Merge remote-tracking branch 'origin/new_caiman_logo' into new_caiman…

…_logo

docs/source/conf.py

@@ -72,5 +72,10 @@
     'titles_only': False
 }
 
+# these links cannot be checked in github actions
+linkcheck_ignore = [
+    "https://crates.io/crates/nwbview",
+]
+
 # -- Build the nwb project analytics in the current directory
-build_project_analytics(target_dir=os.path.dirname(__file__))
+build_project_analytics(target_dir=os.path.dirname(__file__))

docs/source/conf_extlinks.py

@@ -47,7 +47,7 @@
     'nwb-main': ('https://www.nwb.org/%s', '%s'),
     'nwb-helpdesk': ('https://github.com/dandi/helpdesk/discussions/%s', '%s'),
     'nwb-mailing-list': ('https://mailchi.mp/fe2a9bc55a1a/nwb-signup/%s', '%s'),
-    'datajoint': ('https://www.datajoint.org/%s', '%s'),
+    'datajoint': ('https://www.datajoint.com/%s', '%s'),
     'datajoint-elements': ('https://www.datajoint.com/elements/%s', '%s'),
     'openscope-databook': ('https://alleninstitute.github.io/openscope_databook/%s', '%s'),
     'openscope-project': ('https://alleninstitute.org/what-we-do/brain-science/research/mindscope-program/openscope/%s',

docs/source/tools/acquisition_tools_home.rst

@@ -14,6 +14,7 @@ Acquisition and Control Tools
     openephys/openephys
     visiomode/visiomode
     arcontrol/arcontrol
+    bmtk/bmtk
 
 
 This page is a collection of tools we are cataloging as a convenience reference for NWB users. This is not a comprehensive list of NWB tools. Many of these tools are built and supported by other groups, and are in active development. If you would like to contribute a tool, please see the instructions :nwb-overview-src:`here <>`.
@@ -78,6 +79,22 @@ Controlling and Recoding Behavioral Tasks
 
     <br/>
 
+.. raw:: html
+
+    <hr>
+    <br />
+
+Brain Data Modeling and Simulation
+-----------------------------------
+
+.. image:: bmtk/bmtk_icon.png
+    :class: align-left
+    :width: 180
+
+.. include::  bmtk/bmtk.rst
+        :start-after: .. short_description_start
+        :end-before: .. short_description_end
+
 .. note::
 
         **Disclaimer:** Reference herein to any specific product, process, or service

docs/source/tools/analysis_tools_home.rst

@@ -12,11 +12,13 @@ Analysis and Visualization Tools
     nwbwidgets/nwbwidgets
     neurosift/neurosift
     nwbexplorer/nwbexplorer
+    nwbview/nwbview
     hdftools/hdftools
     spikeinterface/spikeinterface
     cellexplorer/cellexplorer
     ecogvis/ecogvis
     neo/neo
+    eeglab/eeglab
     caiman/caiman
     suite2p/suite2p
     ciatah/ciatah
@@ -87,6 +89,19 @@ Exploring NWB Files
     <br/>
     <br/>
 
+.. image:: nwbview/nwbview-icon.png
+    :class: align-left
+    :width: 180
+
+.. include::  nwbview/nwbview.rst
+        :start-after: .. short_description_start
+        :end-before: .. short_description_end
+
+.. raw:: html
+
+    <br/>
+    <br/>
+
 .. image:: hdftools/jupyterlab_h5web_nwb_example.png
     :class: align-left
     :width: 180
@@ -163,9 +178,22 @@ Extracellular Electrophysiology Tools
 .. raw:: html
 
     <br />
-    <hr>
     <br />
 
+.. image:: eeglab/400px-Eeglab_small.jpg
+    :class: align-left
+    :width: 180
+
+.. include::  eeglab/eeglab.rst
+        :start-after: .. short_description_start
+        :end-before: .. short_description_end
+
+
+.. raw:: html
+
+    <br />
+    <hr>
+    <br />
 
 .. _analysistools-ophys:
 

docs/source/tools/bmtk/bmtk.rst

@@ -0,0 +1,24 @@
+.. _analysistools-bmtk:
+
+Brain Modeling Toolkit (BMTK)
+-----------------------------
+
+.. short_description_start
+
+:ref:`analysistools-bmtk`, SONATA, and Visual Neuronal Dynamics (VND) are mutually integrated software tools that are particularly suited to support large-scale bio-realistic brain modeling, but are applicable to a variety of neuronal modeling applications. BMTK is a suite for building and simulating network models at multiple levels of resolution, from biophysically-detailed, to point-neuron, to population-statistics approaches. The modular design of BMTK allows users to easily work across different scales of resolution and different simulation engines using the same code interface. The model architecture and parameters, as well as simulation configuration, input, and output are stored together in the SONATA data format. Models and their output activity can then be visualized with the powerful rendering capabilities of VND. :bdg-link-primary:`Docs <https://alleninstitute.github.io/bmtk>` :bdg-link-primary:`Tutorial <https://alleninstitute.github.io/bmtk/tutorials.html>` :bdg-link-primary:`NWB Spike Stimulus <https://alleninstitute.github.io/bmtk/ecephys_probe.html>`  :bdg-link-primary:`Source <https://github.com/AllenInstitute/bmtk>`
+
+.. image:: https://img.shields.io/github/stars/AllenInstitute/bmtk?style=social
+    :alt: GitHub Repo stars for BTMK
+    :target: https://github.com/AllenInstitute/bmtk
+
+.. short_description_end
+
+
+.. image:: bmtk_levels_of_resolution_sm.png
+    :class: align-left
+    :width: 800
+
+
+**Reference:**
+
+Dai et al. Brain Modeling Toolkit: An open-source software suite for multiscale modeling of brain circuits. PLoS Comput Biol 16(11): e1008386. https://doi.org/10.1371/journal.pcbi.1008386

docs/source/tools/caiman/caiman.rst

@@ -8,6 +8,10 @@ CaImAn
 :ref:`analysistools-caiman` is a computational toolbox for large scale Calcium Imaging Analysis, including movie
 handling, motion correction, source extraction, spike deconvolution and result visualization. CaImAn now supports reading and writing data in NWB 2.0. :bdg-link-primary:`NWB Demo  <https://github.com/flatironinstitute/caiman_use_cases/blob/main/use_cases/NWB/demo_pipeline_nwb.ipynb>` :bdg-link-primary:`Second Demo <https://github.com/flatironinstitute/CaImAn/blob/master/demos/general/demo_pipeline_NWB.py>` :bdg-link-primary:`Video Tutorial <https://www.youtube.com/watch?v=wUhKkNtSu_s>` :bdg-link-primary:`Docs <https://caiman.readthedocs.io/en/latest/>` :bdg-link-primary:`Source <https://github.com/flatironinstitute/CaImAn>`.
 
+.. image:: https://img.shields.io/github/stars/flatironinstitute/CaImAn?style=social
+    :alt: GitHub Repo stars for CaImAn
+    :target: https://github.com/flatironinstitute/CaImAn
+
 .. short_description_end
 
 .. image:: caiman_logo.png

docs/source/tools/cebra/cebra.rst

@@ -15,5 +15,9 @@ CEBRA
 :bdg-link-primary:`Docs <https://cebra.ai/docs/>`
 :bdg-link-primary:`NWB tutorial <https://stes.io/NeuroDataReHack2023/>`.
 
+.. image:: https://img.shields.io/github/stars/AdaptiveMotorControlLab/cebra?style=social
+    :alt: GitHub Repo stars for CEBRA
+    :target: https://github.com/AdaptiveMotorControlLab/cebra
+
 
 .. short_description_end

docs/source/tools/cellexplorer/cellexplorer.rst

@@ -7,6 +7,10 @@ CellExplorer
 
 :ref:`analysistools-cellexplorer`  is a graphical user interface (GUI), a standardized processing module and data structure for exploring and classifying single cells acquired using extracellular electrodes. :bdg-link-primary:`NWB Tutorial  <https://cellexplorer.org/tutorials/nwb-tutorial/>`  :bdg-link-primary:`Intro Video  <https://www.youtube.com/watch?v=GR1glNhcGIY>` :bdg-link-primary:`Video Tutorial  <https://www.youtube.com/watch?v=x2x0KkRuSak>` :bdg-link-primary:`Docs  <https://cellexplorer.org/>` :bdg-link-primary:`Source <https://github.com/petersenpeter/CellExplorer>`.
 
+.. image:: https://img.shields.io/github/stars/petersenpeter/CellExplorer?style=social
+    :alt: GitHub Repo stars for CellExplorer
+    :target: https://github.com/petersenpeter/CellExplorer
+
 .. short_description_end
 
 .. image:: CellExplorerInterface.jpeg

docs/source/tools/ciatah/ciatah.rst

@@ -7,6 +7,10 @@ CIAtah
 
 :ref:`analysistools-ciatah` (pronounced cheetah; formerly calciumImagingAnalysis) is a Matlab software package for analyzing one- and two-photon calcium imaging datasets. :bdg-link-primary:`Video tutorial <https://www.youtube.com/watch?v=I6abW3uuJJw>` :bdg-link-primary:`Docs <https://bahanonu.github.io/ciatah/>` :bdg-link-primary:`Source <https://github.com/bahanonu/calciumImagingAnalysis>`.
 
+.. image:: https://img.shields.io/github/stars/bahanonu/calciumImagingAnalysis?style=social
+    :alt: GitHub Repo stars for CIAtah
+    :target: https://github.com/bahanonu/calciumImagingAnalysis
+
 .. short_description_end
 
 .. image:: ciatah_pipeline.png

docs/source/tools/deeplabcut/deeplabcut.rst

@@ -13,6 +13,10 @@ of this framework by tracking various body parts in multiple species across a
 broad collection of behaviors.
 :bdg-link-primary:`Documentation <http://www.mackenziemathislab.org/deeplabcut>`
 
+.. image:: https://img.shields.io/github/stars/DeepLabCut/DeepLabCut?style=social
+    :alt: GitHub Repo stars for DeepLabCut
+    :target: https://github.com/DeepLabCut/DeepLabCut
+
 .. short_description_end
 
 

docs/source/tools/ecogvis/ecogvis.rst

@@ -7,6 +7,10 @@ EcogVIS
 
 :ref:`analysistools-ecogvis`  is a Python-based, time series visualizer for Electrocorticography (ECoG) signals stored in NWB files. EcogVIS makes it intuitive and simple to visualize ECoG signals from selected channels, brain regions, make annotations and mark intervals of interest. Signal processing and analysis tools will soon be added. :bdg-link-primary:`Source <https://github.com/catalystneuro/ecogVIS>`.
 
+.. image:: https://img.shields.io/github/stars/catalystneuro/ecogVIS?style=social
+    :alt: GitHub Repo stars for ecogVIS
+    :target: https://github.com/catalystneuro/ecogVIS
+
 .. short_description_end
 
 .. image:: ecogvis_screenshot.png

docs/source/tools/eeglab/eeglab.rst

@@ -0,0 +1,18 @@
+.. _analysistools-eeglab:
+
+EEGLAB
+------
+
+.. short_description_start
+
+:ref:`analysistools-eeglab` is a MATLAB-based electrophysiology (ECoG/iEEG/EEG) software to process and visualize data stored in NWB files. After installing the NWB-IO EEGLAB plugins, time series, channel information, spike timing, and event information may be imported, processed, and visualized using the EEGLAB graphical interface or scripts. MEF3, EDF, and Brain Vision Exchange format may also be converted to NWB files (and vice versa). :bdg-link-primary:`Docs <https://eeglab.org/>`  :bdg-link-primary:`Source <https://github.com/sccn/EEGLAB>` :bdg-link-primary:`NWB-io EEGLAB plugin  <https://github.com/sccn/nwbio>`
+
+.. image:: https://img.shields.io/github/stars/sccn/eeglab?style=social
+    :alt: GitHub Repo stars for EEGLAB
+    :target: https://github.com/sccn/EEGLAB
+
+.. short_description_end
+
+.. image:: 400px-Eeglab_small.jpg
+    :class: align-left
+    :width: 400

docs/source/tools/extract/extract.rst

@@ -13,6 +13,10 @@ performance.
 :bdg-link-primary:`NWB tutorials <https://github.com/schnitzer-lab/EXTRACT-public/tree/master/Learning%20materials/NWB%20Tutorials>`
 :bdg-link-primary:`Publication <https://www.biorxiv.org/content/10.1101/2021.03.24.436279v2>`
 
+.. image:: https://img.shields.io/github/stars/schnitzer-lab/EXTRACT-public?style=social
+    :alt: GitHub Repo stars for EXTRACT
+    :target: https://github.com/schnitzer-lab/EXTRACT-public
+
 .. short_description_end
 
 

docs/source/tools/graft/graft.rst

@@ -10,4 +10,8 @@ GraFT
 :bdg-link-primary:`NWB tutorials  <https://github.com/adamshch/GraFT-analysis/tree/main/code/nwb_tutorials>`
 :bdg-link-primary:`Cite  <https://pubmed.ncbi.nlm.nih.gov/35533160/>`
 
+.. image:: https://img.shields.io/github/stars/adamshch/GraFT-analysis?style=social
+    :alt: GitHub Repo stars for GraFT
+    :target: https://github.com/adamshch/GraFT-analysis
+
 .. short_description_end

docs/source/tools/hdftools/hdftools.rst

@@ -14,7 +14,7 @@ that can be useful for developers (e.g., *h5ls* and *h5dump* to introspect,
 While these tools do not provide NWB-specific functionality, they are useful
 (mainly for developers) to debug and browse NWB HDF5 files.
 :bdg-link-primary:`HDFView <https://www.hdfgroup.org/downloads/hdfview/>`
-:bdg-link-primary:`HDF5 CLI tools <https://portal.hdfgroup.org/display/HDF5/HDF5+Command-line+Tools>`
+:bdg-link-primary:`HDF5 CLI tools <https://docs.hdfgroup.org/hdf5/v1_14/_view_tools_command.html>`
 :bdg-link-primary:`vscode-h5web <https://marketplace.visualstudio.com/items?itemName=h5web.vscode-h5web>`
 :bdg-link-primary:`h5glance <https://github.com/European-XFEL/h5glance>`
 :bdg-link-primary:`jupyterlab-h5web <https://github.com/silx-kit/jupyterlab-h5web>`
@@ -64,33 +64,33 @@ HDF5 Command-line Tools
 """""""""""""""""""""""
 
 The HDF5 software distribution ships with a broad range of
-`HDF5 command-line utilities <https://portal.hdfgroup.org/display/HDF5/HDF5+Command-line+Tools>`_ that
+`HDF5 command-line utilities <https://docs.hdfgroup.org/hdf5/v1_14/_view_tools_command.html>`_ that
 cover a broad range of tasks useful for debugging and inspecting HDF5 files, for example:
 
 * **CLI tools for inspecting HDF5 files:**
 
-    * `h5ls <https://portal.hdfgroup.org/display/HDF5/h5ls>`_  lists selected information about file objects in the specified format
+    * ``h5ls``  lists selected information about file objects in the specified format
 
         .. tip::
 
             *h5ls* can also be used with remote files on S3 via ``h5ls --vfd=ros3 -r <s3path>`` or on Windows
             via ``h5ls --vfd=ros3 --s3-cred="(,,)" <s3path>``
 
-    * `h5dump <https://portal.hdfgroup.org/display/HDF5/h5dump>`_ enables the user to examine the contents of an HDF5 file and dump those contents to an ASCII file.
-    * `h5diff <https://portal.hdfgroup.org/display/HDF5/h5diff>`_ compares two HDF5 files and reports the differences. *h5diff* is for serial use while *ph5diff* is for use in parallel environments.
-    * `h5check <https://portal.hdfgroup.org/display/HDF5/h5check>`_ verifies that an HDF5 file is encoded according to the HDF5 specification.
-    * `h5stat <https://portal.hdfgroup.org/display/HDF5/h5stat>`_ displays object and metadata information for an HDF5 file.
-    * `h5watch <https://portal.hdfgroup.org/display/HDF5/h5watch>`_ Outputs new records appended to a dataset as the dataset grows similar to the Unix user command ``tail``.
-    * *h5debug* debugs an existing HDF5 file at a low level.
+    * ``h5dump`` enables the user to examine the contents of an HDF5 file and dump those contents to an ASCII file.
+    * ``h5diff`` compares two HDF5 files and reports the differences. *h5diff* is for serial use while *ph5diff* is for use in parallel environments.
+    * ``h5check`` verifies that an HDF5 file is encoded according to the HDF5 specification.
+    * ``h5stat`` displays object and metadata information for an HDF5 file.
+    * ``h5watch`` Outputs new records appended to a dataset as the dataset grows similar to the Unix user command ``tail``.
+    * ``h5debug`` debugs an existing HDF5 file at a low level.
 
 * **CLI tools to copy, clean, and edit HDF5 files:**
 
-    * `h5repack <https://portal.hdfgroup.org/display/HDF5/h5repack>`_  copies an HDF5 file to a new file with or without compression/chunking and is typically used to apply HDF5 filters to an input file and saving the output in a new output file.
-    * `h5copy <https://portal.hdfgroup.org/display/HDF5/h5copy>`_ copies an HDF5 object (a dataset, named datatype, or group) from an input HDF5 file to an output HDF5 file.
-    * `h5repart <https://portal.hdfgroup.org/display/HDF5/h5repart>`_ repartitions a file or family of files, e.g,. to  join a family of files into a single file or to copy one family of files to another while changing the size of the family members.
-    *  `h5clear <https://portal.hdfgroup.org/display/HDF5/h5clear>`_  clears superblock status_flags field, removes metadata cache image, prints EOA and EOF, or sets EOA of a file.
+    * ``h5repack``  copies an HDF5 file to a new file with or without compression/chunking and is typically used to apply HDF5 filters to an input file and saving the output in a new output file.
+    * ``h5copy`` copies an HDF5 object (a dataset, named datatype, or group) from an input HDF5 file to an output HDF5 file.
+    * ``h5repart`` repartitions a file or family of files, e.g,. to  join a family of files into a single file or to copy one family of files to another while changing the size of the family members.
+    * ``h5clear`` clears superblock status_flags field, removes metadata cache image, prints EOA and EOF, or sets EOA of a file.
 
-These are just a few select tools most relevant to debugging NWB files. See the `HDF5 command-line utilities page <https://portal.hdfgroup.org/display/HDF5/HDF5+Command-line+Tools>`_ for a more detailed overview.
+These are just a few select tools most relevant to debugging NWB files. See the `HDF5 command-line utilities page <https://docs.hdfgroup.org/hdf5/v1_14/_view_tools_command.html>`_ for a more detailed overview.
 
 
 .. _analysistools-hdftools-jupyter:

docs/source/tools/mies/mies.rst

@@ -7,6 +7,10 @@ MIES
 
 :ref:`analysistools-mies` is a sweep based data acquisition tool written in Igor Pro. MIES has three primary user interfaces: 1) the ``WaveBuilder`` to generate stimulus sets 2) the ``DA_Ephys`` GUI to control and observe data acquisition in real time, and 3) the ``DataBrowser`` to browse acquired data. All three interfaces are intended to be operated in parallel. :bdg-link-primary:`Video tutorial <https://www.youtube.com/watch?v=Y3I-LDX-R2Q>` :bdg-link-primary:`MIES NWB Module <https://alleninstitute.github.io/MIES/IPNWB/index.html>`  :bdg-link-primary:`Docs <https://alleninstitute.github.io/MIES/index.html>` :bdg-link-primary:`Source <https://github.com/AllenInstitute/MIES>`.
 
+.. image:: https://img.shields.io/github/stars/AllenInstitute/MIES?style=social
+    :alt: GitHub Repo stars for MIES
+    :target: https://github.com/AllenInstitute/MIES
+
 .. short_description_end
 
 

docs/source/tools/neo/neo.rst

@@ -7,16 +7,19 @@ Neo
 :ref:`analysistools-neo` Neo is a Python package for working with
 electrophysiology data in Python, together with support for reading
 and writing a wide range of neurophysiology file formats (see the
-`list of supported formats <https://neo.readthedocs.io/en/stable/io.html?highlight=NWBIO#module-neo.io>`_).
+`list of supported formats <https://neo.readthedocs.io/en/latest/rawiolist.html>`_).
 The goal of Neo is to improve interoperability between Python tools for analyzing,
 visualizing and generating electrophysiology data, by providing a common, shared
 object model. In order to be as lightweight a dependency as possible, Neo
 is deliberately limited to representation of data, with no functions for data analysis
-or visualization. :bdg-link-primary:`Docs <https://neo.readthedocs.io/en/stable/>`
-:bdg-link-primary:`Neo NWBIO Docs <https://neo.readthedocs.io/en/stable/io.html#neo.io.NWBIO>`
+or visualization. :bdg-link-primary:`Docs <https://neo.readthedocs.io/>`
+:bdg-link-primary:`Neo NWBIO Example <https://neo.readthedocs.io/en/latest/examples/convert_to_nwb.html>`
 :bdg-link-primary:`Website <https://neuralensemble.org/neo/>`
 :bdg-link-primary:`Source <https://github.com/NeuralEnsemble/python-neo>`.
 
+.. image:: https://img.shields.io/github/stars/NeuralEnsemble/python-neo?style=social
+    :alt: GitHub Repo stars for NEO
+    :target: https://github.com/NeuralEnsemble/python-neo
 
 .. short_description_end
 

docs/source/tools/neurosift/neurosift.rst

@@ -8,6 +8,10 @@ Neurosift
 :ref:`analysistools-neurosift` provides interactive neuroscience visualizations in the browser. Neurosift caters to both individual users through its local mode, allowing the visualization of views directly from your device, as well as a remote access function for presenting your findings to other users on different machines.
 :bdg-link-primary:`Source <https://github.com/flatironinstitute/neurosift>`
 
+.. image:: https://img.shields.io/github/stars/flatironinstitute/neurosift?style=social
+    :alt: GitHub Repo stars for neurosift
+    :target: https://github.com/flatironinstitute/neurosift
+
 .. short_description_end
 
 With Neurosift, you have the ability to construct a multitude of synchronized visuals such as spike raster plots, audio spectrograms, videos, video annotations, position decode fields, timeseries graphs, and more.