- 
                Notifications
    You must be signed in to change notification settings 
- Fork 4
Add Community Gallery section with resources and images #60
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
          
     Merged
      
        
      
    
  
     Merged
                    Changes from all commits
      Commits
    
    
            Show all changes
          
          
            14 commits
          
        
        Select commit
          Hold shift + click to select a range
      
      23a2890
              
                Add Community Gallery section with resources and images
              
              
                bendichter f470bb2
              
                Update community gallery with new brainmap image
              
              
                bendichter 629d89a
              
                Merge branch 'main' into port-community-gallery
              
              
                bendichter 095c0e0
              
                Merge branch 'main' into port-community-gallery
              
              
                rly 50113b2
              
                Merge branch 'main' into port-community-gallery
              
              
                bendichter 6e6ea5e
              
                Merge branch 'main' into port-community-gallery
              
              
                bendichter f25bbcd
              
                Update menus.yaml
              
              
                bendichter 59642b8
              
                Merge branch 'main' into port-community-gallery
              
              
                bendichter fb4685b
              
                Update content/community/gallery.md
              
              
                bendichter 05acec6
              
                Update content/community/gallery.md
              
              
                bendichter 73248d0
              
                Update content/community/gallery.md
              
              
                bendichter 0a3b6b2
              
                Merge branch 'main' into port-community-gallery
              
              
                bendichter 8f9451c
              
                Merge branch 'main' into port-community-gallery
              
              
                oruebel b452974
              
                Enhance Community Gallery layout and content
              
              
                bendichter File filter
Filter by extension
Conversations
          Failed to load comments.   
        
        
          
      Loading
        
  Jump to
        
          Jump to file
        
      
      
          Failed to load files.   
        
        
          
      Loading
        
  Diff view
Diff view
There are no files selected for viewing
  
    
      This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
      Learn more about bidirectional Unicode characters
    
  
  
    
              
  
    
      This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
      Learn more about bidirectional Unicode characters
    
  
  
    
              
  
    
      This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
      Learn more about bidirectional Unicode characters
    
  
  
    
              | Original file line number | Diff line number | Diff line change | 
|---|---|---|
| @@ -0,0 +1,4 @@ | ||
| --- | ||
| title: "Community" | ||
| weight: 5 | ||
| --- | 
  
    
      This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
      Learn more about bidirectional Unicode characters
    
  
  
    
              | Original file line number | Diff line number | Diff line change | 
|---|---|---|
| @@ -0,0 +1,57 @@ | ||
| --- | ||
| title: "Community Gallery" | ||
| weight: 1 | ||
| gallery_section: | ||
| enable: true | ||
| title: "Data Conversion" | ||
| content: "Tools and resources for converting data to NWB format" | ||
| boxes: | ||
| - title: "NeuroConv Catalog" | ||
| content: "A collection of real-world examples of labs using NeuroConv to convert their data to NWB files. Each project listed contains a description and a link to an open GitHub repository. Many of the projects listed use advanced customization features beyond what is demonstrated in the core NeuroConv conversion gallery." | ||
| image: "/images/community_gallery/neuroconv_gallery.png" | ||
| url: "https://neuroconv.readthedocs.io/en/stable/conversion_examples_gallery/index.html" | ||
| - title: "Bristol Neuroscience Data Guide" | ||
| content: "The Bristol Neuroscience Data Guide includes tutorials for converting data to NWB for extracellular electrophysiology data and optical physiology data using both the PyNWB and MatNWB APIs for NWB." | ||
| image: "/images/community_gallery/bristol_neuroscience_data_guide.png" | ||
| url: "https://dervinism.github.io/bristol-neuroscience-data-guide/tutorials/Bristol%20GIN%20for%20Silicon%20Probe%20Data.html" | ||
|  | ||
| analysis_section: | ||
| enable: true | ||
| title: "Data Analysis and Reuse" | ||
| content: "Examples and resources for analyzing and reusing NWB data" | ||
| boxes: | ||
| - title: "DANDI Example Notebooks" | ||
| content: "DANDI (Distributed Archives for Neurophysiology Data Integration) maintains a collection of example notebooks associated with datasets, conference tools, or more generally notebooks that illustrate the use of data on DANDI." | ||
| image: "/images/community_gallery/dandi_example_notebooks.png" | ||
| url: "https://github.com/dandi/example-notebooks" | ||
| - title: "OpenScope Databook" | ||
| content: "The OpenScope Databook provides scripts and documentation used for brain data analysis and visualization, primarily working with NWB files and the DANDI archive. Through Jupyter Book, this code is structured as a series of notebooks intended to explain and educate users on how to work with brain data." | ||
| image: "/images/community_gallery/openscope_databook.png" | ||
| url: "https://alleninstitute.github.io/openscope_databook/" | ||
| - title: "IBL Brain-wide Map" | ||
| content: "The International Brain Laboratory (IBL) released a Brainwide Map of neural activity during decision-making, consisting of 547 Neuropixel recordings of 32,784 neurons across 194 regions of the mouse brain. The IBL team provides tutorials on Using IBL data with NWB." | ||
| image: "/images/community_gallery/ibl_brainmap.png" | ||
| url: "https://colab.research.google.com/drive/1zr6lP_zzRgPZuHs3nB5oGnFtPKrduQ3L" | ||
| - title: "INCF MATLAB Examples" | ||
| content: "The INCF working group on NWB has created a library of MATLAB examples using DANDI datasets authored as MATLAB live scripts." | ||
| url: "https://github.com/INCF/example-live-scripts" | ||
| - title: "Neuromatch-AJILE12" | ||
| content: "A package for exploratory analysis of long-term naturalistic human intracranial neural recordings and pose data as part of Dandiset 000055." | ||
| url: "https://github.com/neurovium/Neuromatch-AJILE12" | ||
|  | ||
| publications_section: | ||
| enable: true | ||
| title: "Publications That Reuse NWB Data" | ||
| content: "The NWB team maintains a running database of publications that reuse publicly available NWB data, particularly from the DANDI Archive." | ||
| boxes: | ||
| - title: "NWB Data Reuse Publications" | ||
| content: "A collection of publications that reuse publicly available NWB data." | ||
| image: "/images/publications-citing.png" | ||
| url: "https://www.notion.so/rly1/8b1d1f08841e41b89fdd9ab21d486d31?v=99f8e0f855a5486b8fc521066b34d4b3" | ||
|  | ||
| disclaimer: | ||
| enable: true | ||
| content: "**Disclaimer:** Reference herein to any specific product, process, or service by its trade name, trademark, manufacturer, or otherwise, does not constitute or imply its endorsement, recommendation, or favoring by the NWB development team, United States Government or any agency thereof, or The Regents of the University of California. Use of the NeurodataWithoutBorders name for endorsements is prohibited." | ||
| --- | ||
|  | ||
| This page is a collection of community conversion and analysis projects cataloged here as a convenient reference for NWB users. This list is not comprehensive and many of the projects and resources are built and supported by other groups, and are in active development. | ||
  
    
      This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
      Learn more about bidirectional Unicode characters
    
  
  
    
              | Original file line number | Diff line number | Diff line change | 
|---|---|---|
| @@ -0,0 +1,35 @@ | ||
| {{ define "main" }} | ||
| {{/* Hero Section */}} | ||
| <section class="hero teamSect d-flex justify-content-center align-items-center position-relative" | ||
| style="background: radial-gradient(#063053e5, #062e52e5), url('/images/essentials/aboutBg.png');"> | ||
| <h1 class="inter-700 text-48 text-white text-center z-4">{{ .Title | markdownify }}</h1> | ||
| <div class="position-absolute ellipses"> | ||
| <img src="/images/essentials/ellipses.png" alt="" class="ellipseW"> | ||
| </div> | ||
| </section> | ||
| {{/* End Hero Section */}} | ||
|  | ||
| <section class="section bg-dark-100"> | ||
| <div class="container-lg"> | ||
| <div class="row"> | ||
| <div class="col-12"> | ||
| {{ .Content }} | ||
| </div> | ||
| <div class="col-12 mt-4"> | ||
| <div class="row g-4"> | ||
| {{ range .Pages }} | ||
| <div class="col-12 col-md-6 col-lg-4"> | ||
| <a href="{{ .Permalink }}" class="text-decoration-none"> | ||
| <div class="bg-white rounded-3 p-4 shadow-sm h-100"> | ||
| <h4 class="inter-700 text-24 dark-900 mb-3">{{ .Title }}</h4> | ||
| <p class="inter-400 text-16 dark-700">{{ .Summary }}</p> | ||
| </div> | ||
| </a> | ||
| </div> | ||
| {{ end }} | ||
| </div> | ||
| </div> | ||
| </div> | ||
| </div> | ||
| </section> | ||
| {{ end }} | 
  
    
      This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
      Learn more about bidirectional Unicode characters
    
  
  
    
              | Original file line number | Diff line number | Diff line change | 
|---|---|---|
| @@ -0,0 +1,148 @@ | ||
| {{ define "main" }} | ||
| <div class="community-gallery"> | ||
| {{/* Hero Section */}} | ||
| <section class="hero teamSect d-flex justify-content-center align-items-center position-relative" | ||
| style="background: radial-gradient(#063053e5, #062e52e5), url('/images/essentials/aboutBg.png');"> | ||
| <h1 class="inter-700 text-48 text-white text-center z-4">{{ .Title | markdownify }}</h1> | ||
| <div class="position-absolute ellipses"> | ||
| <img src="/images/essentials/ellipses.png" alt="" class="ellipseW"> | ||
| </div> | ||
| </section> | ||
| {{/* End Hero Section */}} | ||
|  | ||
| <section class="section bg-white"> | ||
| <div class="container-lg"> | ||
| <div class="row"> | ||
| <div class="col-12"> | ||
| {{ .Content }} | ||
| </div> | ||
| </div> | ||
| </div> | ||
| </section> | ||
|  | ||
| {{/* Data Conversion Section */}} | ||
| {{ with .Params.gallery_section }} | ||
| {{ if .enable }} | ||
| <section class="section bg-dark-100"> | ||
| <div class="container-lg"> | ||
| <h3 class="inter-700 text-40 dark-900 mb-3">{{ .title | markdownify }}</h3> | ||
| <p class="inter-400 text-16 dark-700 lh-base">{{ .content | markdownify }}</p> | ||
| <div class="row g-4 justify-content-center pt-4"> | ||
| {{ range .boxes }} | ||
| <div class="col-12 col-md-6"> | ||
| <div class="bg-white h-100 rounded-3 p-4 shadow-sm"> | ||
| <div class="d-flex flex-row"> | ||
| {{ if .image }} | ||
| <div class="me-4 flex-shrink-0"> | ||
| <a href="{{ .url }}" target="_blank"> | ||
| <img src="{{ .image }}" alt="{{ .title }}" class="rounded-3 gallery-card-image" style="width: 100px; height: 100px; object-fit: cover;" onerror="this.parentElement.parentElement.style.display='none';"> | ||
| </a> | ||
| </div> | ||
| {{ end }} | ||
| <div class="flex-grow-1"> | ||
| <a href="{{ .url }}" class="text-decoration-none" target="_blank"> | ||
| <h5 class="inter-700 text-18 dark-900 mb-2 text-decoration-underline">{{ .title | markdownify }}</h5> | ||
| </a> | ||
| <p class="inter-400 text-14 dark-700">{{ .content | markdownify }}</p> | ||
| </div> | ||
| </div> | ||
| </div> | ||
| </div> | ||
| {{ end }} | ||
| </div> | ||
| </div> | ||
| </section> | ||
| {{ end }} | ||
| {{ end }} | ||
| {{/* End Data Conversion Section */}} | ||
|  | ||
| {{/* Data Analysis Section */}} | ||
| {{ with .Params.analysis_section }} | ||
| {{ if .enable }} | ||
| <section class="section bg-white"> | ||
| <div class="container-lg"> | ||
| <h3 class="inter-700 text-40 dark-900 mb-3">{{ .title | markdownify }}</h3> | ||
| <p class="inter-400 text-16 dark-700 lh-base">{{ .content | markdownify }}</p> | ||
| <div class="row g-4 justify-content-center pt-4"> | ||
| {{ range .boxes }} | ||
| <div class="col-12 col-md-6"> | ||
| <div class="bg-dark-100 h-100 rounded-3 p-4 shadow-sm"> | ||
| <div class="d-flex flex-row"> | ||
| {{ if .image }} | ||
| <div class="me-4 flex-shrink-0"> | ||
| <a href="{{ .url }}" target="_blank"> | ||
| <img src="{{ .image }}" alt="{{ .title }}" class="rounded-3 gallery-card-image" style="width: 100px; height: 100px; object-fit: cover;" onerror="this.parentElement.parentElement.style.display='none';"> | ||
| </a> | ||
| </div> | ||
| {{ end }} | ||
| <div class="flex-grow-1"> | ||
| <a href="{{ .url }}" class="text-decoration-none" target="_blank"> | ||
| <h5 class="inter-700 text-18 dark-900 mb-2 text-decoration-underline">{{ .title | markdownify }}</h5> | ||
| </a> | ||
| <p class="inter-400 text-14 dark-700">{{ .content | markdownify }}</p> | ||
| </div> | ||
| </div> | ||
| </div> | ||
| </div> | ||
| {{ end }} | ||
| </div> | ||
| </div> | ||
| </section> | ||
| {{ end }} | ||
| {{ end }} | ||
| {{/* End Data Analysis Section */}} | ||
|  | ||
| {{/* Publications Section */}} | ||
| {{ with .Params.publications_section }} | ||
| {{ if .enable }} | ||
| <section class="section bg-dark-100"> | ||
| <div class="container-lg"> | ||
| <h3 class="inter-700 text-40 dark-900 mb-3">{{ .title | markdownify }}</h3> | ||
| <p class="inter-400 text-16 dark-700 lh-base">{{ .content | markdownify }}</p> | ||
| <div class="row g-4 justify-content-center pt-4"> | ||
| {{ range .boxes }} | ||
| <div class="col-12 col-md-6"> | ||
| <div class="bg-white h-100 rounded-3 p-4 shadow-sm"> | ||
| <div class="d-flex flex-row"> | ||
| <div class="me-4"> | ||
| <a href="{{ .url }}" target="_blank"> | ||
| <img src="{{ .image }}" alt="{{ .title }}" class="rounded-3" style="width: 100px; height: 100px; object-fit: cover;"> | ||
| </a> | ||
| </div> | ||
| <div class="flex-grow-1"> | ||
| <a href="{{ .url }}" class="text-decoration-none" target="_blank"> | ||
| <h5 class="inter-700 text-18 dark-900 mb-2 text-decoration-underline">{{ .title | markdownify }}</h5> | ||
| </a> | ||
| <p class="inter-400 text-14 dark-700">{{ .content | markdownify }}</p> | ||
| </div> | ||
| </div> | ||
| </div> | ||
| </div> | ||
| {{ end }} | ||
| </div> | ||
| </div> | ||
| </section> | ||
| {{ end }} | ||
| {{ end }} | ||
| {{/* End Publications Section */}} | ||
|  | ||
| {{/* Disclaimer Section */}} | ||
| {{ with .Params.disclaimer }} | ||
| {{ if .enable }} | ||
| <section class="section bg-white"> | ||
| <div class="container-lg"> | ||
| <div class="row"> | ||
| <div class="col-12"> | ||
| <div class="p-4 bg-light rounded-3"> | ||
| <p class="inter-400 text-14 dark-700 lh-base">{{ .content | markdownify }}</p> | ||
| </div> | ||
| </div> | ||
| </div> | ||
| </div> | ||
| </section> | ||
| {{ end }} | ||
| {{ end }} | ||
| {{/* End Disclaimer Section */}} | ||
|  | ||
| </div> | ||
| {{ end }} | 
      
      Loading
      
  Sorry, something went wrong. Reload?
      Sorry, we cannot display this file.
      Sorry, this file is invalid so it cannot be displayed.
      
    
      
      Loading
      
  Sorry, something went wrong. Reload?
      Sorry, we cannot display this file.
      Sorry, this file is invalid so it cannot be displayed.
      
    
      
      Loading
      
  Sorry, something went wrong. Reload?
      Sorry, we cannot display this file.
      Sorry, this file is invalid so it cannot be displayed.
      
    
      
      Loading
      
  Sorry, something went wrong. Reload?
      Sorry, we cannot display this file.
      Sorry, this file is invalid so it cannot be displayed.
      
    
      
      Loading
      
  Sorry, something went wrong. Reload?
      Sorry, we cannot display this file.
      Sorry, this file is invalid so it cannot be displayed.
      
    
      
      Oops, something went wrong.
        
    
  
  Add this suggestion to a batch that can be applied as a single commit.
  This suggestion is invalid because no changes were made to the code.
  Suggestions cannot be applied while the pull request is closed.
  Suggestions cannot be applied while viewing a subset of changes.
  Only one suggestion per line can be applied in a batch.
  Add this suggestion to a batch that can be applied as a single commit.
  Applying suggestions on deleted lines is not supported.
  You must change the existing code in this line in order to create a valid suggestion.
  Outdated suggestions cannot be applied.
  This suggestion has been applied or marked resolved.
  Suggestions cannot be applied from pending reviews.
  Suggestions cannot be applied on multi-line comments.
  Suggestions cannot be applied while the pull request is queued to merge.
  Suggestion cannot be applied right now. Please check back later.
  
    
  
    
Uh oh!
There was an error while loading. Please reload this page.