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About spe-1

Information about spe-1 (simultaneous patch clamp and extracellular 1).


In this dataset, we recorded simultaneously from the same cortical neuron using patch-clamp and extracellular (Neuropixel, 384 channel) probes, in urethane-anaesthetized rats (no stimulus, just spontaneous activity). A total of 43 neurons were recorded from in primary motor and somatosensory cortex. 38 neurons were recorded in cell-attached mode and 5 in whole-cell. Out of the 43 neurons that we patched, 21 showed clear extracellular spike waveforms, and for 10 of these the peak-peak amplitude exceeded 50 µV. For each neuron, we provide the raw extracellular recording file (action potential band, high-pass filtered at 300 Hz) and the corresponding patch-clamp recording, as well as sync channels for the two modalities, sample number for spike peaks in the patch-clamp recording, and corresponding sample numbers in the extracellular recording. Results from the experiments and detailed information about the dataset are described in:

Recording from the same neuron with high-density CMOS probes and patch-clamp: a ground-truth dataset and an experiment in collaboration.  André Marques-Smith, Joana Pereira Neto, Gonçalo Lopes, Joana Nogueira, Lorenza Calcaterra, João Frazão, Danbee Kim, Matthew G. Phillips, George Dimitriadis, Adam Kampff. bioRxiv 370080; doi:

We have also set up a companion repository featuring all the code used in the above publication, indications on how to load and interact with the dataset, and proposed follow-up projects for collaboration. Interested parties are welcome and encouraged to collaborate on these projects:

Format of the data.

The data is stored in CSV and binary format.  Scripts for using the data are provided.  Details of the formats are in the given in the data description document, linked to at the bottom of this page. Total size of the data is about 276 GB

How to download the data.

The data must be downloaded from:

A account is required.  This link allows bulk downloading of multiple files using the download script as described in the "Alternative download method" section on the download page.

Getting help using the data.

You can get help with the data set by posting any questions on the forum for using data sets, by raising an issue at the GitHub repository, or through direct email contact to [email protected]. We warmly encourage and welcome collaborations and suggestions on follow-up analytical projects through the GitHub repository, as well as corrections on any bugs or mistakes we may have missed.

How to cite the data

If you publish any work using the data, please cite the publications above (Marques-Smith et. al, 2018), as well as the dataset itself:

André Marques-Smith, Joana P. Neto, Gonçalo Lopes, Joana Nogueira, Lorenza Calcaterra, João Frazão, Danbee Kim, Matthew G. Phillips, George Dimitriadis and Adam R. Kampff (2018); Simultaneous patch-clamp and dense CMOS probe extracellular recordings from the same cortical neuron in anaesthetized rats.

The above citation uses a Digital Object Identifier (DOI) which is assigned to the data set.  The DOI was created using DataCite ( and the California Digital Library, "EZID" system (

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