Brain-related Tools

Databases

• NeuroMorpho.org, inventory of software and digitally reconstructed neurons.
• WormAtlas.org.

Chemicals:

• Molecular Probes at invitrogen
  • Calcium and Magnesium Indicators.
• Sigma-Aldrich.

Electrodes:

• Multi Channel Systems, for in vitro electrodes.
• NeuroNexus Technologies, for in vivo electrodes.

Software:

• Computational neuroscience software (maintained by Jim Perlewitz).

• Chronux analysis software (Mitra lab), for spectra and coherences.
• Cvapp, tool for editing and converting morphology files, e.g., Neurolucida to .swc format.
• ICA: Independent Component Analysis.
• ImageJ.
• L-Measure, free analysis tool for dendrite properties.
• NEST: Neural Simulation Technology Initiative.
• Netlab, neural network software for data analysis and pattern recognition.
• neurALC, for analysis of multi-electrode recordings.
• Neuromantic, free program for neuronal reconstruction.
• Neuroptikon, visualization software for neurobiology-related networks.
• Simulators:
  • csmi_lifnet, simulator for networks of leaky-integrate-and-fire neurons. C with Matlab interface.
  • Genesis simulation code.
  • Neuron:
    • Draft of Neuron book.
    • ModelDB, collection of computational neuroscience models, compatible with NeuronDB.
    • Neuron examples.
    • Neuron tutorial by Gillies and Steratt.
    • Summer courses on Neuron.
• Spine analysis:
  • NeuronIQ, software by Stephen Wong to study spine properties.
  • NeuronStudio, free Windows-based software for analyzing spines from images. Other imaging programs are available, see Computational Neurobiology and Imaging Center.
• Spike-sorting:
  • Buzsaki lab software:
    • Neuroscope and the Neuroscope Handbook.
    • NDManager and the NDManager Handbook.
    • Klusters and the Klusters Handbook.
    • KlustaKwik based on the AutoClass algorithm that is described in the 1996 book chapter Bayesian Classification(AutoClass): Theory and Results by Peter Cheesman and John Stutz.
  • MCLUST, clustering software for 1, 2, or 4 electrodes.
  • Mulab analysis tools, George Gerstein at U. Penn.
  • Wave_clus spike sorting/clustering software of Rodrigo Quiroga.