Parsing skeleton IDs

All functions that require neurons/skeleton IDs as inputs (e.g. get_neuron()) accept either:

1. skeleton ID(s) (int or str):

   n = pymaid.get_neuron(16)
   nl = pymaid.get_neuron([16, 57241])
   

2. neuron name(s) (str):

   n = pymaid.get_neuron('PN glomerulus DC3 57242 ML')
   nl = pymaid.get_neuron(['PN glomerulus DC3 57242 ML', 'PN glomerulus VA6 017 DB'])
   

3. annotation(s) (str):

   n = pymaid.get_neuron('annotation:glomerulus VA6')
   nl = pymaid.get_neuron(['annotation:glomerulus DC3', 'annotation:glomerulus VA6'])
   

4. CatmaidNeuron or CatmaidNeuronList object:

   n = pymaid.get_neuron(16)
   cn_table = pymaid.get_partners(n)
   

Regex

By default, annotations and neuron names must match exactly. You can use regex on names and annotations, using a leading /:

# Get all neurons that have 'VA6' in their name
nl = pymaid.get_neuron('/VA6')

# Get all neurons annotated with a 'VA6'-containing annotation
nl = pymaid.get_neuron('annotation:/VA6')

# Get all skeleton IDs that have an annotation starting with 'AV1.R':
skids = pymaid.get_skids_by_annotation('/^AV1.R')

See here for detailed explanation of regex patterns.