diff --git a/content/events/cosyne-2023.md b/content/events/cosyne-2023.md index d0e8877..b147f52 100644 --- a/content/events/cosyne-2023.md +++ b/content/events/cosyne-2023.md @@ -26,7 +26,7 @@ The [Neurodata Without Borders (NWB)](https://www.nwb.org/) team is holding a tu The DANDI Archive now has 100+ publicly available neurophysiology datasets stored using the NWB data standard. -The NWB project is an effort to standardize the description and storage of neurophysiology data and metadata. NWB enables data sharing and reuse and reduces the energy-barrier to applying data analytics both within and across labs. NWB is more than just a file format but it defines an [ecosystem](https://nwb-overview.readthedocs.io/en/latest/tools/tools_home.html) of tools, methods, and standards for storing, sharing, and analyzing complex neurophysiology data. +The NWB project is an effort to standardize the description and storage of neurophysiology data and metadata. NWB enables data sharing and reuse and reduces the energy-barrier to applying data analytics both within and across labs. NWB is more than just a file format but it defines an [ecosystem](https://nwb.org/nwb-software/) of tools, methods, and standards for storing, sharing, and analyzing complex neurophysiology data. ## What You'll Learn @@ -48,7 +48,7 @@ Bring your laptop to work along with the demonstration. To get familiar with NWB - **9:20 - 9:50**: How to analyze NWB data using popular data processing and visualization tools - Using [SpikeInterface](https://github.com/SpikeInterface/spikeinterface#spikeinterface-a-unified-framework-for-spike-sorting) to sort raw extracellular electrophysiology recording data streamed from DANDI & write the output back to NWB - Storing [DeepLabCut](http://www.mackenziemathislab.org/deeplabcut) and [SLEAP](https://sleap.ai/) pose estimation data in NWB - - Using calcium imaging analysis tools, such as [CaImAn](https://github.com/flatironinstitute/CaImAn#caiman) and [suite2p](https://www.suite2p.org/) to process and segment raw imaging data and write the output to NWB + - Using calcium imaging analysis tools, such as [CaImAn](https://github.com/flatironinstitute/CaImAn#caiman) and [suite2p](https://suite2p.readthedocs.io) to process and segment raw imaging data and write the output to NWB ## Survey diff --git a/content/events/hck04-2018-seattle.md b/content/events/hck04-2018-seattle.md index d4dcd9d..d1063a2 100644 --- a/content/events/hck04-2018-seattle.md +++ b/content/events/hck04-2018-seattle.md @@ -25,7 +25,7 @@ resources: ## Objective -The [Neurodata Without Borders: Neurophysiology](http://www.nwb.org/nwb-neurophysiology/) (NWB:N) Hackathon is a hands-on activity lasting several days in which neurophysiology researchers create solutions using the open source NWB:N software packages. +The [Neurodata Without Borders: Neurophysiology](http://www.nwb.org) (NWB:N) Hackathon is a hands-on activity lasting several days in which neurophysiology researchers create solutions using the open source NWB:N software packages. Participants work collaboratively on solutions that use the NWB unified data format for cellular-based neurophysiology data, which is focused on the dynamics of groups of neurons measured under a large range of experimental conditions. In contrast to conferences and workshops where the primary focus is to report results, the objective of the Hackathon is to provide a venue for creators and users of neurophysiology open-source software to collaboratively work on any related research projects. diff --git a/content/events/hck07-2020-seattle.md b/content/events/hck07-2020-seattle.md index aa1037f..69157cb 100644 --- a/content/events/hck07-2020-seattle.md +++ b/content/events/hck07-2020-seattle.md @@ -28,7 +28,7 @@ This event was centered around core NWB development, bringing together developer ## Logistics - **Hotel:** The Allen Institute organized a special rate at the Staybridge Suites, just 3 blocks from the institute. -- **Transportation:** Attendees were encouraged to use public transportation or park at a local garage. Additional details on getting to the Allen Institute are available [here](https://alleninstitute.org/events-training/getting-allen-institute/). +- **Transportation:** Attendees were encouraged to use public transportation or park at a local garage. Additional details on getting to the Allen Institute are available [here](https://alleninstitute.org/getting-to-the-allen-institute/). - **Food:** Lunch was provided at the Allen Institute. Breakfast and dinner were on attendees' own. ## Additional Organizational Support diff --git a/content/events/hck08-2020-remote.md b/content/events/hck08-2020-remote.md index 443a33a..a481be0 100644 --- a/content/events/hck08-2020-remote.md +++ b/content/events/hck08-2020-remote.md @@ -38,7 +38,7 @@ In contrast to conferences, where the primary focus is to report results, the ob * Create a project page with an outline for your workshop project. * Have example datasets that you need for your workshop project ready. For any lab-specific data (i.e., data not in NWB) you should know how to read the data using Python or MATLAB and ideally have scripts ready for reading the data. * Install the Python or MATLAB software for NWB: - * PyNWB (Python): [https://pynwb.readthedocs.io/en/stable/getting_started.html](https://pynwb.readthedocs.io/en/stable/getting_started.html) + * PyNWB (Python): [https://pynwb.readthedocs.io](https://pynwb.readthedocs.io) * MatNWB (MATLAB): [https://neurodatawithoutborders.github.io/matnwb/](https://neurodatawithoutborders.github.io/matnwb/) * For an overview of NWB, see also: [https://www.nwb.org/](https://www.nwb.org/) diff --git a/content/events/hck15-2023-janelia.md b/content/events/hck15-2023-janelia.md index ac6cac1..5daef3f 100644 --- a/content/events/hck15-2023-janelia.md +++ b/content/events/hck15-2023-janelia.md @@ -69,11 +69,11 @@ resources: data not in NWB), you should know how to read the data using Python or MATLAB and ideally have scripts ready for reading the data. * Bring your laptop with appropriate software installed. For installation instructions see: - * [**PyNWB (Python)**](https://pynwb.readthedocs.io/en/stable/install_users.html). If you are a developer and want to contribute to PyNWB see the [**Installing PyNWB for Developers**](https://pynwb.readthedocs.io/en/stable/install_developers.html) instructions. - * [**MatNWB (Matlab)**](https://neurodatawithoutborders.github.io/matnwb/) + * [**PyNWB (Python)**](https://pynwb.readthedocs.io). If you are a developer and want to contribute to PyNWB see the [**Installing PyNWB for Developers**](https://pynwb.readthedocs.io/en/stable/install_developers.html) instructions. + * [**MatNWB (Matlab)**](https://matnwb.readthedocs.io) * For an overview of NWB software, see also: - * [**Glossary of Core NWB Tools**](https://nwb-overview.readthedocs.io/en/latest/core_tools/core_tools_home.html) - * [**Glossary of Analysis and Visualization Tools**](https://nwb-overview.readthedocs.io/en/latest/tools/tools_home.html) + * [**Glossary of Core NWB Tools**](https://nwb.org/tools/core/) + * [**Glossary of Analysis and Visualization Tools**](https://nwb.org/tools/analysis/) * For an overview of NWB see the [**NWB Overview Docs**](https://nwb-overview.readthedocs.io) ## Objective diff --git a/content/grants-and-projects/_index.md b/content/grants-and-projects/_index.md index 0766050..859f60c 100644 --- a/content/grants-and-projects/_index.md +++ b/content/grants-and-projects/_index.md @@ -5,7 +5,7 @@ sponsered_projects: boxes: - title: Advancing Standardization of Neurophysiology Data Through Dissemination of NWB - content: The National Institute of Health, through project 5U24NS120057, funded + content: The National Institute of Health, through project 5U24NS120057, funded Oliver Rübel (Lawrence Berkeley National Laboratory) and Benjamin Dichter (CatalystNeuro) to disseminate Neurodata Without Borders (NWB) neurophysiology technologies developed as part of the NIH BRAIN @@ -18,7 +18,7 @@ sponsered_projects: image: /images/nwb_elife_fig1.jpg - title: "DANDI: Distributed Archives for Neurophysiology Data Integration" image: /images/dandi-logo-square_sw.png - content: "The National Institutes of Health, through project 1R24MH117295, funded Satrajit Ghosh (Massachusetts Institute of Technology) and Yaroslav Halchenko (Center for Open Neuroscience) to create the DANDI archive for neurophysiology Data. + content: "The National Institutes of Health, through project 1R24MH117295, funded Satrajit Ghosh (Massachusetts Institute of Technology) and Yaroslav Halchenko (Center for Open Neuroscience) to create the DANDI archive for neurophysiology Data. * Provides a cloud platform for versioned neurophysiology data storage for the purposes of collaboration, archiving, and preservation. @@ -186,7 +186,7 @@ past_projects_section: - image: /images/project_components.png title: "NWB: A Data Standard and Software Ecosystem for Neurophysiology" content: The National Institutes of Health, through project 1R24MH116922, funded Oliver Rübel (Lawrence + href='https://reporter.nih.gov/search/39Cu1-L5zUap7i3X41dBTA/project-details/9582696'>1R24MH116922, funded Oliver Rübel (Lawrence Berkeley National Laboratory) and Lydia Ng (Allen Institute for Brain Science) to continue development of the NWB data format and software ecosystem to enable standardization, sharing, and @@ -196,7 +196,7 @@ past_projects_section: this project see our Progress Reports page. - image: /images/enabling_sharing_nwb.png title: Enabling Shared Analysis and Processing of Large Neurophysiology Data - content: The National Institutes of Health, through project 1R44MH115731, funded + content: The National Institutes of Health, through project 1R44MH115731, funded William Schroeder (Kitware, Inc.) to create software tools to browse, process, analyze, and visualize NWB data. This funding is part of the NIH’s BRAIN Initiative Small Business Innovation Research (SBIR) grant @@ -223,5 +223,5 @@ boxes: content: The Simons Foundation funds projects (Aug.2017 – present) to develop and expand the NWB2.0 Matlab API MatNWB to allow for adoption by a larger portion of the neuroscience community. - image: "https://github.com/NeurodataWithoutBorders/matnwb/raw/master/logo/logo_matnwb_small.png" + image: "https://github.com/NeurodataWithoutBorders/matnwb/raw/main/logo/logo_matnwb_small.png" --- diff --git a/content/tools/analysis/datajoint.md b/content/tools/analysis/datajoint.md index a988ceb..6fcdc5b 100644 --- a/content/tools/analysis/datajoint.md +++ b/content/tools/analysis/datajoint.md @@ -28,5 +28,5 @@ DataJoint Elements support automatic conversion to NWB format. For example, the ## Resources -- [DataJoint Elements](https://datajoint.com/elements) +- [DataJoint Elements](https://docs.datajoint.com/elements/) - [NWB Export Documentation](https://github.com/datajoint/element-array-ephys/blob/main/element_array_ephys/export/nwb/README.md) diff --git a/content/tools/analysis/hdftools.md b/content/tools/analysis/hdftools.md index ae04a9b..90f492e 100644 --- a/content/tools/analysis/hdftools.md +++ b/content/tools/analysis/hdftools.md @@ -29,7 +29,7 @@ HDFView uses the Java HDF Object Package, which implements HDF4 and HDF5 data ob ## HDF5 Command-line Tools -The HDF5 software distribution ships with a broad range of [HDF5 command-line utilities](https://docs.hdfgroup.org/hdf5/v1_14/_view_tools_command.html) that cover various tasks useful for debugging and inspecting HDF5 files. +The HDF5 software distribution ships with a broad range of [HDF5 command-line utilities](https://support.hdfgroup.org/documentation/hdf5/latest/_view_tools_view.html) that cover various tasks useful for debugging and inspecting HDF5 files. ### CLI tools for inspecting HDF5 files: diff --git a/content/tools/analysis/nwbexplorer.md b/content/tools/analysis/nwbexplorer.md index 5bdb06e..50f81aa 100644 --- a/content/tools/analysis/nwbexplorer.md +++ b/content/tools/analysis/nwbexplorer.md @@ -3,7 +3,7 @@ title: "NWB Explorer" description: "A web application developed by MetaCell for reading, visualizing and exploring the content of NWB 2 files. The portal comes with built-in visualization for many data types, and provides an interface to a jupyter notebook for custom analyses and open exploration." category: "exploration" image: "/images/tools/nwbexplorer/nwbexplorer_screenshot.png" -docs_url: "http://nwbexplorer.opensourcebrain.org/" +docs_url: "https://nwbexplorer.v2.opensourcebrain.org" weight: 30 --- @@ -15,4 +15,4 @@ NWB Explorer is a web application developed by MetaCell for reading, visualizing ![NWB Explorer Demo](/images/tools/nwbexplorer/nwbexplorer.gif) -You can try NWB Explorer online at [nwbexplorer.opensourcebrain.org](http://nwbexplorer.opensourcebrain.org/). +You can try NWB Explorer online at [https://nwbexplorer.v2.opensourcebrain.org](https://nwbexplorer.v2.opensourcebrain.org).