Merge branch 'master' into merge_ap_lfp_neuropix

Author: DradeAW

doc/api.rst

@@ -149,6 +149,7 @@ spikeinterface.preprocessing
     .. autofunction:: correct_lsb
     .. autofunction:: detect_bad_channels
     .. autofunction:: filter
+    .. autofunction:: highpass_filter
     .. autofunction:: highpass_spatial_filter
     .. autofunction:: interpolate_bad_channels
     .. autofunction:: normalize_by_quantile
@@ -159,6 +160,7 @@ spikeinterface.preprocessing
     .. autofunction:: scale
     .. autofunction:: whiten
     .. autofunction:: zero_channel_pad
+    .. autofunction:: zscore
 
 
 spikeinterface.postprocessing

doc/index.rst

@@ -7,7 +7,7 @@ Welcome to SpikeInterface's documentation!
   :align: center
 
 
-Spikeinterface is a Python module to analyze extracellular electrophysiology data.
+SpikeInterface is a Python module to analyze extracellular electrophysiology data.
 
 With a few lines of code, SpikeInterface enables you to load and pre-process the recording, run several 
 state-of-the-art spike sorters, post-process and curate the output, compute quality metrics, and visualize the results.
@@ -29,7 +29,7 @@ SpikeInterface is made of several modules to deal with different aspects of the
 - compare and benchmark spike sorting outputs.
 - compute quality metrics to validate and curate spike sorting outputs.
 - visualize recordings and spike sorting outputs.
-- export report and export to Phy.
+- export a report and/or export to Phy.
 - offer a powerful Qt-based viewer in a separate package `spikeinterface-gui <https://https://github.com/SpikeInterface/spikeinterface-gui>`_
 - have some powerful sorting components to build your own sorter.
 
@@ -63,7 +63,7 @@ To get started with SpikeInterface, you can take a look at the following additio
   | figures of SpikeInterface-based papers and to showcase the latest features of SpikeInterface.
 
 - | The `2020 eLife paper <https://elifesciences.org/articles/61834>`_ introduces the concept and motivation and 
-  | performs an in-depth comparison of multiple sorters (spolier alert: they strongly disagree between each other!). 
+  | performs an in-depth comparison of multiple sorters (spoiler alert: they strongly disagree with each other!). 
   | **Note**: the code-base and implementation have changed a lot since the "paper" version published in 2020. 
   | For detailed documentation we therefore suggest more recent resources, like this documentation and :code:`spiketutorials`.
 

doc/install_sorters.rst

@@ -4,18 +4,18 @@ Installing Spike Sorters
 ========================
 
 
-An important aspect of spikeinterface is the :py:mod:`spikeinterface.sorters` module.
+An important aspect of SpikeInterface is the :py:mod:`spikeinterface.sorters` module.
 This module wraps many popular spike sorting tools, allowing you to run multiple sorters on the same dataset with
 only a few lines of code and through Python.
 
 Installing spike sorters can be painful! Many of them come with several requirements that could cause conflicts in 
-your Python environment. To make things easier, we have created docker images for most of these sorters, 
-and in many cases the easiest way to run them is to do so via docker or singularity. 
+your Python environment. To make things easier, we have created Docker images for most of these sorters, 
+and in many cases the easiest way to run them is to do so via Docker or Singularity. 
 **This is the approach we recommend for all users.** 
 To run containerized sorters see our documentation here: :ref:`containerizedsorters`.
 
 There are some cases where users will need to install the spike sorting algorithms in their own environment. If you
-are on a system where it is infeasible to run docker or singularity containers, or if you are actively developing the
+are on a system where it is infeasible to run Docker or Singularity containers, or if you are actively developing the
 spike sorting software, you will likely need to install each spike sorter yourself.
 
 Some of theses sorters are written in Matlab, so you will also need to install Matlab if you want
@@ -50,6 +50,7 @@ Herdingspikes2
 
     pip install herdingspikes
 
+
 HDSort
 ^^^^^^
 
@@ -62,18 +63,20 @@ HDSort
       # provide installation path by setting the HDSORT_PATH environment variable
       # or using HDSortSorter.set_hdsort_path()
 
+
 IronClust
 ^^^^^^^^^
 
 * Matlab
 * Url: https://github.com/jamesjun/ironclust
 * Authors: James J. Jun
-* Installation need Matlab::
+* Installation needs Matlab::
 
       git clone https://github.com/jamesjun/ironclust
       # provide installation path by setting the IRONCLUST_PATH environment variable
       # or using IronClustSorter.set_ironclust_path()
 
+
 Kilosort
 ^^^^^^^^
 
@@ -86,7 +89,8 @@ Kilosort
       # provide installation path by setting the KILOSORT_PATH environment variable
       # or using KilosortSorter.set_kilosort_path()
 
-* See also for Matlab/cuda: https://www.mathworks.com/help/parallel-computing/gpu-support-by-release.html
+* See also for Matlab/CUDA: https://www.mathworks.com/help/parallel-computing/gpu-support-by-release.html
+
 
 Kilosort2
 ^^^^^^^^^
@@ -100,7 +104,7 @@ Kilosort2
       # provide installation path by setting the KILOSORT2_PATH environment variable
       # or using Kilosort2Sorter.set_kilosort2_path()
 
-* See also for Matlab/cuda: https://www.mathworks.com/help/parallel-computing/gpu-support-by-release.html
+* See also for Matlab/CUDA: https://www.mathworks.com/help/parallel-computing/gpu-support-by-release.html
 
 
 Kilosort2.5
@@ -115,7 +119,8 @@ Kilosort2.5
       # provide installation path by setting the KILOSORT2_5_PATH environment variable
       # or using Kilosort2_5Sorter.set_kilosort2_path()
 
-* See also for Matlab/cuda: https://www.mathworks.com/help/parallel-computing/gpu-support-by-release.html
+* See also for Matlab/CUDA: https://www.mathworks.com/help/parallel-computing/gpu-support-by-release.html
+
 
 Kilosort3
 ^^^^^^^^^
@@ -129,12 +134,13 @@ Kilosort3
       # provide installation path by setting the KILOSORT3_PATH environment variable
       # or using Kilosort3Sorter.set_kilosort3_path()
 
-* See also for Matlab/cuda: https://www.mathworks.com/help/parallel-computing/gpu-support-by-release.html
+* See also for Matlab/CUDA: https://www.mathworks.com/help/parallel-computing/gpu-support-by-release.html
+
 
 pyKilosort
 ^^^^^^^^^^
 
-* Python, requires cuda
+* Python, requires CUDA
 * Url: https://github.com/int-brain-lab/pykilosort / https://github.com/MouseLand/pykilosort
 * Authors: Marius Pachitariu, Shashwat Sridhar, Alexander Morley, Cyrille Rossant, Kush Bunga
 
@@ -175,10 +181,9 @@ Mountainsort4
       pip install mountainsort4
 
 
-SpykingCircus
+SpyKING CIRCUS
 ^^^^^^^^^^^^^
 
-
 * Python, requires MPICH
 * Url: https://spyking-circus.readthedocs.io
 * Authors: Pierre Yger, Olivier Marre
@@ -201,12 +206,13 @@ Tridesclous
 
 * Optional installation of opencl ICD and pyopencl for hardware acceleration::
 
-        sudo apt-get install beignet (optional if intel GPU)
-        sudo apt-get install nvidia-opencl-XXX (optional if nvidia GPU)
+        sudo apt-get install beignet (optional if Intel GPU)
+        sudo apt-get install nvidia-opencl-XXX (optional if NVIDIA GPU)
         sudo apt-get install pocl-opencl-icd (optional for multi core CPU)
         sudo apt-get install opencl-headers ocl-icd-opencl-dev libclc-dev ocl-icd-libopencl1
         pip install pyopencl
 
+
 Waveclus
 ^^^^^^^^
 
@@ -250,11 +256,11 @@ Klusta (LEGACY)
 
 * See also: https://github.com/kwikteam/phy
 
+
 Yass (LEGACY)
 ^^^^^^^^^^^^^
 
-
-* Python, cuda, torch
+* Python, CUDA, torch
 * Requires SpikeInterface<0.96.0 (and Python 3.7)
 * Url: https://github.com/paninski-lab/yass
 * Authors: JinHyung Lee, Catalin Mitelut, Liam Paninski
@@ -286,4 +292,4 @@ working not only at peak times but at all times, recovering more spikes close to
 
         pip install hdbscan
         pip install spikeinterface
-        pip install numba  (or conda install numba as recommended by conda authors)
+        pip install numba  (or conda install numba as recommended by conda authors)