Dorkenwald et al., 2023
    - Schlegel et al., 2023 + Schlegel et al., 2023
    Male CNS
    - Berg et al., 2025 + Berg et al., 2025
    From 8cf9ae5a3e727c5c802c5f5f6cc1b2d55e7a4fab Mon Sep 17 00:00:00 2001 From: Jody Clements Date: Thu, 18 Dec 2025 09:26:22 -0500 Subject: [PATCH 2/2] feat: Adds external link icon to all external links. --- src/components/About.jsx | 12 ++- src/components/Admin.jsx | 4 +- src/components/DevSiteBanner.jsx | 4 +- src/components/Help/HelpContents.jsx | 16 +-- src/components/HelpPage.jsx | 12 ++- src/components/ImageCollections.jsx | 4 +- src/components/Landing.jsx | 24 ++--- src/components/MatchModal/Citations.jsx | 4 +- src/components/MatchModal/Download3D.jsx | 8 +- src/components/NoSearch.jsx | 8 +- src/components/References.jsx | 120 ++++++++++++----------- 11 files changed, 119 insertions(+), 97 deletions(-) diff --git a/src/components/About.jsx b/src/components/About.jsx index 7290d6ae..8a1f3a1e 100644 --- a/src/components/About.jsx +++ b/src/components/About.jsx @@ -1,6 +1,8 @@ import React from "react"; import { Typography, Row, Col } from "antd"; import { Link } from "react-router-dom"; +import { faExternalLink } from "@fortawesome/pro-regular-svg-icons"; +import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; import References from "./References"; import config from "../config"; @@ -16,8 +18,8 @@ export default function About() { quick to look up by identifier. You can also upload your own data and match it against these public data sets. - More information about the software infrastructure is available in our published paper and {" "} - AWS blog post. + More information about the software infrastructure is available in our published paper and {" "} + AWS blog post . @@ -69,7 +71,7 @@ export default function About() { Release Notes @@ -86,13 +88,13 @@ export default function About() { Site Feedback Survey Please take a moment to fill out our{" "} - site feedback survey. + site feedback survey . Source Code You can find all of the code for this website and the supporting infrastructure in our{" "} - GitHub repositories. + GitHub repositories . diff --git a/src/components/Admin.jsx b/src/components/Admin.jsx index 8b23ff51..78e5a8b0 100644 --- a/src/components/Admin.jsx +++ b/src/components/Admin.jsx @@ -1,6 +1,8 @@ import React, { useState, useEffect, useContext } from "react"; import { Auth } from "aws-amplify"; import { Switch } from "antd"; +import { faExternalLink } from "@fortawesome/pro-regular-svg-icons"; +import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; import { AppContext } from "../containers/AppContext"; import AnnouncementsCreate from "./AnnouncementsCreate"; @@ -35,7 +37,7 @@ export default function Admin() { <>

    Admin Page

    - Custom search admin site + Custom search admin site

    Bearer token: