Get Fly Connectome.

python

#!/usr/bin/env python
# coding: utf-8
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from tqdm.notebook import tqdm
import navis
import pickle
import os
import navis
import navis.interfaces.neuprint as neu
from neuprint import Client
import os
NC = neu.NeuronCriteria
client = neu.Client('https://neuprint.janelia.org', dataset='hemibrain:v1.1', token='redacted')
# First grab all neurons that have either pre- or postsynapses 
# (we don't really care about neurons without connectivity for this analysis)
all_meta1, roi1 = neu.fetch_neurons(NC(min_post=1))
all_meta2, roi2 = neu.fetch_neurons(NC(min_pre=1))
# Combine above dataframes
all_roi = pd.concat([roi1, roi2], axis=0).drop_duplicates(['bodyId', 'roi'])
meta = pd.concat([all_meta1, all_meta2], axis=0).drop_duplicates('bodyId')
meta.tail(2)
os.system("mkdir flybrain")
export_dir="flybrain"
_, edges = neu.fetch_adjacencies(include_nonprimary=True, export_dir=export_dir, batch_size=200)
with open("drosophila_connectome.p","wb") as f:
    pickle.dump(edges,f)