Spike Sorting and Reproducibility for Next Generation Electrophysiology

24. and 25. June 2019 Informatics Forum, University of Edinburgh

The analysis of extracellular recordings is a computationally and conceptually complex task with multiple sources of error and bias that can affect subsequent data interpretation. The advent of high-density extracellular micro-electrode arrays (MEAs) now allows recording from hundreds to thousands of channels that poses significant challenges. Additionally, current analysis workflows lack standardisation, and few attempts have been made to make perform systematic comparisons between different solutions and approaches.

This workshop will bring together electrophysiologists and developers of tools for the analysis of extracellular recordings, with the following goals:

  • to showcase new approaches to analyse large scale recordings
  • to discuss approaches for validation and quality control
  • to discuss how elements of reproducibility and provenance can be added to typical analysis workflows
If there is interest, the workshop will also include hands-on spike sorting tutorials for Mountainsort, Ironclust (formerly JRClust), HS2 and SpykingCircus. Bring your own data or use the example data provided.

The meeting will consist of a series of invited talks and discussion sessions on the topics of spike sorting and reproducible data analysis. We hope to not only summarise the state of the art, but to also develop recommendations for new solutions. We invite poster presentations to be held on 24. June.

Invited Speakers

Alessio Buccino, Oslo
David Jaeckel, MaxWell
Espen Hagen, Oslo
Felix Franke, ETHZ
Samuel Garcia, CNRS
James Jun, Flatiron Institute
Jeremy Magland, Flatiron Institute
André Marques Smith, UCL
Olivier Marre, Institut de la vision
Hernan G Rey, Leicester
Gerrit Hilgen, Newcastle
Olivier Winter, Champalimaud
Pierre Yger, Institut de la vision

Registration and Submission

Registation is now closed.


24 June
9:30 coffee
10:20 welcome
10:30 Olivier Winter: Spike Sorting Roadmap for Large Scale Neurophysiology at IBL.
11:00 James Jun: Drift-resistant, real-time spike sorting based on anatomical similarity for high channel-count silicon probes.
11:30 coffee
12:00 Felix Franke: Template-matching-based spike sorting for large scale high-density electrode arrays. Past and future challenges
12:30 Pierre Yger: A real-time spike sorting software for hundreds of electrodes.
13:00 lunch
14:30 André Marques Smith: Recording from the same neuron using Neuropixel probes and patch-clamp - a ground-truth dataset.
15:00 Espen Hagen: Forward-model based generation of test data with ground truth for spike-sorting algorithms using ViSAPy and LFPy.
15:30 Alessio Buccino: MEArec: a fast and customizable testbench simulatorfor ground-truth extracellular spiking activity.
16:00 coffee, posters and demonstrations
19:00 dinner

25 June
9:30 Olivier Marre: Spike sorting: a few lessons from the retina.
10:00 Gerrit Hilgen: A Large-scale, high-density recordings of light responses from mouse retinal ganglion cells.
10:30 coffee
11:00 David Jaeckel: Challenges and Opportunities of Analyzing MEA Recordings of iPSC-derived Neurons
11:30 Cole Hurwitz: SpikeInterface: An open-source framework for sorting, analysis, and evaluation of extracellular recordings.
12:00 Samuel Garcia: Reproducible evaluation of different spike sorters using spiketoolkit - concept and examples.
12:30 lunch
13:30 Jeremy Magland: SpikeForest: a web-based spike sorting validation platform and analysis framework.
14:00 Hernan Rey: How do we pick the right spike sorting approach for a given application?
14:30 coffee, tutorials and discussion
16:30 closing session


By train the nearest station is Edinburgh Waverley, which is less than a 15 minute walk from the Informatics Forum. See National Rail Enquiries for train information.
For those coming from further afield, information about travel to and from Edinburgh Airport is available. A taxi to the city centre from the airport costs about 22GBP to 24GBP one way. There is an express bus from the airport called Airlink that terminates in the city centre (7.50GBP return), and a tram travelling the same route (8.50GBP return, get off at Princess street). Journey time is about 30 minutes.


Matthias Hennig, Edinburgh
Cole Hurwitz, Edinburgh
Jeremy Magland, Flatiron
Alessio Buccino, Oslo