Discovery

!pip install vfb-connect --upgrade
!pip install python-catmaid --upgrade

# Import libs and initialise API objects
from vfb_connect.cross_server_tools import VfbConnect
import pandas as pd
vc = VfbConnect()

import pymaid
import navis

navis.set_pbars(jupyter=False)
pymaid.set_pbars(jupyter=False)

# Connect to the VFB CATMAID server hosting the FAFB data
rm = pymaid.connect_catmaid(server="https://fafb.catmaid.virtualflybrain.org/", api_token=None, max_threads=10)

# Test call to see if connection works 
print(f'Server is running CATMAID version {rm.catmaid_version}')

DA3adPN = vc.get_instances("adult Drosulfakinin neuron", summary=True)
pd.DataFrame.from_records(DA3adPN)

# Find neurons by location. The following query works across multiple data sources and both sides of the brain.  
# Results may be incomplete & may include minor overlap inferred from low synapse counts

neurons_in_DA3 = vc.get_instances("'neuron' that 'overlaps' some 'antennal lobe glomerulus DA3'", summary=True)
neurons_in_DA3_tab = pd.DataFrame.from_records(neurons_in_DA3)
neurons_in_DA3_tab[0:5]

# Find local interneurons (intrinsic neurons) of the AL, overlapping DA3:

local_in_DA3 = vc.get_instances("'local interneuron of adult antennal lobe' that 'overlaps' some 'antennal lobe glomerulus DA3'",
                                summary=True)
local_in_DA3_tab = pd.DataFrame.from_records(local_in_DA3)
local_in_DA3_tab

# Find neurons by dataset/paper - on CATMAID

bates = pymaid.find_neurons(annotations='Paper: Bates and Schlegel et al 2020')
bates

# Inspect what datasets are available on VFB

ds = vc.neo_query_wrapper.get_datasets(summary=True)
ds_tab = pd.DataFrame.from_records(ds)
ds_tab.sort_values(by=['id'])

sayin_tab = pd.DataFrame.from_records(vc.get_instances_by_dataset('Sayin2019', summary=True))
sayin_tab

vc.get_connected_neurons_by_type(upstream_type='LNd', downstream_type='adult descending neuron', weight=20)

# Intra pacemaker neuron neuron connections

vc.get_connected_neurons_by_type(upstream_type='pacemaker neuron', downstream_type='pacemaker neuron', weight=20)

vc.get_connected_neurons_by_type(upstream_type='adult neuron', downstream_type='adult Drosulfakinin neuron', weight=20)