We hope you enjoyed the last Monthly Must-Reads about Neurons and Viruses. In the other months this year we mainly highlighted scientific topics such as Axons in January, Retina in February and last month we highlighted Organoids.

This month we want to highlight a topic that complements the above four editions perfection! During times of COVID-19 and the significant amount of home-office hours, you might have more time to analyse all of your data. Therefore we have decided to pick five articles. that allow you to delve deeper into the topic of Spikesorting! The five papers we decided to highlight this month are a mere snippet of the wide range of publications out there but are a great read during these unconventional times.

In the subsequent section you can find the highlighted paper and four other educational articles. For this month we decided to highlight the article Buccino et al. concerning SpikeInterface!

SpikeInterface, a unified framework for spike sorting.
by Alessio P. Buccino, Cole L. Hurwitz, Jeremy Magland, Samuel Garcia, Joshua H. Siegle, Roger Hurwitz, and Matthias H. Hennig. bioRxiv. October 2019.

With the development of high density micro electrode arrays and multichannel silicone probes, scientists can now simultaneously record extracellular activity from thousands of neurons at once. In order to analyze these signals at the single cell resolution the generated raw voltage traces need to be separated and clustered based on the similarity of their shapes. Recently several automatic unsupervised algorithms where developed in order to spike sort large datasets generated by high density devices. Since most of these have different file format and hardware requirements they reduce interoperability, and make it challenging to cross compare results. In this months featured preprint article, Buccino and coworkers highlight SpikeInterface, a framework that unifies existing automatic sorting algorithms to one code base. Authors demonstrate how it can improve the accessibility, reliability, and reproducibility of spike sorting of large scale datasets.

Read the paper here.

Besides the above-mentioned paper, four other publications that are highly relevant to the topic of Spike Sorting can be found below:

  1. A spike sorting toolbox for up to thousands of electrodes validated with ground truth recordings in vitro and in vivo.
    by Pierre Yger, Giulia LB Spampinato, Elric Esposito, Baptiste Lefebvre, Stephane Deny, Christophe Gardella, Marcel Stimberg, Florian Jetter, Guenther Zeck, Serge Picaud, Jens Duebel and Olivier Marre. eLife. March 2018.
    Read the paper here.
  2. Automatic spike sorting for high-density microelectrode arrays.
    by Roland Diggelmann, Michele Fiscella, Andreas Hierleman and Felix Franke. The Mouse Visual System. December 2018.
    Read the paper here.
  3. Unsupervised Spike Sorting for Large-Scale, High-Density Multielectrode Arrays.
    by Gerrit Hilgen, Martino Sorbaro, Sahar Pirmoradian, Jens-Oliver Muthmann, Ibolya Edit Kepiro, Simona Ullo, Cesar Juarez Ramirez, Albert Puente Encinas, Alessandro Maccione, Luca Berdondini, Vittorio Murino, Diego Sona, Francesca Cella Zanacchi, Evelyne Sernagor and Matthias Helge Hennig. Cell Reports. March 2017.
    Read the paper here. 
  4. Kilosort: realtime spike-sorting for extracellular electrophysiology with hundreds of channels.
    by Marius Pachitariu, Nicholas Steinmetz, Shabnam Kadir, Matteo Carandini and Kenneth D. Harris. bioRxiv. June 2016.
    Read the paper here.