Dataset Open Access
Ground truth recordings for validation of spike sorting algorithms
Giulia LB Spampinato;
Elric Esposito;
Pierre Yger;
Jens Duebel;
Serge Picaud;
Olivier Marre
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<subfield code="a"><p><strong>Ground-truth recordings for validation of spike sorting algorithms</strong><br>
&nbsp;</p>
<p>This datasets is composed of simultaneous loose patch recordings of Ganglion Cells in mice retina, combined with dense extra-cellular recordings (252 channels). The details of the dataset can be found here <a href="https://elifesciences.org/articles/34518">https://elifesciences.org/articles/34518</a></p>
<p><strong>Probe layout</strong></p>
<p>The probe layout can be found as mea_256.prb. This is a 16x16 Multi Electrode Array with 30um spacing. Only 252 channels are extra-cellular signals, and the 4 corners are devoted to triggers/sync/juxta.</p>
<p><strong>Struture of the data</strong></p>
<p>In this dataset, you will find several individual recordings, at max 5min long each (but please do not hesitate to contact us if interested by longer recordings).&nbsp;The extra-cellular data are saved as 16bits unsigned integer, with a variable offset at the beginning of the file. The value of this offset is given, for every datafile, in the additional text file (padding value (see following for more details)).&nbsp;The files have already been filtered with a Butterworth filter of order 3 with a cut-off frequency at 100Hz</p>
<p><strong>Structure of a given dataset</strong></p>
<p>Please read carefully the following to understand how to load and perform spike sorting with the data. In every .tar.gz file, you will find:</p>
<ul>
<li>&nbsp;a jpg image, displaying a small chunk of the juxta-cellular signal (top left), with detected peaks and threshold. The extra-cellular spike triggered waveform, across all channels, for the juxta-spike times (top right). In the bottom, you can see the juxta-cellular spikes, for all the detected triggers (left), and on the right the voltage on the channel where the Spike Triggered Average of the extra-cellular waveform is peaking the most.</li>
<li>a file .juxta.raw, as float32, with the juxta-cellular trace at 20kHz, no data offset</li>
<li>a file .raw, as uint16, with the extra-cellular signals recorded for 256 channels at a sampling rate of 20kHZ. In fact, only 252 channels are extra-cellular signals, the 4 corners of the arrays are devoted to juxta-cellular and sync signals (see probe layout mea_256.prb)</li>
<li>a file .triggers.npy containing the spike times of the juxta-cellular spikes, detected using a threshold of k.MAD. The exact value of k can vary on a per dataset basis, and is written in the .txt file (threshold)</li>
<li>a .txt file describing some information for a given dataset, such as the threshold value used to detect the spikes, the channel in the raw file where the juxta-cellular signal is located, the minimal value of the peak for the STA (and on which channel it is located), and the header size to read the raw data</li>
<li>a .params file, if you want to analyze the data with SpyKING CIRCUS</li>
</ul>
<p><strong>How to load the raw data in numpy</strong></p>
<pre><code class="language-python">#Using the offset value from the txt file, we can load the data with memmap arrays
data=numpy.memmap('mydata.raw', dtype='uint16', offset=offset, mode='r')
data=data.reshape(len(data)//256, 256)
#Then for example, to display the first second of channel 0
one_channel = data[:20000, 0].astype('float32')
#If we want to center data around 0
one_channel -= 2**15 - 1
#And if we want to display data in micro volt, we must use the gain factor of 0.1042 provided in the header
one_channel *= 0.1042</code></pre>
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1,886
1,131
views
downloads
| All versions | This version | |
|---|---|---|
| Views | 1,886 | 1,898 |
| Downloads | 1,131 | 1,131 |
| Data volume | 1.7 TB | 1.7 TB |
| Unique views | 1,692 | 1,704 |
| Unique downloads | 407 | 407 |
Indexed in
- Publication date:
- March 22, 2018
- DOI:
-
- Keyword(s):
- neuroscience, spike sorting, ground-truth, spyking circus
- Published in:
- Elife:.
- License (for files):
- Creative Commons Attribution 4.0 International