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Challenge Level 1

Abstractions and simplifications

The first sophistication level of the WBE Challenge features these characteristics and simplifications of virtual brain data:

  • Empty extracellular space: There are no glia, vasculature or other components in the exracellular space. Only neural cell bodies and their processes are present.

  • Very small sample size: The number of neurons in the sample is very small.

  • Two types of neurons: Only 2 types of neurons are present, a generic principal neuron and a generic interneuron. The two types are easily distinguished.

  • Zeroth order morphology: Neuron morphologies are simplified to the point where neurons are composed of only 1 soma compartment and 1 axon compartment. Synaptic connections are made directly onto the soma of a target cell.

  • Two receptor types: Connections use one of 2 receptor types, one used in inhibitory connections from presynaptic interneurons (a GABA type), and one used in excitatory connections from presynaptic principal neurons (an AMPA type).

  • Zeroth order synaptic connections: Synaptic connectivity between any pair of neurons, where present, is achieved by a single synapse (seen in EM as a single postsynaptic density).

Challenge data set

EM Images

The EM image stack was produced using a virtual FIBSEM process.

  • There is 1 imaged sample region.
  • The total sample volume imaged is ??.
  • The z-distance between successive imaging depths is ??.
  • The x-y pixel resolution is ?? on each axis.
  • Each image contains 1024x1024 pixels.
  • Image overlap in both x and y is ??.
  • The data set comprises a total of ?? images with a total size of ??.

Calcium Imaging

To be added.

Extracellular Electrode Recording

The data from each recording electrode is contained in a JSON file with the following format:

{
  "Name": string,         # Unique name of the electrode.
  "TipPosition": list,    # X,Y,Z coordinates of the electrode tip in the sample.
  "EndPosition": list,    # X,Y,Z coordinates of the end of the electrode.
  "Sites": list of lists, # Relative X,Y,Z locations of each recording site on the electrode (see below).
  "TimeStamp_ms": list,   # List of recording time points.
  "ElectricField_mV": list of lists, # For each site, a list of recorded voltages at each time point.
}

The relative X,Y,Z location of a recording site on an electrode is expressed as a ratio of the electrode X,Y,Z dimensions. For example, a site at [0, 0, 0.5] is located at an X,Y edge of an electrode, halfway up its Z length.

  • This data set contains JSON files with recordings from ?? electrodes.
  • Each recording was made over a time interval of ?? ms.

Minimum electrode spacing is 250 um and was based on the spacing between shanks of a four-shank Neuropixels electrode ref.

Warning

Download links currently disabled - will be enabled upon release.

Download the complete data set as a compressed file at this link:

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The WBE Challenge is developed and supported by the Virtual Brain Platform (VBP) and Neural Emulation System (NES) groups of the BrainGenix division of the Carboncopies Foundation R&D. The Carboncopies Foundation (CCF) is a 501(c)3 non-profit research and education organization. You can read more about the CCF at https://carboncopies.org, and BrainGenix at https://braingenix.org.

For questions or comments, please write to wbechallenge@carboncopies.org.