count_synapses - jaybgager/tracertools GitHub Wiki

Description

Arguments:

• datstack (string, mandatory)
  • the name of the CAVE datastack the segment IDs are from (e.g. "brain_and_nerve_cord")
• seg_ids (list of integers, mandatory)
  • a list of segment IDs to
• detailed_results (boolean, optional, default=False)
  • optional toggle to get dictionary output with incoming and outgoing numbers
  • default value of False just returns total synapse count

Returns:

• synapses (varies, see description)
  • default behavior returns a list of total synapse counts as integers in the same order as the seg IDs submitted
  • if detailed_counts is set to True, returns a dictionary with seg ID keys and detailed synapse counts as values (see examples)

Examples

Default Behavior

INPUT:

import tracertools as tt

synapses = tt.count_synapses(
    datastack = "brain_and_nerve_cord", 
    seg_ids = [
        720575940380068115, # nucleus, no synapses #
        720575941609391725, # rough unproofread cell, some synapses #
        720575941354901552, # full cell, many synapses #
    ], 
)

print(synapses)

OUTPUT:

[0, 336, 8246]

Detailed Results

INPUT:

import tracertools as tt

synapses = tt.count_synapses(
    datastack = "brain_and_nerve_cord", 
    seg_ids = [
        720575940380068115, # nucleus, no synapses #
        720575941609391725, # rough unproofread cell, some synapses #
        720575941354901552, # full cell, many synapses #
    ],
    detailed_results = True, 
)

print(synapses)

OUTPUT:

{
    720575940380068115: {'in': 0, 'out': 0, 'all': 0},
    720575941609391725: {'in': 45, 'out': 291, 'all': 336},
    720575941354901552: {'in': 2822, 'out': 5424, 'all': 8246}
}