From efc241e2a5cf99602c1907f1806dcbc530d425f9 Mon Sep 17 00:00:00 2001 From: bendichter Date: Sun, 5 Nov 2023 12:50:40 -0500 Subject: [PATCH 1/3] add github stars --- docs/source/tools/neurosift/neurosift.rst | 4 ++++ docs/source/tools/nwbwidgets/nwbwidgets.rst | 6 +++++- 2 files changed, 9 insertions(+), 1 deletion(-) diff --git a/docs/source/tools/neurosift/neurosift.rst b/docs/source/tools/neurosift/neurosift.rst index 2ddf0d5..dcfd83a 100644 --- a/docs/source/tools/neurosift/neurosift.rst +++ b/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 ` +.. 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. diff --git a/docs/source/tools/nwbwidgets/nwbwidgets.rst b/docs/source/tools/nwbwidgets/nwbwidgets.rst index d1194f7..70b22de 100644 --- a/docs/source/tools/nwbwidgets/nwbwidgets.rst +++ b/docs/source/tools/nwbwidgets/nwbwidgets.rst @@ -6,7 +6,11 @@ NWB Widgets .. short_description_start :ref:`analysistools-nwbwidgets` is a library of widgets for visualization NWB data in a Jupyter notebook (or lab). -The widgets make it easy to navigate through the hierarchical structure of the NWB file and visualize specific data elements. It is designed to work out-of-the-box with NWB 2.0 files and to be easy to extend. :bdg-link-primary:`Source ` :bdg-link-primary:`Docs ` +The widgets make it easy to navigate through the hierarchical structure of the NWB file and visualize specific data elements. It is designed to work out-of-the-box with NWB 2.0 files and to be easy to extend. :bdg-link-primary:`Source ` :bdg-link-primary:`Docs ` + +.. image:: https://img.shields.io/github/stars/NeurodataWithoutBorders/nwbwidgets?style=social + :alt: GitHub Repo stars for NWB Widgets + :target: https://github.com/NeurodataWithoutBorders/nwbwidgets .. short_description_end From d9ad1ca3248f09cabb6344d5953162c47e479f8f Mon Sep 17 00:00:00 2001 From: bendichter Date: Sat, 2 Dec 2023 16:59:48 +0100 Subject: [PATCH 2/3] add github stars --- docs/source/tools/caiman/caiman.rst | 4 ++++ docs/source/tools/cebra/cebra.rst | 4 ++++ docs/source/tools/cellexplorer/cellexplorer.rst | 4 ++++ docs/source/tools/ciatah/ciatah.rst | 4 ++++ docs/source/tools/deeplabcut/deeplabcut.rst | 4 ++++ docs/source/tools/ecogvis/ecogvis.rst | 4 ++++ docs/source/tools/extract/extract.rst | 4 ++++ docs/source/tools/graft/graft.rst | 4 ++++ docs/source/tools/mies/mies.rst | 4 ++++ docs/source/tools/openephys/openephys.rst | 4 ++++ docs/source/tools/optinist/optinist.rst | 5 +++++ docs/source/tools/patchview/patchview.rst | 4 ++++ docs/source/tools/pynapple/pynapple.rst | 6 +++++- docs/source/tools/sleap/sleap.rst | 6 +++++- docs/source/tools/spikeinterface/spikeinterface.rst | 4 ++++ docs/source/tools/spyglass/spyglass.rst | 4 ++++ docs/source/tools/suite2p/suite2p.rst | 4 ++++ docs/source/tools/visiomode/visiomode.rst | 4 ++++ 18 files changed, 75 insertions(+), 2 deletions(-) diff --git a/docs/source/tools/caiman/caiman.rst b/docs/source/tools/caiman/caiman.rst index 52ed854..561a495 100644 --- a/docs/source/tools/caiman/caiman.rst +++ b/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 ` :bdg-link-primary:`Second Demo ` :bdg-link-primary:`Video Tutorial ` :bdg-link-primary:`Docs ` :bdg-link-primary:`Source `. +.. 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 diff --git a/docs/source/tools/cebra/cebra.rst b/docs/source/tools/cebra/cebra.rst index a844e8c..824d030 100644 --- a/docs/source/tools/cebra/cebra.rst +++ b/docs/source/tools/cebra/cebra.rst @@ -15,5 +15,9 @@ CEBRA :bdg-link-primary:`Docs ` :bdg-link-primary:`NWB tutorial `. +.. 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 diff --git a/docs/source/tools/cellexplorer/cellexplorer.rst b/docs/source/tools/cellexplorer/cellexplorer.rst index 05265df..12d0a53 100644 --- a/docs/source/tools/cellexplorer/cellexplorer.rst +++ b/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 ` :bdg-link-primary:`Intro Video ` :bdg-link-primary:`Video Tutorial ` :bdg-link-primary:`Docs ` :bdg-link-primary:`Source `. +.. 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 diff --git a/docs/source/tools/ciatah/ciatah.rst b/docs/source/tools/ciatah/ciatah.rst index 229cd49..6782944 100644 --- a/docs/source/tools/ciatah/ciatah.rst +++ b/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 ` :bdg-link-primary:`Docs ` :bdg-link-primary:`Source `. +.. 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 diff --git a/docs/source/tools/deeplabcut/deeplabcut.rst b/docs/source/tools/deeplabcut/deeplabcut.rst index 76bd7f0..47bc76a 100644 --- a/docs/source/tools/deeplabcut/deeplabcut.rst +++ b/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 ` +.. 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 diff --git a/docs/source/tools/ecogvis/ecogvis.rst b/docs/source/tools/ecogvis/ecogvis.rst index 07bfe3a..1ed7c0c 100644 --- a/docs/source/tools/ecogvis/ecogvis.rst +++ b/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 `. +.. 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 diff --git a/docs/source/tools/extract/extract.rst b/docs/source/tools/extract/extract.rst index 3c0f1fe..2230db5 100644 --- a/docs/source/tools/extract/extract.rst +++ b/docs/source/tools/extract/extract.rst @@ -13,6 +13,10 @@ performance. :bdg-link-primary:`NWB tutorials ` :bdg-link-primary:`Publication ` +.. 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 diff --git a/docs/source/tools/graft/graft.rst b/docs/source/tools/graft/graft.rst index 488615c..271a5c1 100644 --- a/docs/source/tools/graft/graft.rst +++ b/docs/source/tools/graft/graft.rst @@ -10,4 +10,8 @@ GraFT :bdg-link-primary:`NWB tutorials ` :bdg-link-primary:`Cite ` +.. 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 \ No newline at end of file diff --git a/docs/source/tools/mies/mies.rst b/docs/source/tools/mies/mies.rst index 9235f55..bf3e344 100644 --- a/docs/source/tools/mies/mies.rst +++ b/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 ` :bdg-link-primary:`MIES NWB Module ` :bdg-link-primary:`Docs ` :bdg-link-primary:`Source `. +.. 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 diff --git a/docs/source/tools/openephys/openephys.rst b/docs/source/tools/openephys/openephys.rst index 5269b85..f28c2cf 100644 --- a/docs/source/tools/openephys/openephys.rst +++ b/docs/source/tools/openephys/openephys.rst @@ -7,6 +7,10 @@ OpenEphys GUI :ref:`acquisitiontools-openephys` is a modular, open-source software for extracellular electrophysiology. Built by neuroscientists, for neuroscientists, OpenEphys GUI has all the features needed to acquire and visualize electrophysiology data, while making it easy to add new modules written in C++. The GUI allows the user to configure processing pipelines by mixing and matching modules. Using the NWB format plugin, users can record data directly in NWB format via the OpenEphys GUI. --- **OpenEphys GUI:** :bdg-link-primary:`Docs ` :bdg-link-primary:`Website ` :bdg-link-primary:`Source ` --- **NWB Plugin for OpenEphys**: :bdg-link-primary:`Docs ` :bdg-link-primary:`Source ` +.. image:: https://img.shields.io/github/stars/open-ephys-plugins/nwb-format?style=social + :alt: GitHub Repo stars for the NWB format plugin + :target: https://github.com/open-ephys-plugins/nwb-format + .. short_description_end .. image:: openephys_gui_screenshot.png diff --git a/docs/source/tools/optinist/optinist.rst b/docs/source/tools/optinist/optinist.rst index 645f10e..a055a48 100644 --- a/docs/source/tools/optinist/optinist.rst +++ b/docs/source/tools/optinist/optinist.rst @@ -7,6 +7,11 @@ OptiNiSt :ref:`analysistools-optinist` (Optical Neuroimage Studio) is a GUI based workflow pipeline tools for processing two-photon calcium imaging data. :bdg-link-primary:`Source ` :bdg-link-primary:`Docs ` +.. image:: https://img.shields.io/github/stars/oist/optinist?style=social + :alt: GitHub Repo stars for Optinist + :target: https://github.com/oist/optinist + + .. short_description_end OptiNiSt helps researchers try multiple data analysis methods, visualize the results, and construct the data analysis pipelines easily and quickly on GUI. OptiNiSt's data-saving format follows NWB standards. diff --git a/docs/source/tools/patchview/patchview.rst b/docs/source/tools/patchview/patchview.rst index c456d98..bf9a764 100644 --- a/docs/source/tools/patchview/patchview.rst +++ b/docs/source/tools/patchview/patchview.rst @@ -10,6 +10,10 @@ PatchView :bdg-link-primary:`Source ` :bdg-link-primary:`Publication ` +.. image:: https://img.shields.io/github/stars/ZeitgeberH/patchview?style=social + :alt: GitHub Repo stars for PatchView + :target: https://github.com/ZeitgeberH/patchview + .. short_description_end .. image:: patchview.png diff --git a/docs/source/tools/pynapple/pynapple.rst b/docs/source/tools/pynapple/pynapple.rst index 545aa32..d694ca4 100644 --- a/docs/source/tools/pynapple/pynapple.rst +++ b/docs/source/tools/pynapple/pynapple.rst @@ -1,13 +1,17 @@ .. _analysistools-pynapple: pynapple ------------- +--------- .. short_description_start :ref:`analysistools-pynapple` is a unified toolbox for integrated analysis of multiple data sources. Designed to be "plug & play", users define and import their own time-relevant variables. Supported data sources include, but are not limited to, electrophysiology, calcium imaging, and motion capture data. Pynapple contains integrated functions for common neuroscience analyses, including cross-correlograms, tuning curves, decoding and perievent time histogram. :bdg-link-primary:`Docs ` :bdg-link-primary:`DANDI Demo ` :bdg-link-primary:`Source ` :bdg-link-primary:`Twitter ` +.. image:: https://img.shields.io/github/stars/pynapple-org/pynapple?style=social + :alt: GitHub Repo stars for pynapple + :target: https://github.com/pynapple-org/pynapple + .. short_description_end .. image:: GraphicAbstract.png diff --git a/docs/source/tools/sleap/sleap.rst b/docs/source/tools/sleap/sleap.rst index 84da57e..5fa6a20 100644 --- a/docs/source/tools/sleap/sleap.rst +++ b/docs/source/tools/sleap/sleap.rst @@ -1,7 +1,7 @@ .. _analysistools-sleap: SLEAP ----------- +----- .. short_description_start @@ -11,6 +11,10 @@ number of animals and includes an advanced labeling/training GUI for active learning and proofreading. :bdg-link-primary:`Documentation ` +.. image:: https://img.shields.io/github/stars/talmolab/sleap?style=social + :alt: GitHub Repo stars for SLEAP + :target: https://github.com/talmolab/sleap + .. short_description_end diff --git a/docs/source/tools/spikeinterface/spikeinterface.rst b/docs/source/tools/spikeinterface/spikeinterface.rst index 3e18377..b9e98ba 100644 --- a/docs/source/tools/spikeinterface/spikeinterface.rst +++ b/docs/source/tools/spikeinterface/spikeinterface.rst @@ -7,6 +7,10 @@ SpikeInterface :ref:`analysistools-spikeinterface` is a collection of Python modules designed to improve the accessibility, reliability, and reproducibility of spike sorting and all its associated computations. :bdg-link-primary:`Video tutorial ` :bdg-link-primary:`Demo Notebook ` :bdg-link-primary:`Docs ` :bdg-link-primary:`Source ` +.. image:: https://img.shields.io/github/stars/SpikeInterface/spikeinterface?style=social + :alt: GitHub Repo stars for SpikeInterface + :target: https://github.com/SpikeInterface/spikeinterface + .. short_description_end With SpikeInterface, users can: diff --git a/docs/source/tools/spyglass/spyglass.rst b/docs/source/tools/spyglass/spyglass.rst index 1d4ad11..f5897b6 100644 --- a/docs/source/tools/spyglass/spyglass.rst +++ b/docs/source/tools/spyglass/spyglass.rst @@ -9,6 +9,10 @@ Spyglass :bdg-link-primary:`Docs ` :bdg-link-primary:`Source `. +.. image:: https://img.shields.io/github/stars/LorenFrankLab/spyglass?style=social + :alt: GitHub Repo stars for Spyglass + :target: https://github.com/LorenFrankLab/spyglass + .. short_description_end .. image:: Spyglass.png diff --git a/docs/source/tools/suite2p/suite2p.rst b/docs/source/tools/suite2p/suite2p.rst index 90e539b..8eb746b 100644 --- a/docs/source/tools/suite2p/suite2p.rst +++ b/docs/source/tools/suite2p/suite2p.rst @@ -7,6 +7,10 @@ suite2p :ref:`analysistools-suite2p` is an imaging processing pipeline written in Python . suite2p includes modules for 1) Registration, 2) Cell detection, 3) Spike detection, and a 4) Visualization GUI. :bdg-link-primary:`Video Tutorial ` :bdg-link-primary:`Docs ` :bdg-link-primary:`Source `. +.. image:: https://img.shields.io/github/stars/MouseLand/suite2p?style=social + :alt: GitHub Repo stars for suite2p + :target: https://github.com/MouseLand/suite2p + .. short_description_end .. only:: html diff --git a/docs/source/tools/visiomode/visiomode.rst b/docs/source/tools/visiomode/visiomode.rst index 0239d8c..d6b8635 100644 --- a/docs/source/tools/visiomode/visiomode.rst +++ b/docs/source/tools/visiomode/visiomode.rst @@ -7,6 +7,10 @@ Visiomode :ref:`analysistools-visiomode` is an open-source platform for building touchscreen-based behavioral tasks for rodents. It leverages the inherent flexibility of touchscreens to offer a simple yet adaptable software and hardware platform. Visiomode is built on the Raspberry Pi computer combining a web-based interface and powerful plug-in system with an operant chamber that can be adapted to generate a wide range of behavioral tasks. :bdg-link-primary:`Docs ` :bdg-link-primary:`Source ` :bdg-link-primary:`Publication ` +.. image:: https://img.shields.io/github/stars/DuguidLab/visiomode?style=social + :alt: GitHub Repo stars for visiomode + :target: https://github.com/DuguidLab/visiomode + .. short_description_end .. image:: visiomode_graphical_abstract.png From 930241b3e3270a4565f428f0e2317cd57bd1686d Mon Sep 17 00:00:00 2001 From: bendichter Date: Sat, 2 Dec 2023 17:59:07 +0100 Subject: [PATCH 3/3] add star for neo --- docs/source/tools/neo/neo.rst | 3 +++ 1 file changed, 3 insertions(+) diff --git a/docs/source/tools/neo/neo.rst b/docs/source/tools/neo/neo.rst index 54561bd..9d6acea 100644 --- a/docs/source/tools/neo/neo.rst +++ b/docs/source/tools/neo/neo.rst @@ -17,6 +17,9 @@ or visualization. :bdg-link-primary:`Docs ` :bdg-link-primary:`Source `. +.. 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