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Challenge Level 2¶
Abstractions and simplifications¶
The first sophistication level of the WBE Challenge features these characteristics and simplifications of virtual brain data:
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Empty extracellular space: There are no glia, vasculature or other components in the exracellular space. Only neural cell bodies and their processes are present.
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Very small sample size: The number of neurons in the sample is very small.
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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.
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First order morphology: Neuron morphologies are simplified such that straight compartments connect successive branch points on axons and dendrites. Soma are highly simplified. Synaptic connections occur between axon and dendrite pieces.
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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).
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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 150 um x 150 um x 40 um.
- The z-distance between successive imaging depths is 40 nm.
- The x-y pixel resolution is 20 nm on each axis.
- Each image contains 1024x1024 pixels.
- Image overlap in both x and y is 10%.
- The data set comprises a total of 81,000 images with a total size of 3.6GB.
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.
Download Link¶
Warning
Download links currently disabled - will be enabled upon release.
Download the complete data set as a compressed file at this link:
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.