Skip to content

Commit

Permalink
Small rewrites for community, getting started, resources.
Browse files Browse the repository at this point in the history
  • Loading branch information
JoeZiminski committed Jul 5, 2024
1 parent 52f4e44 commit 1c6096f
Show file tree
Hide file tree
Showing 3 changed files with 29 additions and 30 deletions.
2 changes: 1 addition & 1 deletion docs/source/ephys_at_swc/community.md
Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ Please don't hesitate to contact us
For information and advice on electrophysiology from the SWC community, the
best place to go is the `#forum-extracellular-ephys` channel on the SWC Slack.

Outside the SWC, you can address any questions or issues for
Outside the SWC, you can address any questions or issues about
[SpikeInterface](https://github.com/SpikeInterface)
by raising an issue on their
[GitHub repository](https://github.com/SpikeInterface/spikeinterface/issues).
Expand Down
23 changes: 12 additions & 11 deletions docs/source/ephys_at_swc/getting_started.md
Original file line number Diff line number Diff line change
@@ -1,10 +1,11 @@
# Getting Started

Getting started with extracellular electrophysiology can be intimidating!
With numerous acquisition setups, software packages, preprocessing, postprocessing,
and analysis steps to consider, it's understandable to feel daunted.
With the numerous acquisition setups, software packages, preprocessing, postprocessing,
and analysis steps to consider, how to get started with extracellular electrophysiology
is not always clear.

A good first step in getting started is to ask for advice. Every setup
A good first step is to ask for advice around your particular
experimental setup and research question. Every setup
and experiment is different, and it's often most effective to
seek guidance early on. See the [Community](community)
sections for details on where to get help.
Expand All @@ -14,11 +15,11 @@ for the history and landscape of extracellular electrophysiology.
See the resources section for [general introductions](#general-introduction)
as well as more technical reading for deeper background.

INTRODUCE SPIKEINTERFACE

To get started with pipeline building, the
[SpikeInterface](#spikeinterface) resources are a good starting point.
We also have
For preprocessing and spike sorting, we recommend
[SpikeInterace](https://github.com/SpikeInterface/spikeinterface),
an open source community toolkit for extracellular electrophysiology. To get
started with pipeline building, the
[SpikeInterface](https://spikeinterface.readthedocs.io/en/stable/)
documentation is a good starting point. We also have
[Examples](gallery/index)
from researchers at the
SWC who'd be happy to answer any questions you might have.
from researchers at the SWC who'd be happy to answer any questions you might have.
34 changes: 16 additions & 18 deletions docs/source/ephys_at_swc/resources.md
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
# Resources

This section provides articles and videos providing
This section includes articles and videos providing
background and technical detail on extracellular
electrophysiology data preprocessing and analysis.

Expand All @@ -23,25 +23,25 @@ and overview of the extracellular electrophysiology landscape:

## Technical Introduction

Below are more technical resources on the different stages of
This section includes more technical resources on the different stages of
extracellular electrophysiology analysis.

A particularly useful resource is the
[Neuropixels](https://www.ucl.ac.uk/neuropixels/courses) course, with their videos published online
(e.g. [2023](https://www.ucl.ac.uk/neuropixels/training/2023-neuropixels-course)).
While these are particularly useful for Neuropixels users, they are
useful resources for any researcher
While these are targeted towards for Neuropixels users, they are
valuable resources for any researcher
approaching electrophysiology preprocessing and analysis.

### Preprocessing

The [IBL white paper](https://figshare.com/articles/online_resource/Spike_sorting_pipeline_for_the_International_Brain_Laboratory/19705522)
contains a clearly written overview of preprocessing steps. Similarly,
[Bill Karsh's guide](https://billkarsh.github.io/SpikeGLX/help/catgt_tshift/catgt_tshift/) on the
SpikeGLX website also gives a useful overview.
contains a clearly written overview of common preprocessing steps. Similarly,
[Bill Karsh's guide](https://billkarsh.github.io/SpikeGLX/help/catgt_tshift/catgt_tshift/) on
SpikeGLX preprocessing tools gives a useful overview.

[de Cheveigné & Nelken (2019)](https://pubmed.ncbi.nlm.nih.gov/30998899/)
provide a more technical treatment of digital filtering, a key step in preprocessing and analysis.
provide a technical treatment of digital filtering, a key step in preprocessing and analysis.

### Spike Sorting

Expand Down Expand Up @@ -85,21 +85,19 @@ in their documentation.
Visit the SpikeInterface
[GitHub](https://github.com/SpikeInterface/spikeinterface)
and
[Documentation](https://spikeinterface.readthedocs.io/en/latest/index.html)
to get started. Note their documentation currently points to the developer
version, select your installed version from the list at the bottom-left
of the page.
[Documentation](https://spikeinterface.readthedocs.io/en/stable/)
to get started.

## Other Community Tools

### Analysis

SpikeInterface
is mainly focused on preprocessing, spike sorting and quality metrics.
[Pynapple](https://github.com/pynapple-org/pynapple)
and
[Elephant]( https://neuralensemble.org/elephant/)
both provide nice toolboxes for analysing data post-sorting.
[Pynapple](https://github.com/pynapple-org/pynapple),
[Elephant]( https://neuralensemble.org/elephant/),
and [Nemos](https://github.com/flatironinstitute/nemos)
all provide nice toolboxes for analysing data post-sorting.

The [SpikeForest](https://spikeforest.flatironinstitute.org/)
project is an excellent resource for assessing the performance of
Expand All @@ -111,5 +109,5 @@ different spike-sorting algorithms across probe types and brain regions.

[The IBL sorting pipeline](https://github.com/int-brain-lab/ibl-neuropixel)

[Neuropixels Utils](https://djoshea.github.io/neuropixel-utils/) package
(MATLAB) and related [NeuroPyxels](https://github.com/m-beau/NeuroPyxels).
For working with NeuroPixels, [Neuropixels Utils](https://djoshea.github.io/neuropixel-utils/) package
(MATLAB) and [NeuroPyxels](https://github.com/m-beau/NeuroPyxels) (Python).

0 comments on commit 1c6096f

Please sign in to comment.