catalystneuro · bendichter · Feb 7, 2024 · Feb 7, 2024 · Feb 7, 2024 · Feb 16, 2024
diff --git a/docs/conf.py b/docs/conf.py
@@ -112,3 +112,7 @@ def setup(app):  # This makes the data-interfaces signatures display on the docs
     "format-request-form": ("https://github.com/catalystneuro/neuroconv/issues/new?assignees=&labels=enhancement"
                             "%2Cdata+interfaces&template=format_request.yml&title=%5BNew+Format%5D%3A+", "")
 }
+
+html_sidebars = {
+    "conversion_example_gallery": ["page-toc", "edit-this-page", "sourcelink"]
+}
diff --git a/docs/conversion_example_gallery.rst b/docs/conversion_example_gallery.rst
@@ -0,0 +1,105 @@
+.. _conversion_gallery:
+:html_theme.sidebar_secondary.remove:
+
+##################
+Conversion Gallery
+##################
+
+The examples here are guaranteed to be running correctly with our testing suite. Their aim is to be a showcase of the
+library capabilities and to get you to hit the ground running with your own conversion.
+
+*******************************
+Extracellular electrophysiology
+*******************************
+
+Recording
+---------
+
+.. include:: conversion_examples_gallery/recording/alphaomega.rst
+.. include:: conversion_examples_gallery/recording/axona.rst
+.. include:: conversion_examples_gallery/recording/biocam.rst
+.. include:: conversion_examples_gallery/recording/blackrock.rst
+.. include:: conversion_examples_gallery/recording/edf.rst
+.. include:: conversion_examples_gallery/recording/intan.rst
+.. include:: conversion_examples_gallery/recording/maxone.rst
+.. include:: conversion_examples_gallery/recording/mcsraw.rst
+.. include:: conversion_examples_gallery/recording/mearec.rst
+.. include:: conversion_examples_gallery/recording/neuralynx.rst
+.. include:: conversion_examples_gallery/recording/neuroscope.rst
+.. include:: conversion_examples_gallery/recording/openephys.rst
+.. include:: conversion_examples_gallery/recording/plexon.rst
+.. include:: conversion_examples_gallery/recording/spike2.rst
+.. include:: conversion_examples_gallery/recording/spikegadgets.rst
+.. include:: conversion_examples_gallery/recording/spikeglx.rst
+.. include:: conversion_examples_gallery/recording/tdt.rst
+
+Sorting
+-------
+
+.. include:: conversion_examples_gallery/sorting/blackrock.rst
+.. include:: conversion_examples_gallery/sorting/cellexplorer.rst
+.. include:: conversion_examples_gallery/sorting/kilosort.rst
+.. include:: conversion_examples_gallery/sorting/neuralynx.rst
+.. include:: conversion_examples_gallery/sorting/neuroscope.rst
+.. include:: conversion_examples_gallery/sorting/phy.rst
+.. include:: conversion_examples_gallery/sorting/plexon.rst
+
+*******************************
+Intracellular electrophysiology
+*******************************
+
+.. include:: conversion_examples_gallery/recording/abf.rst
+
+******************
+Optical physiology
+******************
+
+Imaging
+-------
+
+.. include:: conversion_examples_gallery/imaging/brukertiff.rst
+.. include:: conversion_examples_gallery/imaging/hdf5imaging.rst
+.. include:: conversion_examples_gallery/imaging/micromanagertiff.rst
+.. include:: conversion_examples_gallery/imaging/miniscope.rst
+.. include:: conversion_examples_gallery/imaging/scanbox.rst
+.. include:: conversion_examples_gallery/imaging/scanimage.rst
+.. include:: conversion_examples_gallery/imaging/tiff.rst
+
+
+Segmentation
+------------
+
+.. include:: conversion_examples_gallery/segmentation/caiman.rst
+.. include:: conversion_examples_gallery/segmentation/cnmfe.rst
+.. include:: conversion_examples_gallery/segmentation/extract.rst
+.. include:: conversion_examples_gallery/segmentation/suite2p.rst
+
+********
+Behavior
+********
+
+.. include:: conversion_examples_gallery/behavior/audio.rst
+.. include:: conversion_examples_gallery/behavior/deeplabcut.rst
+.. include:: conversion_examples_gallery/behavior/fictrac.rst
+.. include:: conversion_examples_gallery/behavior/lightningpose.rst
+.. include:: conversion_examples_gallery/behavior/sleap.rst
+.. include:: conversion_examples_gallery/behavior/video.rst
+.. include:: conversion_examples_gallery/behavior/neuralynx_nvt.rst
+
+Text
+----
+
+.. include:: conversion_examples_gallery/text/csv.rst
+.. include:: conversion_examples_gallery/text/excel.rst
+
+*****************************
+Common interface combinations
+*****************************
+
+.. include:: conversion_examples_gallery/combinations/spikeglx_and_phy.rst
+.. include:: conversion_examples_gallery/combinations/tiff_and_suite2p.rst
+.. include:: conversion_examples_gallery/combinations/ecephys_pose_estimation.rst
+
+.. note::
+  If you do not see the format you need, feel free to :format-request-form:`request it<>` or
+  :ref:`build-data-interface`.
diff --git a/docs/conversion_examples_gallery/behavior/audio.rst b/docs/conversion_examples_gallery/behavior/audio.rst
@@ -1,5 +1,5 @@
-Audio data conversion
----------------------
+Audio
+-----
 
 Install NeuroConv with the additional dependencies necessary for reading audio data.
 

diff --git a/docs/conversion_examples_gallery/behavior/deeplabcut.rst b/docs/conversion_examples_gallery/behavior/deeplabcut.rst
@@ -1,5 +1,5 @@
-DeepLabCut data conversion
---------------------------
+DeepLabCut
+----------
 
 Install NeuroConv with the additional dependencies necessary for reading DeepLabCut data.
 

diff --git a/docs/conversion_examples_gallery/behavior/fictrac.rst b/docs/conversion_examples_gallery/behavior/fictrac.rst
@@ -1,5 +1,5 @@
-FicTrac data conversion
---------------------------
+FicTrac
+-------
 
 Install NeuroConv with the additional dependencies necessary for reading `FicTrac <https://rjdmoore.net/fictrac/>`_ data.
 

diff --git a/docs/conversion_examples_gallery/behavior/lightningpose.rst b/docs/conversion_examples_gallery/behavior/lightningpose.rst
@@ -1,5 +1,5 @@
-LightningPose data conversion
---------------------------
+LightningPose
+-------------
 
 Install NeuroConv with the additional dependencies necessary for reading LightningPose data.
 

diff --git a/docs/conversion_examples_gallery/behavior/neuralynx_nvt.rst b/docs/conversion_examples_gallery/behavior/neuralynx_nvt.rst
@@ -1,5 +1,5 @@
-Neuralynx NVT data conversion
------------------------------
+Neuralynx NVT
+-------------
 
 Neuralynx NVT files contain information about position tracking. This interface requires no additional dependencies,
 so you can install NeuroConv using:

diff --git a/docs/conversion_examples_gallery/behavior/sleap.rst b/docs/conversion_examples_gallery/behavior/sleap.rst
@@ -1,5 +1,5 @@
-SLEAP data conversion
----------------------
+SLEAP
+-----
 
 Install NeuroConv with the additional dependencies necessary for reading SLEAP data.
 

diff --git a/docs/conversion_examples_gallery/behavior/video.rst b/docs/conversion_examples_gallery/behavior/video.rst
@@ -1,13 +1,13 @@
-Video data conversion (multimedia formats)
-------------------------------------------
+Video (multimedia formats)
+--------------------------
 
 Install NeuroConv with the additional dependencies necessary for reading multimedia data.
 
 .. code-block:: bash
 
     pip install neuroconv[video]
 
-This interface can handle conversions from avi, mov, mp4, wmv, flv and most FFmpeg_ supported formats to NWB using the
+This interface can handle conversions from .avi, .mov, .mp4, .wmv, .flv and most FFmpeg_-supported formats to NWB using the
 :py:class:`~neuroconv.datainterfaces.behavior.video.videodatainterface.VideoInterface` class.
 
 .. _FFmpeg: https://ffmpeg.org/

diff --git a/docs/conversion_examples_gallery/conversion_example_gallery.rst b/docs/conversion_examples_gallery/conversion_example_gallery.rst
diff --git a/docs/conversion_examples_gallery/imaging/brukertiff.rst b/docs/conversion_examples_gallery/imaging/brukertiff.rst
@@ -1,5 +1,5 @@
-Bruker TIFF data conversion
----------------------------
+Bruker TIFF
+^^^^^^^^^^^
 
 Install NeuroConv with the additional dependencies necessary for reading Bruker TIFF data.
 

diff --git a/docs/conversion_examples_gallery/imaging/hdf5imaging.rst b/docs/conversion_examples_gallery/imaging/hdf5imaging.rst
@@ -1,5 +1,5 @@
-HDF5 data conversion
---------------------
+HDF5 Imaging
+^^^^^^^^^^^^
 
 Install NeuroConv with the additional dependencies necessary for reading HDF5 data.
 

diff --git a/docs/conversion_examples_gallery/imaging/micromanagertiff.rst b/docs/conversion_examples_gallery/imaging/micromanagertiff.rst
@@ -1,5 +1,5 @@
-Micro-Manager TIFF data conversion
-----------------------------------
+Micro-Manager TIFF
+^^^^^^^^^^^^^^^^^^
 
 Install NeuroConv with the additional dependencies necessary for reading Micro-Manager TIFF data.
 

diff --git a/docs/conversion_examples_gallery/imaging/miniscope.rst b/docs/conversion_examples_gallery/imaging/miniscope.rst
@@ -1,5 +1,5 @@
-Miniscope data conversion
--------------------------
+Miniscope
+^^^^^^^^^
 
 Install NeuroConv with the additional dependencies necessary for reading Miniscope data.
 

diff --git a/docs/conversion_examples_gallery/imaging/scanbox.rst b/docs/conversion_examples_gallery/imaging/scanbox.rst
@@ -1,5 +1,5 @@
-Scanbox data conversion
------------------------
+Scanbox
+^^^^^^^
 
 Install NeuroConv with the additional dependencies necessary for reading Scanbox data.
 

diff --git a/docs/conversion_examples_gallery/imaging/scanimage.rst b/docs/conversion_examples_gallery/imaging/scanimage.rst
@@ -1,5 +1,5 @@
-ScanImage data conversion
--------------------------
+ScanImage
+^^^^^^^^^
 
 Install NeuroConv with the additional dependencies necessary for reading ScanImage data.
 

diff --git a/docs/conversion_examples_gallery/imaging/tiff.rst b/docs/conversion_examples_gallery/imaging/tiff.rst
@@ -1,5 +1,5 @@
-TIFF data conversion
---------------------
+TIFF
+^^^^
 
 Install NeuroConv with the additional dependencies necessary for reading TIFF data.
 

diff --git a/docs/conversion_examples_gallery/recording/abf.rst b/docs/conversion_examples_gallery/recording/abf.rst
@@ -1,5 +1,5 @@
-ABF data conversion
--------------------
+ABF
+---
 
 Install NeuroConv with the additional dependencies necessary for reading ABF data.
 

diff --git a/docs/conversion_examples_gallery/recording/alphaomega.rst b/docs/conversion_examples_gallery/recording/alphaomega.rst
@@ -1,5 +1,5 @@
-AlphaOmega conversion
----------------------
+AlphaOmega
+^^^^^^^^^^
 
 Install NeuroConv with the additional dependencies necessary for reading AlphaOmega data.
 

diff --git a/docs/conversion_examples_gallery/recording/axona.rst b/docs/conversion_examples_gallery/recording/axona.rst
@@ -1,5 +1,5 @@
-Axona data conversion
----------------------
+Axona
+^^^^^
 
 Install NeuroConv with the additional dependencies necessary for reading Axona data.
 

diff --git a/docs/conversion_examples_gallery/recording/biocam.rst b/docs/conversion_examples_gallery/recording/biocam.rst
@@ -1,5 +1,5 @@
-Biocam conversion
------------------
+Biocam
+^^^^^^
 
 Install NeuroConv with the additional dependencies necessary for reading Biocam data.
 

diff --git a/docs/conversion_examples_gallery/recording/blackrock.rst b/docs/conversion_examples_gallery/recording/blackrock.rst
@@ -1,6 +1,5 @@
-Blackrock data conversion
--------------------------
-
+Blackrock recording
+^^^^^^^^^^^^^^^^^^^
 Install NeuroConv with the additional dependencies necessary for reading Blackrock data.
 
 .. code-block:: bash