Potter Lab Data, Code and Designs

Potter Lab Data, Code and Designs

MEA Data Sharing

We have been sharing multi-electrode array data for years, long before the NIH and NSF began to ask for “data sharing” policies in grant proposals. One of our best-cited papers describes how cortical cultures develop interesting patterns of activity in vitro. This was the work of Daniel Wagenaar, when he was a PhD student at Caltech. We have made the entire dataset (over 40 GB) freely available for you to analyze further. A number of independent labs have done this and published their own findings about the data.

  • Wagenaar, D. A., Pine, J. and Potter, S. M. (2006). An extremely rich repertoire of bursting patterns during the development of cortical cultures. BMC Neuroscience 7:11.Reprint (2.79 MB PDF).

This dataset can be accessed by clicking here.

OptoClamp

We also have many gigs worth of MEA data recorded from cultures undergoing optogenetic control using our OptoClamp closed-loop system. This is the work of former PhD students, Jonathan Newman and Ming-fai Fong, as described in these papers:

  • Newman, J. P., Fong, M-f, Millard, D. C., Whitmire, C. J., Stanley, G. B., & Potter, S. M. (2015) Optogenetic feedback control of neural activity. eLife 2015;4:e07192 Online Open-Access Paper
  • Fong, M.-F., Newman, J. P., Potter, S. M., & Wenner, P. (2015). Upward synaptic scaling is dependent on neurotransmission rather than spiking. Nature Communications, 6, 6339. Online Open-Access Paper

Access the recommendation on F1000Prime

Data associated with these OptoClamp papers can be found here.


Code and Electronics Sharing

NeuroRighter

The details of how to make your own NeuroRighter multi-unit electrophysiology system can be found here. NeuroRighter was created and used in vivo by former MD/PhD student John Rolston, and re-created, added to, and tested in vivo and in vitro by former PhD student Jonathan Newman (and our collaborators in Garrett Stanley’s lab). Jon Newman also created the high-speed LED controller for optogenetic experiments, Cyclops, that made the OptoClamp possible. He has made detailed plans for it available as part of the OpenEphys project, here.

  • Newman, J. P, Zeller-Townson, R, Fong, M.-f., Arcot Desai, S., Gross, R. E., and Potter, S. M. (2103) Closed-Loop, Multichannel Experimentation Using the Open-Source NeuroRighter Electrophysiology Platform. Frontiers in neural circuits, 6(January):98. Online Open Access paper
  • Rolston, J. D., Gross, R. E., & Potter, S. M. (2010). Closed-loop, open-source electrophysiology (Invited Focused Review). Frontiers in Neuroscience, 4(31), 1-8. Online Open-Access paper
  • Rolston, J. D., Gross, R. E., & Potter, S. M. (2009). A low-cost multielectrode system for data acquisition and real-time processing with rapid recovery from stimulation artifacts. Frontiers in Neuroengineering, 2(12), 1-17. Online Open-Access paper.

MEABench

The precursor to NeuroRighter was Daniel Wagenaar’s MEABench, a set of software and hardware tools that made closed-loop all-electrode stimulation and MEA electrophysiology possible for the first time. Here is the MEABench web page. MEABench-related papers include:

  • Wagenaar, D. A., DeMarse, T. B., & Potter, S. M. (2005). MeaBench: A toolset for multi-electrode data acquisition and on-line analysis. 2nd Intl. IEEE EMBS Conference on Neural Engineering, 518-521. Reprint (1 MB PDF)
  • Wagenaar, D. A. and Potter, S. M. (2004). A versatile all-channel stimulator for electrode arrays, with real-time control. Journal of Neural Engineering 1: 39-45. Reprint (335 Kb PDF).
  • Wagenaar, D. A. and S. M. Potter (2002). “Real-time multi-channel stimulus artifact suppression by local curve fitting.” J. Neurosci. Methods 120: 113-120. Full Text (308 Kb PDF) (Abstract).
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