fafbseg.google.find_autoseg_fragments¶

fafbseg.google.find_autoseg_fragments(x, autoseg_instance, min_node_overlap=3, min_nodes=1, verbose=True, raise_none_found=True)[source]¶

Find autoseg tracings constituting a given neuron.

This function works by querying the segmentation IDs along the neurites of your query neuron and then fetching the corresponding skeletons in autoseg_instance.

Parameters:

x (navis.Neuron/List) – Neuron to collect fragments for.
autoseg_instance (pymaid.CatmaidInstance) – Catmaid instance which contains autoseg fragments.
min_node_overlap (int, optional) – Minimal overlap between x and a segmentation [in nodes].
min_nodes (int, optional) – Minimum node count for returned neurons.
verbose (bool, optional) – If True, will be print summary of who has contributed to the autoseg fragments by merging or tracing nodes.
raise_none_found (bool, optional) – If True and none of the requested segments were found, will raise ValueError

Returns:

CatmaidNeurons of the overlapping fragments.

Return type:

pymaid.CatmaidNeuronList

Examples

Setup:

>>> import pymaid                                       
>>> import fafbseg                                      

>>> manual = pymaid.CatmaidInstance('MANUAL_SERVER_URL', 'HTTP_USER',   
...                                 'HTTP_PW', 'API_TOKEN')             
>>> auto = pymaid.CatmaidInstance('AUTO_SERVER_URL', 'HTTP_USER',       
...                               'HTTP_PW', 'API_TOKEN')               

>>> # Call one of the fafbseg.use_... to set a source for segmentation IDs
>>> fafbseg.google.use_google_storage("https://storage.googleapis.com/fafb-ffn1-20190805/segmentation") 

Find autoseg fragments overlapping with a manually traced neuron:

>>> x = pymaid.get_neuron(16, remote_instance=manual)       
>>> frags_of_x = fafbseg.google.find_autoseg_fragments(x, remote_instance=auto) 