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updated doc
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petersenpeter committed Dec 23, 2022
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5 changes: 5 additions & 0 deletions docs/interface/neuroscope2.md
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Expand Up @@ -43,6 +43,11 @@ NeuroScope2 is substantially faster than the original NeuroScope. The below figu

![Benchmarks of NeuroScope2](https://raw.githubusercontent.com/petersenpeter/common_resources/main/images/benchmark_window_duration-01.png)

{: .note-title}
> Raw data performance
>
> Matlab's plot performance scales non-linearly with the number of raw data points, but linearly with the number of channels plotted. Adjust the window duration to optimize this. For a recording with 128 channels sampled at 20kHz, the window duration should be kept below 1.2 sec for optimized performance. The window duration should be kept below 0.55 sec for a Neuropixels recording with 384 channels sampled at 30kHz.
## Metadata
NeuroScope2 uses the [session struct](https://cellexplorer.org/datastructure/data-structure-and-format/#session-metadata) for session-level metadata. Please see [this tutorial](https://cellexplorer.org/tutorials/metadata-tutorial/) on how to generate and fill out the metadata. Metadata can be imported from multiple sources: an existing `basename.xml` file (NeuroSuite), from Intan's `info.rhd` file, from KiloSort's `rez.mat` file and from a `basename.sessionInfo.mat` (Buzcode) file.

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10 changes: 8 additions & 2 deletions docs/tutorials/neuropixels-tutorial.md
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Expand Up @@ -110,7 +110,6 @@ basepaths = {'/your/data/path/basename1/','/your/data/path/basename2/'};
basenames = {'basename1','basename2'};
cell_metrics = loadCellMetricsBatch('basepaths',basepaths,'basenames',basenames);
cell_metrics = CellExplorer('metrics',cell_metrics);
```

Expand All @@ -122,7 +121,14 @@ cd('/Volumes/Peter_SSD_4/CellExplorerTutorial/MS22/Peter_MS22_180629_110319_conc
NeuroScope2
```

{: .note-title }
{: .note-title}
> Example dataset shown in NeuroScope2 is available to download
>
> Please see the [download instructions](https://cellexplorer.org/datastructure/data-structure-and-format/#example-dataset). The dataset contains a raw dat file, an lfp file, session metadata, spikes, brain states, behavior, events data, and digital and analog traces.
{: .note-title}
> Viewing a Neuropixels recording in NeuroScope2
>
> Matlab's plot performance scales non-linearly with the number of raw data points, but linearly with the number of channels plotted. For optimized performance, the windows duration should be kept below 0.6 sec when viewing the raw data for a Neuropixels recording with 384 channels sampled at 30kHz.
> Neuropixels recordings has a DC offset that is recommended to remove when viewing the traces by selecting "Remove DC from ephys traces" from the settings menu in NeuroScope2.

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