diff --git a/docs/source/ephys_at_swc/community.md b/docs/source/ephys_at_swc/community.md index d1eff6a..ecedbf7 100644 --- a/docs/source/ephys_at_swc/community.md +++ b/docs/source/ephys_at_swc/community.md @@ -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). diff --git a/docs/source/ephys_at_swc/getting_started.md b/docs/source/ephys_at_swc/getting_started.md index e2c8fbf..ab37760 100644 --- a/docs/source/ephys_at_swc/getting_started.md +++ b/docs/source/ephys_at_swc/getting_started.md @@ -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. @@ -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. diff --git a/docs/source/ephys_at_swc/resources.md b/docs/source/ephys_at_swc/resources.md index 93096d1..6629ab5 100644 --- a/docs/source/ephys_at_swc/resources.md +++ b/docs/source/ephys_at_swc/resources.md @@ -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. @@ -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 @@ -85,10 +85,8 @@ 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 @@ -96,10 +94,10 @@ of the page. 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 @@ -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).