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Software/Data Downloads

Data downloads

  • Error neurons in MFC: data release (OSF). This contains the data for Fu et al. 2022, Science
  • Cognitive boundary neurons: data release in NWB (DANDI). This contains the data for Zheng et al. 2022, Nat Neurosci
  • Single neurons and LFP in MTL during free viewing of faces: data release (OSF). This contains the data for Staudigl, Minxha et al., Science Advances
  • Single neurons and LFP in STN during stop signal task: data release (OSF). This contains the data for Mosher et al. 2021, Neuron
  • MFC/MTL neurons for task switching: data release (OSF). This contains the data for Minxha et al. 2020, Science
  • NWB-formatted single-neuron dataset during recognition memory: Scientific Data data descriptor and data release (OSF). This contains 1863 neurons from 59 subjects across 3 sites (NIH ROH consortium). A subset of this data constitutes Rutishauser et al. 2015, Nat Neurosci.
  • Single-neuron dataset during recognition memory: Scientific Data data descriptor and data release (Dryad) of over 1500 human single neurons during new/old recognition memory task.
  • Example single-neuron recordings: Provided as part of Osort.
  • NIH NDAR releases for our projects: Project 2449 and Project 2417
  • Eye tracking. Zenodo open archive of eye tracking data and model code for our binocular rivalry study Marx et al.

Active software projects (open source)

  • Github repository: Lab Github repository. Note that many of the projects listed below are in their own repositories and thus will not show up here.

  • Online Spike sorting: Osort - a Matlab implementation of my online spike sorting/unsupervised clustering algorithm. Available together with example files, documentation and the original paper.

  • Closed-loop visual stimulus display: StimOmatic - Software package (Matlab/Python) for closed-loop control and visual stimulus display, conditional on phase and power of oscillations in the LFP measured in realtime.

  • Neuralynx file reader and writer (neurophysiology file formats) for matlab on unix / linux / Mac OS X. Project homepage.

  • Implementing DFAs with Winner-take all networks: Matlab/Java package for automatically converting arbitrary deterministic state automatons to winner-take-all networks. Accompanies our recently published paper. Includes a tutorial.

  • Solving constraint solving problems with winner-take-all networks: Matlab code for converting arbitrary constraint satisfaction problems (graph coloring, sudoku, maximum independent set) into neural networks (WTAs) and simulating them to find a solution.

Inactive software projects

  • ABI: Adaptive Building Intelligence. An opensource java framework for online learning from sparse events. Its usefulness is demonstrated by applying it to an intelligent building (integration with LON). The original ABI can be found here. New versions, originally based on ABI, can be found here.
  • Java SCEP: A SCEP (Cisco Simple Certificate Enrollment Protocol) client, including proxy for PKCS#12 key requests so that browsers can use SCEP for key requests. A SCEP server can be found here. The JAVA SCEP client is available here.


    A completely retyped version in latex (courtesy of Akram S. Sadek, Caltech) of the classic Probabilistic logics and the synthesis of reliable organisms from unreliable components by J. von Neumann, originally published in C. E. Shannon and J. McCarthy (editors), Automata Studies, 1956. Also note the article "Parallel information and computation with restitution for noise-tolerant nanoscale logic networks" by Akram S Sadek et al 2004 Nanotechnology 15:192-210 for an application to new physical substractes of computation (link).

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