Get meta information for hemibrain neurons

Source: R/hemibrain_meta.R

Read meta data for hemibrain neurons from NeuPrint and supplement this with other data available in this package. Specifically, neuron lineage, class, olfactory system layer and FAFB match information, as well as numbers related to neurons' putative axon-dendrite split, e.g. for synapses or cable_length.

hemibrain_get_meta(x, ...)

Arguments

x

a vector of bodyids that can be read from 'https://neuprint.janelia.org/'.
...

arguments passed to neuprintr::neuprint_get_meta.

Value

a data.frame with columns that can give a user neuron lineage and class information, as well as numbers related to neurons' putative axon-dendrite split.

#'

  • "bodyid" - unique identifier for a single hemibrain neuron.

  • "pre" - the number of presynapses (outputs) a neuron contains. Each of this is polyadic.

  • "post" - the number of postsynapses (inputs) to the neuron.

  • "upstream" - the number of incoming connections to a neuron.

  • "downstream" - the number of outgoing connections from a neuron.

  • "soma" - neuron size in voxels.

  • "sid" - which brain hemisphere contains the neuron's soma.

  • "voxels" - whether the neuron has a soma in the hemibrain volume.

  • "name" - the name of this neuron.

  • "connectivity.type" - the neuPrint designated 'type' for the neuron. A subset of neurons within a cell_type that share similar connectivity. A connectivity type is distinguished from a cell_type by an ending _letter, defined using CBLAST (Scheffer et al. 2020).

  • "cell_type" - neurons of a shared morphology that take the same cell body fibre tract and come from the same hemilineage (Bates 2019).

  • "cellBodyFiber" - The cell body fiber for a neuron, as read from neuPrint and annotated by a team under Kei Ito.

  • "putative.classic.transmitter" - putative neurotransmitter based on what neurons in the hemilineage in question has been shown to express, out of acetylcholine, GABA, glutamate.

  • "ito_lee_hemilineage" - the hemilineage that we reckon this cell_type belongs to, based on expert review of light level data from the K. Ito and T. Lee groups (Yu 2013, Ito 2013). See hemibrain_hemilineages.

  • "hartenstein_hemilineage" - the hemilineage that we reckon this cell_type belongs to, based on expert review of light level data from the V. Hartenstein Lee group (Wong 2013, Lovick 2013). See hemibrain_hemilineages.

  • "FAFB.match" - the ID of the manual match from the FAFB data set. ID indicates a neuron reconstructed in FAFBv14 CATMAID. Many of these neurons will be available through Virtual Fly Brain.

  • "FAFB.match.quality" - the matcher makers qualitative assessment of how good this match is: a poor match could be a neuron from a very similar same cell_type or a highly untraced neuron that may be the correct cell_type. An okay match should be a neuron that looks to be from the same morphological cell_type but there may be some discrepancies in its arbour. A good match is a neuron that corresponds well between FAFB and the hemibrain data.

  • "layer" - probabilistic mean path length from neuron from ALRNs, depends on connection strengths.

  • "layer.ct"- the mean layer for cell_type, rounded to the nearest whole number.

  • "axon_outputs"- number of outgoing connections from the neuron's predicted axon.

  • "dend_outputs"- number of outgoing connections from the neuron's predicted dendrite.

  • "axon_inputs"- number of incoming connections from the neuron's predicted axon.

  • "dend_inputs"- number of incoming connections from the neuron's predicted dendrite.

  • "total_length"- total cable_length of the neuron in micrometers.

  • "axon_length"- total axon cable_length of the neuron in micrometers.

  • "dend_length"- total dendrite cable_length of the neuron in micrometers.

  • "pd_length"- total cable_length of the primary dendrite 'linker' between axon and dendrite.

  • "segregation_index"- a quantification of how polarised a neuron is, in terms of its segregation of inputs onto its predicted dendrite and outputs onto its axon, where 0 is no-polarisation and 1 is totally polarised (Schneider-Mizell 2016).

See also

hemibrain_splitpoints, hemibrain_flow_centrality, hemibrain_somas, hemibrain_precomputed_splitpoints, hemibrain_metrics,hemibrain_olfactory_layers hemibrain_hemilineages, classed.ids, hemibrain_read_neurons

Examples

# \donttest{
if (FALSE) {

# Get neurons
meta = hemibrain_get_meta("763730414")
View(meta)

}# }