Connectomics

[1]:
# Install all used libraries
!pip install -r ../../../requirements.txt --quiet
!pip install ../../../ --quiet

[2]:
# Import libs and initialise API objects
from vfb_connect import vfb
import pandas as pd

import pymaid
import navis

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

# Connect to VFB's 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}')

Welcome to the Virtual Fly Brain API
See the documentation at: https://virtualflybrain.org/docs/tutorials/apis/

Establishing connections to https://VirtualFlyBrain.org services...
INFO  : Global CATMAID instance set. Caching is ON. (pymaid)
Session Established!

Type vfb. and press tab to see available queries. You can run help against any query e.g. help(vfb.terms)
Server is running CATMAID version 2020.02.15-102-gce1dee4

VFB provides a simple methods for exploring connectomics data

get_connected_neurons_by_type allows queries for connections between defined upstream and downstream neuron types/classes. This supports a level of abstraction not available without VFB, where grouping of neurons by higher level classifications is limited to extraction of classification from standardised names. The following examples take advantage of the abstract clasifications on VFB to explore direct synaptic connections.

[3]:
vfb.get_terms_by_xref(['Trh-F-500041'], db='FlyCircuit')
[3]:
label symbol id tags description parents_label parents_id data_source accession xrefs templates dataset license
0 Trh-F-500041 VFB_00014110 [Entity, Adult, Anatomy, Cell, Expression_patt... OutAge: Adult 5~15 days [adult neuron, expression pattern fragment] [FBbt_00047095, VFBext_0000004] [FlyCircuit] [Trh-F-500041] [FlyCircuit:Trh-F-500041] [JRC2018Unisex, adult brain template JFRC2] [Chiang2010] []
[4]:
neurons_in_DA3 = vfb.get_instances("'neuron' that 'overlaps' some 'antennal lobe glomerulus DA3'", return_dataframe=True, limit=50)
neurons_in_DA3
Limiting to 50 terms out of 158
[4]:
label symbol id tags description parents_label parents_id data_source accession xrefs templates dataset license
0 ORN_DA1_R (FlyEM-HB:1735054607) ORN_DA1_R VFB_jrchk13v [Entity, Adult, Anatomy, Cell, Chemosensory_sy... tracing status-Leaves, cropped-True [adult olfactory receptor neuron Or67d] [FBbt_00067031] [neuprint_JRC_Hemibrain_1point1] [1735054607] [neuprint_JRC_Hemibrain_1point1:1735054607, ne... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
1 ORN_DA1_R (FlyEM-HB:1735382530) ORN_DA1_R VFB_jrchk14h [Entity, Adult, Anatomy, Cell, Chemosensory_sy... tracing status-Leaves, cropped-True [adult cholinergic neuron, adult olfactory rec... [FBbt_00058205, FBbt_00067031] [neuprint_JRC_Hemibrain_1point1] [1735382530] [neuronbridge:1735382530, neuprint_JRC_Hemibra... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
2 ORN_DA1_R (FlyEM-HB:1735391275) ORN_DA1_R VFB_jrchk14f [Entity, Adult, Anatomy, Cell, Chemosensory_sy... tracing status-Leaves, cropped-True [adult olfactory receptor neuron Or67d] [FBbt_00067031] [neuprint_JRC_Hemibrain_1point1] [1735391275] [neuprint_JRC_Hemibrain_1point1:1735391275, ne... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
3 ORN_DA1_R (FlyEM-HB:1735032816) ORN_DA1_R VFB_jrchk14l [Entity, Adult, Anatomy, Cell, Chemosensory_sy... tracing status-Leaves, cropped-True [adult olfactory receptor neuron Or67d] [FBbt_00067031] [neuprint_JRC_Hemibrain_1point1] [1735032816] [neuprint_JRC_Hemibrain_1point1:1735032816, ne... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
4 ORN_DA1_L (FlyEM-HB:1574160129) ORN_DA1_L VFB_jrchk13s [Entity, Adult, Anatomy, Cell, Chemosensory_sy... tracing status-Leaves, cropped-True [adult olfactory receptor neuron Or67d] [FBbt_00067031] [neuprint_JRC_Hemibrain_1point1] [1574160129] [neuprint_JRC_Hemibrain_1point1:1574160129, ne... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
5 ORN_DA1_L (FlyEM-HB:1672643988) ORN_DA1_L VFB_jrchk143 [Entity, Adult, Anatomy, Cell, Chemosensory_sy... tracing status-Leaves, cropped-True [adult olfactory receptor neuron Or67d] [FBbt_00067031] [neuprint_JRC_Hemibrain_1point1] [1672643988] [neuprint_JRC_Hemibrain_1point1:1672643988, ne... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
6 ORN_D (FlyEM-HB:5812993853) ORN_D VFB_jrchk12n [Entity, Adult, Anatomy, Cell, Chemosensory_sy... tracing status-Leaves, cropped-True [adult olfactory receptor neuron Or69a, adult ... [FBbt_00067034, FBbt_00058205] [neuprint_JRC_Hemibrain_1point1] [5812993853] [neuprint_JRC_Hemibrain_1point1:5812993853, ne... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
7 ORN_DA1_R (FlyEM-HB:1735395524) ORN_DA1_R VFB_jrchk13p [Entity, Adult, Anatomy, Cell, Chemosensory_sy... tracing status-Leaves, cropped-True [adult olfactory receptor neuron Or67d] [FBbt_00067031] [neuprint_JRC_Hemibrain_1point1] [1735395524] [neuprint_JRC_Hemibrain_1point1:1735395524, ne... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
8 ORN_DA1_L (FlyEM-HB:1672311578) ORN_DA1_L VFB_jrchk13h [Entity, Adult, Anatomy, Cell, Chemosensory_sy... tracing status-Leaves, cropped-True [adult olfactory receptor neuron Or67d] [FBbt_00067031] [neuprint_JRC_Hemibrain_1point1] [1672311578] [neuronbridge:1672311578, neuprint_JRC_Hemibra... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
9 ORN_DA1_L (FlyEM-HB:1703342190) ORN_DA1_L VFB_jrchk12z [Entity, Adult, Anatomy, Cell, Chemosensory_sy... tracing status-Leaves, cropped-True [adult olfactory receptor neuron Or67d] [FBbt_00067031] [neuprint_JRC_Hemibrain_1point1] [1703342190] [neuprint_JRC_Hemibrain_1point1:1703342190, ne... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
10 ORN_DA1_R (FlyEM-HB:5813020396) ORN_DA1_R VFB_jrchk13k [Entity, Adult, Anatomy, Cell, Chemosensory_sy... tracing status-Leaves, cropped-True [adult olfactory receptor neuron Or67d] [FBbt_00067031] [neuprint_JRC_Hemibrain_1point1] [5813020396] [neuronbridge:5813020396, neuprint_JRC_Hemibra... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
11 ORN_DA1_L (FlyEM-HB:1766409090) ORN_DA1_L VFB_jrchk13a [Entity, Adult, Anatomy, Cell, Chemosensory_sy... tracing status-Leaves, cropped-True [adult olfactory receptor neuron Or67d] [FBbt_00067031] [neuprint_JRC_Hemibrain_1point1] [1766409090] [neuprint_JRC_Hemibrain_1point1:1766409090, ne... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
12 ORN_DA1_L (FlyEM-HB:1764703552) ORN_DA1_L VFB_jrchk146 [Entity, Adult, Anatomy, Cell, Chemosensory_sy... tracing status-Leaves, cropped-True [adult olfactory receptor neuron Or67d] [FBbt_00067031] [neuprint_JRC_Hemibrain_1point1] [1764703552] [neuronbridge:1764703552, neuprint_JRC_Hemibra... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
13 ORN_DA1_R (FlyEM-HB:1672315788) ORN_DA1_R VFB_jrchk13i [Entity, Adult, Anatomy, Cell, Chemosensory_sy... tracing status-Leaves, cropped-True [adult olfactory receptor neuron Or67d] [FBbt_00067031] [neuprint_JRC_Hemibrain_1point1] [1672315788] [neuronbridge:1672315788, neuprint_JRC_Hemibra... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
14 ORN_DA1_R (FlyEM-HB:1703683156) ORN_DA1_R VFB_jrchk13f [Entity, Adult, Anatomy, Cell, Chemosensory_sy... tracing status-Leaves, cropped-True [adult olfactory receptor neuron Or67d] [FBbt_00067031] [neuprint_JRC_Hemibrain_1point1] [1703683156] [neuronbridge:1703683156, neuprint_JRC_Hemibra... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
15 ORN_DA1_R (FlyEM-HB:1797439276) ORN_DA1_R VFB_jrchk160 [Entity, Adult, Anatomy, Cell, Chemosensory_sy... tracing status-Leaves, cropped-True [adult olfactory receptor neuron Or67d] [FBbt_00067031] [neuprint_JRC_Hemibrain_1point1] [1797439276] [neuronbridge:1797439276, neuprint_JRC_Hemibra... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
16 ORN_DA1_L (FlyEM-HB:1671970212) ORN_DA1_L VFB_jrchk163 [Entity, Adult, Anatomy, Cell, Chemosensory_sy... tracing status-Leaves, cropped-True [adult olfactory receptor neuron Or67d] [FBbt_00067031] [neuprint_JRC_Hemibrain_1point1] [1671970212] [neuronbridge:1671970212, neuprint_JRC_Hemibra... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
17 ORN_DL5_R (FlyEM-HB:1639925326) ORN_DL5_R VFB_jrchk1lb [Entity, Adult, Anatomy, Cell, Chemosensory_sy... tracing status-Leaves, cropped-True [adult cholinergic neuron, adult olfactory rec... [FBbt_00058205, FBbt_00067005] [neuprint_JRC_Hemibrain_1point1] [1639925326] [neuronbridge:1639925326, neuprint_JRC_Hemibra... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
18 ORN_DL5_L (FlyEM-HB:1669933011) ORN_DL5_L VFB_jrchk1li [Entity, Adult, Anatomy, Cell, Chemosensory_sy... tracing status-Leaves, cropped-True [adult cholinergic neuron, adult olfactory rec... [FBbt_00058205, FBbt_00067005] [neuprint_JRC_Hemibrain_1point1] [1669933011] [neuronbridge:1669933011, neuprint_JRC_Hemibra... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
19 ORN_DL5_L (FlyEM-HB:1640050851) ORN_DL5_L VFB_jrchk1lh [Entity, Adult, Anatomy, Cell, Chemosensory_sy... tracing status-Leaves, cropped-True [adult cholinergic neuron, adult olfactory rec... [FBbt_00058205, FBbt_00067005] [neuprint_JRC_Hemibrain_1point1] [1640050851] [neuronbridge:1640050851, neuprint_JRC_Hemibra... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
20 DA3_adPN_R (FlyEM-HB:1703683361) DA3_adPN_R VFB_jrchjtdn [Entity, Adult, Anatomy, Cell, Chemosensory_sy... tracing status-Roughly traced, cropped-False [adult antennal lobe projection neuron DA3 adPN] [FBbt_00100384] [neuprint_JRC_Hemibrain_1point1] [1703683361] [neuronbridge:1703683361, neuprint_JRC_Hemibra... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
21 CSD(5HT1)(AVM03)_L (FlyEM-HB:759810119) CSD(5HT1)(AVM03)_L VFB_jrchjtd6 [Entity, Adult, Anatomy, Cell, Individual, Ner... tracing status-Roughly traced, cropped-False [adult CSD interneuron] [FBbt_00007405] [neuprint_JRC_Hemibrain_1point1] [759810119] [neuronbridge:759810119, neuprint_JRC_Hemibrai... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
22 DA4m_adPN_R (FlyEM-HB:574037266) DA4m_adPN_R VFB_jrchjtdq [Entity, Adult, Anatomy, Cell, Chemosensory_sy... tracing status-Roughly traced, cropped-False [adult antennal lobe projection neuron DA4m adPN] [FBbt_00047714] [neuprint_JRC_Hemibrain_1point1] [574037266] [neuronbridge:574037266, neuprint_JRC_Hemibrai... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
23 DA3_adPN_R (FlyEM-HB:666135689) DA3_adPN_R VFB_jrchjtdo [Entity, Adult, Anatomy, Cell, Chemosensory_sy... tracing status-Roughly traced, cropped-False [adult antennal lobe projection neuron DA3 adPN] [FBbt_00100384] [neuprint_JRC_Hemibrain_1point1] [666135689] [neuronbridge:666135689, neuprint_JRC_Hemibrai... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
24 lLN16b_R (FlyEM-HB:1887168462) lLN16b_R VFB_jrchk89w [Entity, Adult, Anatomy, Cell, Individual, Ner... tracing status-Roughly traced, cropped-False [adult antennal lobe local neuron lLN16B] [FBbt_20003752] [neuprint_JRC_Hemibrain_1point1] [1887168462] [neuronbridge:1887168462, neuprint_JRC_Hemibra... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
25 lLN16a_R (FlyEM-HB:1702318692) lLN16a_R VFB_jrchk89t [Entity, Adult, Anatomy, Cell, Individual, Ner... tracing status-Roughly traced, cropped-False [adult antennal lobe local neuron lLN16A] [FBbt_20003751] [neuprint_JRC_Hemibrain_1point1] [1702318692] [neuronbridge:1702318692, neuprint_JRC_Hemibra... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
26 il3LN6_R (FlyEM-HB:5813018460) il3LN6_R VFB_jrchk88v [Entity, Adult, Anatomy, Cell, GABAergic, Indi... tracing status-Roughly traced, cropped-False [adult serotonergic SE neuron, antennal lobe l... [FBbt_00047319, FBbt_00047710] [neuprint_JRC_Hemibrain_1point1] [5813018460] [neuprint_JRC_Hemibrain_1point1:5813018460, ne... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
27 lLN10_R (FlyEM-HB:1825789179) lLN10_R VFB_jrchk89b [Entity, Adult, Anatomy, Cell, GABAergic, Indi... tracing status-Roughly traced, cropped-False [GABAergic local interneuron of the adult ante... [FBbt_00007402, FBbt_20003744] [neuprint_JRC_Hemibrain_1point1] [1825789179] [neuprint_JRC_Hemibrain_1point1:1825789179, ne... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
28 lLN12a_R (FlyEM-HB:1826445251) lLN12a_R VFB_jrchk89g [Entity, Adult, Anatomy, Cell, Cholinergic, In... tracing status-Roughly traced, cropped-False [cholinergic local interneuron of the adult an... [FBbt_00007403, FBbt_20003746] [neuprint_JRC_Hemibrain_1point1] [1826445251] [neuprint_JRC_Hemibrain_1point1:1826445251, ne... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
29 lLN11_R (FlyEM-HB:2040301572) lLN11_R VFB_jrchk89d [Entity, Adult, Anatomy, Cell, Cholinergic, In... tracing status-Roughly traced, cropped-False [cholinergic local interneuron of the adult an... [FBbt_00007403, FBbt_20003745] [neuprint_JRC_Hemibrain_1point1] [2040301572] [neuronbridge:2040301572, neuprint_JRC_Hemibra... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
30 lLN11_R (FlyEM-HB:1670278227) lLN11_R VFB_jrchk89e [Entity, Adult, Anatomy, Cell, Individual, Ner... tracing status-Roughly traced, cropped-False [adult antennal lobe local neuron lLN11] [FBbt_20003745] [neuprint_JRC_Hemibrain_1point1] [1670278227] [neuprint_JRC_Hemibrain_1point1:1670278227, ne... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
31 lLN2F_b(Full)_R (FlyEM-HB:5813024698) lLN2F_b(Full)_R VFB_jrchk8an [Entity, Adult, Anatomy, Cell, Individual, Ner... tracing status-Roughly traced, cropped-False [adult antennal lobe local neuron lLN2F, adult... [FBbt_00049812, FBbt_00007394] [neuprint_JRC_Hemibrain_1point1] [5813024698] [neuprint_JRC_Hemibrain_1point1:5813024698, ne... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
32 lLN2P_a(Patchy)_R (FlyEM-HB:2041621893) lLN2P_a(Patchy)_R VFB_jrchk8ao [Entity, Adult, Anatomy, Cell, GABAergic, Indi... tracing status-Roughly traced, cropped-False [adult local interneuron of the lateral ALl1 n... [FBbt_00007394, FBbt_00007402, FBbt_00049813] [neuprint_JRC_Hemibrain_1point1] [2041621893] [neuronbridge:2041621893, neuprint_JRC_Hemibra... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
33 lLN2F_b(Full)_R (FlyEM-HB:1640909284) lLN2F_b(Full)_R VFB_jrchk8am [Entity, Adult, Anatomy, Cell, Individual, Ner... tracing status-Roughly traced, cropped-False [adult antennal lobe local neuron lLN2F, adult... [FBbt_00049812, FBbt_00007394] [neuprint_JRC_Hemibrain_1point1] [1640909284] [neuronbridge:1640909284, neuprint_JRC_Hemibra... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
34 lLN2T_a(Tortuous)_R (FlyEM-HB:5813032595) lLN2T_a(Tortuous)_R VFB_jrchk8bd [Entity, Adult, Anatomy, Cell, Individual, Ner... tracing status-Roughly traced, cropped-False [adult antennal lobe local neuron lLN2T, adult... [FBbt_00049816, FBbt_00049526] [neuprint_JRC_Hemibrain_1point1] [5813032595] [neuronbridge:5813032595, neuprint_JRC_Hemibra... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
35 lLN2T_d(Tortuous)_R (FlyEM-HB:1667251683) lLN2T_d(Tortuous)_R VFB_jrchk8bp [Entity, Adult, Anatomy, Cell, Individual, Ner... tracing status-Roughly traced, cropped-False [adult antennal lobe local neuron lLN2T, adult... [FBbt_00049816, FBbt_00049526] [neuprint_JRC_Hemibrain_1point1] [1667251683] [neuronbridge:1667251683, neuprint_JRC_Hemibra... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
36 lLN2P_b(Patchy)_R (FlyEM-HB:1946178096) lLN2P_b(Patchy)_R VFB_jrchk8au [Entity, Adult, Anatomy, Cell, Individual, Ner... tracing status-Roughly traced, cropped-False [adult local interneuron of the lateral ALl1 n... [FBbt_00007394, FBbt_00049813, FBbt_00049526] [neuprint_JRC_Hemibrain_1point1] [1946178096] [neuprint_JRC_Hemibrain_1point1:1946178096, ne... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
37 lLN2T_a(Tortuous)_R (FlyEM-HB:1762354941) lLN2T_a(Tortuous)_R VFB_jrchk8bg [Entity, Adult, Anatomy, Cell, Individual, Ner... tracing status-Roughly traced, cropped-False [adult antennal lobe local neuron lLN2T, adult... [FBbt_00049816, FBbt_00049526] [neuprint_JRC_Hemibrain_1point1] [1762354941] [neuprint_JRC_Hemibrain_1point1:1762354941, ne... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
38 lLN2T_a(Tortuous)_R (FlyEM-HB:5813056598) lLN2T_a(Tortuous)_R VFB_jrchk8bi [Entity, Adult, Anatomy, Cell, Individual, Ner... tracing status-Roughly traced, cropped-False [adult antennal lobe local neuron lLN2T, adult... [FBbt_00049816, FBbt_00049526] [neuprint_JRC_Hemibrain_1point1] [5813056598] [neuprint_JRC_Hemibrain_1point1:5813056598, ne... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
39 lLN2T_e(Tortuous)_R (FlyEM-HB:1640922516) lLN2T_e(Tortuous)_R VFB_jrchk8bs [Entity, Adult, Anatomy, Cell, Individual, Ner... tracing status-Roughly traced, cropped-False [adult serotonergic neuron, adult antennal lob... [FBbt_00049526, FBbt_00049816] [neuprint_JRC_Hemibrain_1point1] [1640922516] [neuprint_JRC_Hemibrain_1point1:1640922516, ne... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
40 lLN2S(Star)_R (FlyEM-HB:1762359683) lLN2S(Star)_R VFB_jrchk8bc [Entity, Adult, Anatomy, Cell, Individual, Ner... tracing status-Roughly traced, cropped-False [adult local interneuron of the lateral ALl1 n... [FBbt_00007394, FBbt_00049526, FBbt_00049815] [neuprint_JRC_Hemibrain_1point1] [1762359683] [neuronbridge:1762359683, neuprint_JRC_Hemibra... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
41 lLN2T_b(Tortuous)_R (FlyEM-HB:1640572741) lLN2T_b(Tortuous)_R VFB_jrchk8bl [Entity, Adult, Anatomy, Cell, Individual, Ner... tracing status-Roughly traced, cropped-False [adult antennal lobe local neuron lLN2T, adult... [FBbt_00049816, FBbt_00049526] [neuprint_JRC_Hemibrain_1point1] [1640572741] [neuronbridge:1640572741, neuprint_JRC_Hemibra... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
42 lLN2T_a(Tortuous)_R (FlyEM-HB:5813054726) lLN2T_a(Tortuous)_R VFB_jrchk8bh [Entity, Adult, Anatomy, Cell, Individual, Ner... tracing status-Roughly traced, cropped-False [adult serotonergic neuron, adult antennal lob... [FBbt_00049526, FBbt_00049816] [neuprint_JRC_Hemibrain_1point1] [5813054726] [neuronbridge:5813054726, neuprint_JRC_Hemibra... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
43 lLN2S(Star)_R (FlyEM-HB:1670627928) lLN2S(Star)_R VFB_jrchk8bb [Entity, Adult, Anatomy, Cell, Individual, Ner... tracing status-Roughly traced, cropped-False [adult antennal lobe local neuron lLN2S, adult... [FBbt_00049815, FBbt_00049526, FBbt_00007394] [neuprint_JRC_Hemibrain_1point1] [1670627928] [neuronbridge:1670627928, neuprint_JRC_Hemibra... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
44 lLN2S(Star)_R (FlyEM-HB:1732995501) lLN2S(Star)_R VFB_jrchk8ba [Entity, Adult, Anatomy, Cell, Individual, Ner... tracing status-Roughly traced, cropped-False [adult antennal lobe local neuron lLN2S, adult... [FBbt_00049815, FBbt_00049526, FBbt_00007394] [neuprint_JRC_Hemibrain_1point1] [1732995501] [neuronbridge:1732995501, neuprint_JRC_Hemibra... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
45 v2LN30_R (FlyEM-HB:1671620613) v2LN30_R VFB_jrchk8e8 [Entity, Adult, Anatomy, Cell, GABAergic, Indi... tracing status-Roughly traced, cropped-False [adult antennal lobe local neuron v2LN30, GABA... [FBbt_20003756, FBbt_00007402] [neuprint_JRC_Hemibrain_1point1] [1671620613] [neuprint_JRC_Hemibrain_1point1:1671620613, ne... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
46 lLN2T_e(Tortuous)_R (FlyEM-HB:1699974843) lLN2T_e(Tortuous)_R VFB_jrchk8br [Entity, Adult, Anatomy, Cell, Individual, Ner... tracing status-Roughly traced, cropped-False [adult antennal lobe local neuron lLN2T, adult... [FBbt_00049816, FBbt_00049526] [neuprint_JRC_Hemibrain_1point1] [1699974843] [neuprint_JRC_Hemibrain_1point1:1699974843, ne... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
47 lLN2T_a(Tortuous)_R (FlyEM-HB:5813055277) lLN2T_a(Tortuous)_R VFB_jrchk8bf [Entity, Adult, Anatomy, Cell, Individual, Ner... tracing status-Roughly traced, cropped-False [adult antennal lobe local neuron lLN2T, adult... [FBbt_00049816, FBbt_00049526] [neuprint_JRC_Hemibrain_1point1] [5813055277] [neuprint_JRC_Hemibrain_1point1:5813055277, ne... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
48 lLN2T_c(Tortuous)_R (FlyEM-HB:1671292719) lLN2T_c(Tortuous)_R VFB_jrchk8bo [Entity, Adult, Anatomy, Cell, Individual, Ner... tracing status-Roughly traced, cropped-False [adult antennal lobe local neuron lLN2T] [FBbt_00049816] [neuprint_JRC_Hemibrain_1point1] [1671292719] [neuronbridge:1671292719, neuprint_JRC_Hemibra... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
49 lLN2T_b(Tortuous)_R (FlyEM-HB:5813034493) lLN2T_b(Tortuous)_R VFB_jrchk8bm [Entity, Adult, Anatomy, Cell, Individual, Ner... tracing status-Roughly traced, cropped-False [adult serotonergic neuron, adult antennal lob... [FBbt_00049526, FBbt_00049816] [neuprint_JRC_Hemibrain_1point1] [5813034493] [neuronbridge:5813034493, neuprint_JRC_Hemibra... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
[5]:
# Find all GABA-regic inputs onto descending neurons

vfb.get_connected_neurons_by_type(upstream_type='GABAergic neuron',
                                 downstream_type='adult descending neuron',
                                 weight=10).sort_values('weight', ascending=False, ignore_index=True)
[5]:
upstream_class upstream_class_id upstream_neuron_id upstream_neuron_name weight downstream_neuron_id downstream_neuron_name downstream_class downstream_class_id up_data_source up_accession down_source down_accession
0 adult superior medial protocerebrum neuron 594 FBbt_20003456 VFB_jrchk79q SMP594(SCB017)_R (FlyEM-HB:976934253) 492 VFB_jrchk70f SMP454_R (FlyEM-HB:326253554) adult superior medial protocerebrum neuron 454 FBbt_20003316 neuprint_JRC_Hemibrain_1point1 976934253 neuprint_JRC_Hemibrain_1point1 326253554
1 adult superior medial protocerebrum neuron 594 FBbt_20003456 VFB_jrchk79q SMP594(SCB017)_R (FlyEM-HB:976934253) 393 VFB_jrchjsri CL138_R (FlyEM-HB:707190304) adult clamp neuron 138 FBbt_20000843 neuprint_JRC_Hemibrain_1point1 976934253 neuprint_JRC_Hemibrain_1point1 707190304
2 adult anterior ventrolateral protocerebrum neu... FBbt_20000189 VFB_jrchjrof AVLP080_R (FlyEM-HB:5813027276) 373 VFB_jrchk4wd PVLP136_R (FlyEM-HB:5813057178) adult posterior ventrolateral protocerebrum ne... FBbt_20002194 neuprint_JRC_Hemibrain_1point1 5813027276 neuprint_JRC_Hemibrain_1point1 5813057178
3 adult anterior optic tubercle neuron 019 FBbt_20000018 VFB_jrchjrek AOTU019(ADM10)_L (FlyEM-HB:1605518663) 362 VFB_jrchk47t PS017_R (FlyEM-HB:5813069484) adult posterior slope neuron 017 FBbt_20001772 neuprint_JRC_Hemibrain_1point1 1605518663 neuprint_JRC_Hemibrain_1point1 5813069484
4 adult anterior ventrolateral protocerebrum neu... FBbt_20000185 VFB_jrchjrob AVLP076_R (FlyEM-HB:1135441187) 349 VFB_jrchk4wd PVLP136_R (FlyEM-HB:5813057178) adult posterior ventrolateral protocerebrum ne... FBbt_20002194 neuprint_JRC_Hemibrain_1point1 1135441187 neuprint_JRC_Hemibrain_1point1 5813057178
... ... ... ... ... ... ... ... ... ... ... ... ... ...
1354 adult superior medial protocerebrum neuron 593 FBbt_20003455 VFB_jrchk79p SMP593(SCB014)_R (FlyEM-HB:549282467) 10 VFB_jrchk4a1 PS066(AVM08)_L (FlyEM-HB:1284675398) adult posterior slope neuron 066 FBbt_20001821 neuprint_JRC_Hemibrain_1point1 549282467 neuprint_JRC_Hemibrain_1point1 1284675398
1355 adult anterior optic tubercle neuron 053 FBbt_20000052 VFB_jrchjrgi AOTU053_R (FlyEM-HB:5813097142) 10 VFB_jrchk4a1 PS066(AVM08)_L (FlyEM-HB:1284675398) adult posterior slope neuron 066 FBbt_20001821 neuprint_JRC_Hemibrain_1point1 5813097142 neuprint_JRC_Hemibrain_1point1 1284675398
1356 adult anterior optic tubercle neuron 019 FBbt_20000018 VFB_jrchjrej AOTU019_R (FlyEM-HB:799868224) 10 VFB_jrchk0ve MDN_R (FlyEM-HB:698016469) adult moonwalker descending neuron FBbt_00111308 neuprint_JRC_Hemibrain_1point1 799868224 neuprint_JRC_Hemibrain_1point1 698016469
1357 adult inferior bridge neuron 060 FBbt_20001237 VFB_jrchjuut IB060(PVL21)_L (FlyEM-HB:760806798) 10 VFB_jrchk7f7 VES029(AVM14)_L (FlyEM-HB:1099800130) adult vest neuron 029 FBbt_20003495 neuprint_JRC_Hemibrain_1point1 760806798 neuprint_JRC_Hemibrain_1point1 1099800130
1358 adult saddle neuron 013 FBbt_20002222 VFB_jrchk4yr SAD013_R (FlyEM-HB:5813024035) 10 VFB_jrchjtg7 DNp04_R (FlyEM-HB:1405231475) descending neuron of the posterior brain DNp04 FBbt_00047637 neuprint_JRC_Hemibrain_1point1 5813024035 neuprint_JRC_Hemibrain_1point1 1405231475

1359 rows × 13 columns

[6]:
# Get connections between pacemaker neurons
clock_neuron_connectome = vfb.get_connected_neurons_by_type(upstream_type='pacemaker neuron',
                                 downstream_type='pacemaker neuron',
                                 weight=10).sort_values('weight', ascending=False)
clock_neuron_connectome
[6]:
upstream_class upstream_class_id upstream_neuron_id upstream_neuron_name weight downstream_neuron_id downstream_neuron_name downstream_class downstream_class_id up_data_source up_accession down_source down_accession
12 DN1a neuron FBbt_00007429 VFB_jrchjtex DN1a_R (FlyEM-HB:264083994) 79 VFB_jrchjzxy LNd_R (FlyEM-HB:5813069648) LNd neuron FBbt_00004045 neuprint_JRC_Hemibrain_1point1 264083994 neuprint_JRC_Hemibrain_1point1 5813069648
15 DN1a neuron FBbt_00007429 VFB_jrchjtey DN1a_R (FlyEM-HB:5813022274) 75 VFB_jrchjzxy LNd_R (FlyEM-HB:5813069648) LNd neuron FBbt_00004045 neuprint_JRC_Hemibrain_1point1 5813022274 neuprint_JRC_Hemibrain_1point1 5813069648
25 DN1a neuron FBbt_00007429 VFB_jrchjtey DN1a_R (FlyEM-HB:5813022274) 63 VFB_jrchk8e0 5th s-LNv (FlyEM-HB:511051477) adult s-LNv neuron FBbt_00007428 neuprint_JRC_Hemibrain_1point1 5813022274 neuprint_JRC_Hemibrain_1point1 511051477
28 DN1a neuron FBbt_00007429 VFB_jrchjtex DN1a_R (FlyEM-HB:264083994) 55 VFB_jrchk8e0 5th s-LNv (FlyEM-HB:511051477) adult s-LNv neuron FBbt_00007428 neuprint_JRC_Hemibrain_1point1 264083994 neuprint_JRC_Hemibrain_1point1 511051477
30 adult LP neuron FBbt_00007432 VFB_jrchk089 LPN_R (FlyEM-HB:480029788) 43 VFB_jrchk08a LPN_R (FlyEM-HB:450034902) adult LP neuron FBbt_00007432 neuprint_JRC_Hemibrain_1point1 480029788 neuprint_JRC_Hemibrain_1point1 450034902
16 adult s-LNv neuron FBbt_00007428 VFB_jrchk8e0 5th s-LNv (FlyEM-HB:511051477) 40 VFB_jrchjzxy LNd_R (FlyEM-HB:5813069648) LNd neuron FBbt_00004045 neuprint_JRC_Hemibrain_1point1 511051477 neuprint_JRC_Hemibrain_1point1 5813069648
24 LNd neuron FBbt_00004045 VFB_jrchjzxy LNd_R (FlyEM-HB:5813069648) 37 VFB_jrchk8e0 5th s-LNv (FlyEM-HB:511051477) adult s-LNv neuron FBbt_00007428 neuprint_JRC_Hemibrain_1point1 5813069648 neuprint_JRC_Hemibrain_1point1 511051477
19 ventro-contralateral-projecting DN1p neuron FBbt_00052273 VFB_jrchjtf0 DN1pA_R (FlyEM-HB:324846570) 37 VFB_jrchjzxy LNd_R (FlyEM-HB:5813069648) LNd neuron FBbt_00004045 neuprint_JRC_Hemibrain_1point1 324846570 neuprint_JRC_Hemibrain_1point1 5813069648
18 ventro-contralateral-projecting DN1p neuron FBbt_00052273 VFB_jrchjtf2 DN1pA_R (FlyEM-HB:387944118) 34 VFB_jrchjzxy LNd_R (FlyEM-HB:5813069648) LNd neuron FBbt_00004045 neuprint_JRC_Hemibrain_1point1 387944118 neuprint_JRC_Hemibrain_1point1 5813069648
26 ventro-contralateral-projecting DN1p neuron FBbt_00052273 VFB_jrchjtf1 DN1pA_R (FlyEM-HB:325529237) 33 VFB_jrchk8e0 5th s-LNv (FlyEM-HB:511051477) adult s-LNv neuron FBbt_00007428 neuprint_JRC_Hemibrain_1point1 325529237 neuprint_JRC_Hemibrain_1point1 511051477
13 ventro-contralateral-projecting DN1p neuron FBbt_00052273 VFB_jrchjtf1 DN1pA_R (FlyEM-HB:325529237) 30 VFB_jrchjzxy LNd_R (FlyEM-HB:5813069648) LNd neuron FBbt_00004045 neuprint_JRC_Hemibrain_1point1 325529237 neuprint_JRC_Hemibrain_1point1 5813069648
31 adult LP neuron FBbt_00007432 VFB_jrchk08a LPN_R (FlyEM-HB:450034902) 30 VFB_jrchk089 LPN_R (FlyEM-HB:480029788) adult LP neuron FBbt_00007432 neuprint_JRC_Hemibrain_1point1 450034902 neuprint_JRC_Hemibrain_1point1 480029788
11 ventro-contralateral-projecting DN1p neuron FBbt_00052273 VFB_jrchjtf3 DN1pA_R (FlyEM-HB:387166379) 30 VFB_jrchjzxy LNd_R (FlyEM-HB:5813069648) LNd neuron FBbt_00004045 neuprint_JRC_Hemibrain_1point1 387166379 neuprint_JRC_Hemibrain_1point1 5813069648
20 LNd neuron FBbt_00004045 VFB_jrchjzxy LNd_R (FlyEM-HB:5813069648) 29 VFB_jrchjzxw LNd_R (FlyEM-HB:5813056917) LNd neuron FBbt_00004045 neuprint_JRC_Hemibrain_1point1 5813069648 neuprint_JRC_Hemibrain_1point1 5813056917
8 adult s-LNv neuron FBbt_00007428 VFB_jrchk8e0 5th s-LNv (FlyEM-HB:511051477) 25 VFB_jrchjzxx LNd_R (FlyEM-HB:5813021192) LNd neuron FBbt_00004045 neuprint_JRC_Hemibrain_1point1 511051477 neuprint_JRC_Hemibrain_1point1 5813021192
29 ventro-contralateral-projecting DN1p neuron FBbt_00052273 VFB_jrchjtf3 DN1pA_R (FlyEM-HB:387166379) 25 VFB_jrchk8e0 5th s-LNv (FlyEM-HB:511051477) adult s-LNv neuron FBbt_00007428 neuprint_JRC_Hemibrain_1point1 387166379 neuprint_JRC_Hemibrain_1point1 511051477
27 ventro-contralateral-projecting DN1p neuron FBbt_00052273 VFB_jrchjtez DN1pA_R (FlyEM-HB:5813010153) 25 VFB_jrchk8e0 5th s-LNv (FlyEM-HB:511051477) adult s-LNv neuron FBbt_00007428 neuprint_JRC_Hemibrain_1point1 5813010153 neuprint_JRC_Hemibrain_1point1 511051477
22 ventro-contralateral-projecting DN1p neuron FBbt_00052273 VFB_jrchjtf0 DN1pA_R (FlyEM-HB:324846570) 25 VFB_jrchk8e0 5th s-LNv (FlyEM-HB:511051477) adult s-LNv neuron FBbt_00007428 neuprint_JRC_Hemibrain_1point1 324846570 neuprint_JRC_Hemibrain_1point1 511051477
23 ventro-contralateral-projecting DN1p neuron FBbt_00052273 VFB_jrchjtf2 DN1pA_R (FlyEM-HB:387944118) 22 VFB_jrchk8e0 5th s-LNv (FlyEM-HB:511051477) adult s-LNv neuron FBbt_00007428 neuprint_JRC_Hemibrain_1point1 387944118 neuprint_JRC_Hemibrain_1point1 511051477
9 LNd neuron FBbt_00004045 VFB_jrchjzxy LNd_R (FlyEM-HB:5813069648) 21 VFB_jrchjzxx LNd_R (FlyEM-HB:5813021192) LNd neuron FBbt_00004045 neuprint_JRC_Hemibrain_1point1 5813069648 neuprint_JRC_Hemibrain_1point1 5813021192
21 adult s-LNv neuron FBbt_00007428 VFB_jrchk8e0 5th s-LNv (FlyEM-HB:511051477) 17 VFB_jrchjzxw LNd_R (FlyEM-HB:5813056917) LNd neuron FBbt_00004045 neuprint_JRC_Hemibrain_1point1 511051477 neuprint_JRC_Hemibrain_1point1 5813056917
14 ventro-contralateral-projecting DN1p neuron FBbt_00052273 VFB_jrchjtez DN1pA_R (FlyEM-HB:5813010153) 15 VFB_jrchjzxy LNd_R (FlyEM-HB:5813069648) LNd neuron FBbt_00004045 neuprint_JRC_Hemibrain_1point1 5813010153 neuprint_JRC_Hemibrain_1point1 5813069648
6 adult s-LNv neuron FBbt_00007428 VFB_jrchk8e0 5th s-LNv (FlyEM-HB:511051477) 14 VFB_jrchjtf3 DN1pA_R (FlyEM-HB:387166379) ventro-contralateral-projecting DN1p neuron FBbt_00052273 neuprint_JRC_Hemibrain_1point1 511051477 neuprint_JRC_Hemibrain_1point1 387166379
4 LNd neuron FBbt_00004045 VFB_jrchjzxy LNd_R (FlyEM-HB:5813069648) 14 VFB_jrchjtf1 DN1pA_R (FlyEM-HB:325529237) ventro-contralateral-projecting DN1p neuron FBbt_00052273 neuprint_JRC_Hemibrain_1point1 5813069648 neuprint_JRC_Hemibrain_1point1 325529237
7 LNd neuron FBbt_00004045 VFB_jrchjzxy LNd_R (FlyEM-HB:5813069648) 13 VFB_jrchjtf3 DN1pA_R (FlyEM-HB:387166379) ventro-contralateral-projecting DN1p neuron FBbt_00052273 neuprint_JRC_Hemibrain_1point1 5813069648 neuprint_JRC_Hemibrain_1point1 387166379
10 ventro-contralateral-projecting DN1p neuron FBbt_00052273 VFB_jrchjtf0 DN1pA_R (FlyEM-HB:324846570) 13 VFB_jrchjzxx LNd_R (FlyEM-HB:5813021192) LNd neuron FBbt_00004045 neuprint_JRC_Hemibrain_1point1 324846570 neuprint_JRC_Hemibrain_1point1 5813021192
3 adult s-LNv neuron FBbt_00007428 VFB_jrchk8e0 5th s-LNv (FlyEM-HB:511051477) 12 VFB_jrchjtf1 DN1pA_R (FlyEM-HB:325529237) ventro-contralateral-projecting DN1p neuron FBbt_00052273 neuprint_JRC_Hemibrain_1point1 511051477 neuprint_JRC_Hemibrain_1point1 325529237
17 anterior-projecting DN1p neuron FBbt_00052272 VFB_jrchjtf5 DN1pB_R (FlyEM-HB:5813071319) 11 VFB_jrchjzxy LNd_R (FlyEM-HB:5813069648) LNd neuron FBbt_00004045 neuprint_JRC_Hemibrain_1point1 5813071319 neuprint_JRC_Hemibrain_1point1 5813069648
0 DN1a neuron FBbt_00007429 VFB_jrchjtey DN1a_R (FlyEM-HB:5813022274) 11 VFB_jrchjtex DN1a_R (FlyEM-HB:264083994) DN1a neuron FBbt_00007429 neuprint_JRC_Hemibrain_1point1 5813022274 neuprint_JRC_Hemibrain_1point1 264083994
1 DN1a neuron FBbt_00007429 VFB_jrchjtex DN1a_R (FlyEM-HB:264083994) 10 VFB_jrchjtey DN1a_R (FlyEM-HB:5813022274) DN1a neuron FBbt_00007429 neuprint_JRC_Hemibrain_1point1 264083994 neuprint_JRC_Hemibrain_1point1 5813022274
5 LNd neuron FBbt_00004045 VFB_jrchjzxy LNd_R (FlyEM-HB:5813069648) 10 VFB_jrchjtez DN1pA_R (FlyEM-HB:5813010153) ventro-contralateral-projecting DN1p neuron FBbt_00052273 neuprint_JRC_Hemibrain_1point1 5813069648 neuprint_JRC_Hemibrain_1point1 5813010153
2 LNd neuron FBbt_00004045 VFB_jrchjzxy LNd_R (FlyEM-HB:5813069648) 10 VFB_jrchjtf2 DN1pA_R (FlyEM-HB:387944118) ventro-contralateral-projecting DN1p neuron FBbt_00052273 neuprint_JRC_Hemibrain_1point1 5813069648 neuprint_JRC_Hemibrain_1point1 387944118
[7]:
# Get connections between visual projectsion neurons and descending neurons
visPN2DC = vfb.get_connected_neurons_by_type(upstream_type='visual projection neuron',
                                 downstream_type='adult descending neuron',
                                 weight=10).sort_values('weight', ascending=False)
visPN2DC
[7]:
upstream_class upstream_class_id upstream_neuron_id upstream_neuron_name weight downstream_neuron_id downstream_neuron_name downstream_class downstream_class_id up_data_source up_accession down_source down_accession
1701 lobula tangential neuron LT51 FBbt_00049861 VFB_jrchk09j LT51(aSP29a)_R (FlyEM-HB:1282348408) 319 VFB_jrchjtfr DNb01_R (FlyEM-HB:1566597156) descending neuron of the anterior ventral brai... FBbt_00047582 neuprint_JRC_Hemibrain_1point1 1282348408 neuprint_JRC_Hemibrain_1point1 1566597156
53 adult vest neuron 044 FBbt_20003510 VFB_jrchk7g6 VES044_R (FlyEM-HB:5812979017) 262 VFB_jrchk7eb VES009_R (FlyEM-HB:1140923511) adult vest neuron 009 FBbt_20003475 neuprint_JRC_Hemibrain_1point1 5812979017 neuprint_JRC_Hemibrain_1point1 1140923511
1332 lobula tangential neuron LT51 FBbt_00049861 VFB_jrchk09h LT51_R (FlyEM-HB:5813069020) 238 VFB_jrchk7e7 VES006_R (FlyEM-HB:642728308) adult vest neuron 006 FBbt_20003472 neuprint_JRC_Hemibrain_1point1 5813069020 neuprint_JRC_Hemibrain_1point1 642728308
1668 lobula tangential neuron FBbt_00003859 VFB_jrchk0bu LT86_R (FlyEM-HB:1285849916) 228 VFB_jrchk7g4 VES042_R (FlyEM-HB:1875284107) adult vest neuron 042 FBbt_20003508 neuprint_JRC_Hemibrain_1point1 1285849916 neuprint_JRC_Hemibrain_1point1 1875284107
11 lobula tangential neuron LT51 FBbt_00049861 VFB_jrchk09c LT51_R (FlyEM-HB:1444351896) 221 VFB_jrchjtfg DNa03_R (FlyEM-HB:1139909038) descending neuron of the anterior dorsal brain... FBbt_00047574 neuprint_JRC_Hemibrain_1point1 1444351896 neuprint_JRC_Hemibrain_1point1 1139909038
... ... ... ... ... ... ... ... ... ... ... ... ... ...
1026 lobula-lobula plate columnar neuron LLPC FBbt_00003881 VFB_jrchjzoi LLPC2a (FlyEM-HB:5813039328) 10 VFB_jrchjtfo DNa10_R (FlyEM-HB:707116522) descending neuron of the posterior brain DNp10 FBbt_00047643 neuprint_JRC_Hemibrain_1point1 5813039328 neuprint_JRC_Hemibrain_1point1 707116522
1020 lobula columnar neuron LC10 FBbt_00100482 VFB_jrchjwwh LC10 (FlyEM-HB:5813016041) 10 VFB_jrchjtfo DNa10_R (FlyEM-HB:707116522) descending neuron of the posterior brain DNp10 FBbt_00047643 neuprint_JRC_Hemibrain_1point1 5813016041 neuprint_JRC_Hemibrain_1point1 707116522
1019 lobula-lobula plate columnar neuron LLPC FBbt_00003881 VFB_jrchjzul LLPC3 (FlyEM-HB:1777956777) 10 VFB_jrchjtfo DNa10_R (FlyEM-HB:707116522) descending neuron of the posterior brain DNp10 FBbt_00047643 neuprint_JRC_Hemibrain_1point1 1777956777 neuprint_JRC_Hemibrain_1point1 707116522
1014 lobula columnar neuron FBbt_00003870 VFB_jrchjy7z LC35_R (FlyEM-HB:1502364155) 10 VFB_jrchjtge DNp10_R (FlyEM-HB:5813026936) descending neuron of the posterior brain DNp10 FBbt_00047643 neuprint_JRC_Hemibrain_1point1 1502364155 neuprint_JRC_Hemibrain_1point1 5813026936
1706 adult inferior bridge neuron 043 FBbt_20001220 VFB_jrchjuts IB043_R (FlyEM-HB:883514695) 10 VFB_jrchjtfr DNb01_R (FlyEM-HB:1566597156) descending neuron of the anterior ventral brai... FBbt_00047582 neuprint_JRC_Hemibrain_1point1 883514695 neuprint_JRC_Hemibrain_1point1 1566597156

1707 rows × 13 columns

[8]:
visPN2DC['upstream_class'].value_counts(normalize=True).plot(kind = 'bar') # Excercise - sum up weights for each type.  Note - some types here subsume others
[8]:
<Axes: xlabel='upstream_class'>
../_images/tutorials_connectomics_9_1.png

Get neurons downstream/downstream of a specific neuron

Starting from an individual neuron, in this case an individual neuron from hemibrain, find all neurons upstream or downstream, restricting to edges >= some specified wieght (synaptic connections) and optionally limiting the output by neuron type/class.

[9]:
# Starting point - let's take one of the individual descending neurons from
# the previous exploratory queries and look for other inputs

upstream_of_DNp04 = vfb.get_neurons_upstream_of('DNp04_R (FlyEM-HB:1405231475)', weight = 20)
upstream_of_DNp04
[9]:
query_neuron_id query_neuron_name weight target_neuron_id target_neuron_name
0 VFB_jrchjy9x LC4 (FlyEM-HB:1938544937) 98 VFB_jrchjtg7 DNp04_R (FlyEM-HB:1405231475)
1 VFB_jrchjy9p LC4 (FlyEM-HB:1815070402) 97 VFB_jrchjtg7 DNp04_R (FlyEM-HB:1405231475)
2 VFB_jrchjyad LC4 (FlyEM-HB:1908226457) 93 VFB_jrchjtg7 DNp04_R (FlyEM-HB:1405231475)
3 VFB_jrchjya0 LC4 (FlyEM-HB:5812998136) 92 VFB_jrchjtg7 DNp04_R (FlyEM-HB:1405231475)
4 VFB_jrchjyah LC4 (FlyEM-HB:1938207942) 90 VFB_jrchjtg7 DNp04_R (FlyEM-HB:1405231475)
... ... ... ... ... ...
82 VFB_jrchk063 LPLC2_R (FlyEM-HB:5813034151) 24 VFB_jrchjtg7 DNp04_R (FlyEM-HB:1405231475)
83 VFB_jrchk4oy PVLP023_R (FlyEM-HB:1598296804) 23 VFB_jrchjtg7 DNp04_R (FlyEM-HB:1405231475)
84 VFB_jrchjrof AVLP080_R (FlyEM-HB:5813027276) 22 VFB_jrchjtg7 DNp04_R (FlyEM-HB:1405231475)
85 VFB_jrchk4p4 PVLP026_R (FlyEM-HB:1570565128) 21 VFB_jrchjtg7 DNp04_R (FlyEM-HB:1405231475)
86 VFB_jrchk4pd PVLP031_R (FlyEM-HB:1630342124) 20 VFB_jrchjtg7 DNp04_R (FlyEM-HB:1405231475)

87 rows × 5 columns

[10]:
vfb.get_TermInfo(upstream_of_DNp04['query_neuron_id'])
[10]:
label symbol id tags description parents_label parents_id data_source accession xrefs templates dataset license
0 LPLC2_R (FlyEM-HB:5813034151) LPLC2_R VFB_jrchk063 [Entity, Adult, Anatomy, Cell, Cholinergic, In... tracing status-Roughly traced, cropped-False [lobula plate-lobula columnar neuron LPLC2] [FBbt_00111763] [neuprint_JRC_Hemibrain_1point1] [5813034151] [neuronbridge:5813034151, neuprint_JRC_Hemibra... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
1 LC4 (FlyEM-HB:1625080038) LC4 VFB_jrchjy9e [Entity, Adult, Anatomy, Cell, Cholinergic, Gl... tracing status-Roughly traced, cropped-False [lobula columnar neuron LC4] [FBbt_00003874] [neuprint_JRC_Hemibrain_1point1] [1625080038] [neuprint_JRC_Hemibrain_1point1:1625080038, ne... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
2 LC4 (FlyEM-HB:1782668028) LC4 VFB_jrchjy9o [Entity, Adult, Anatomy, Cell, Cholinergic, Gl... tracing status-Roughly traced, cropped-False [lobula columnar neuron LC4] [FBbt_00003874] [neuprint_JRC_Hemibrain_1point1] [1782668028] [neuronbridge:1782668028, neuprint_JRC_Hemibra... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
3 LC4 (FlyEM-HB:1874035952) LC4 VFB_jrchjy9z [Entity, Adult, Anatomy, Cell, Cholinergic, Gl... tracing status-Roughly traced, cropped-False [lobula columnar neuron LC4] [FBbt_00003874] [neuprint_JRC_Hemibrain_1point1] [1874035952] [neuprint_JRC_Hemibrain_1point1:1874035952, ne... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
4 LC4 (FlyEM-HB:1810956698) LC4 VFB_jrchjy9j [Entity, Adult, Anatomy, Cell, Cholinergic, Gl... tracing status-Roughly traced, cropped-False [lobula columnar neuron LC4] [FBbt_00003874] [neuprint_JRC_Hemibrain_1point1] [1810956698] [neuprint_JRC_Hemibrain_1point1:1810956698, ne... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
... ... ... ... ... ... ... ... ... ... ... ... ... ...
82 SAD017_R (FlyEM-HB:1630678915) SAD017_R VFB_jrchk4z0 [Entity, Adult, Anatomy, Cell, GABAergic, Indi... tracing status-Roughly traced, cropped-False [adult saddle neuron 017] [FBbt_20002226] [neuprint_JRC_Hemibrain_1point1] [1630678915] [neuronbridge:1630678915, neuprint_JRC_Hemibra... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
83 PVLP142_R (FlyEM-HB:1876565477) PVLP142_R VFB_jrchk4wk [Entity, Adult, Anatomy, Cell, Cholinergic, In... tracing status-Roughly traced, cropped-False [adult cholinergic neuron, adult posterior ven... [FBbt_00058205, FBbt_20002200] [neuprint_JRC_Hemibrain_1point1] [1876565477] [neuronbridge:1876565477, neuprint_JRC_Hemibra... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
84 PVLP151(SCB004)_L (FlyEM-HB:1628973439) PVLP151(SCB004)_L VFB_jrchk4x2 [Entity, Adult, Anatomy, Cell, Cholinergic, In... tracing status-Roughly traced, cropped-False [adult posterior ventrolateral protocerebrum n... [FBbt_20002209] [neuprint_JRC_Hemibrain_1point1] [1628973439] [neuronbridge:1628973439, neuprint_JRC_Hemibra... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
85 PVLP100_R (FlyEM-HB:1375845363) PVLP100_R VFB_jrchk4u3 [Entity, Adult, Anatomy, Cell, GABAergic, Indi... tracing status-Roughly traced, cropped-False [adult posterior ventrolateral protocerebrum n... [FBbt_20002158] [neuprint_JRC_Hemibrain_1point1] [1375845363] [neuronbridge:1375845363, neuprint_JRC_Hemibra... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
86 PVLP094_R (FlyEM-HB:1503733177) PVLP094_R VFB_jrchk4tm [Entity, Adult, Anatomy, Cell, GABAergic, Indi... tracing status-Roughly traced, cropped-False [adult posterior ventrolateral protocerebrum n... [FBbt_20002152] [neuprint_JRC_Hemibrain_1point1] [1503733177] [neuprint_JRC_Hemibrain_1point1:1503733177, ne... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...

87 rows × 13 columns

[11]:
vfb.get_TermInfo(upstream_of_DNp04['query_neuron_id'])
[11]:
label symbol id tags description parents_label parents_id data_source accession xrefs templates dataset license
0 LPLC2_R (FlyEM-HB:5813034151) LPLC2_R VFB_jrchk063 [Entity, Adult, Anatomy, Cell, Cholinergic, In... tracing status-Roughly traced, cropped-False [lobula plate-lobula columnar neuron LPLC2] [FBbt_00111763] [neuprint_JRC_Hemibrain_1point1] [5813034151] [neuronbridge:5813034151, neuprint_JRC_Hemibra... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
1 LC4 (FlyEM-HB:1625080038) LC4 VFB_jrchjy9e [Entity, Adult, Anatomy, Cell, Cholinergic, Gl... tracing status-Roughly traced, cropped-False [lobula columnar neuron LC4] [FBbt_00003874] [neuprint_JRC_Hemibrain_1point1] [1625080038] [neuprint_JRC_Hemibrain_1point1:1625080038, ne... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
2 LC4 (FlyEM-HB:1782668028) LC4 VFB_jrchjy9o [Entity, Adult, Anatomy, Cell, Cholinergic, Gl... tracing status-Roughly traced, cropped-False [lobula columnar neuron LC4] [FBbt_00003874] [neuprint_JRC_Hemibrain_1point1] [1782668028] [neuronbridge:1782668028, neuprint_JRC_Hemibra... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
3 LC4 (FlyEM-HB:1874035952) LC4 VFB_jrchjy9z [Entity, Adult, Anatomy, Cell, Cholinergic, Gl... tracing status-Roughly traced, cropped-False [lobula columnar neuron LC4] [FBbt_00003874] [neuprint_JRC_Hemibrain_1point1] [1874035952] [neuprint_JRC_Hemibrain_1point1:1874035952, ne... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
4 LC4 (FlyEM-HB:1810956698) LC4 VFB_jrchjy9j [Entity, Adult, Anatomy, Cell, Cholinergic, Gl... tracing status-Roughly traced, cropped-False [lobula columnar neuron LC4] [FBbt_00003874] [neuprint_JRC_Hemibrain_1point1] [1810956698] [neuprint_JRC_Hemibrain_1point1:1810956698, ne... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
... ... ... ... ... ... ... ... ... ... ... ... ... ...
82 SAD017_R (FlyEM-HB:1630678915) SAD017_R VFB_jrchk4z0 [Entity, Adult, Anatomy, Cell, GABAergic, Indi... tracing status-Roughly traced, cropped-False [adult saddle neuron 017] [FBbt_20002226] [neuprint_JRC_Hemibrain_1point1] [1630678915] [neuronbridge:1630678915, neuprint_JRC_Hemibra... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
83 PVLP142_R (FlyEM-HB:1876565477) PVLP142_R VFB_jrchk4wk [Entity, Adult, Anatomy, Cell, Cholinergic, In... tracing status-Roughly traced, cropped-False [adult cholinergic neuron, adult posterior ven... [FBbt_00058205, FBbt_20002200] [neuprint_JRC_Hemibrain_1point1] [1876565477] [neuronbridge:1876565477, neuprint_JRC_Hemibra... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
84 PVLP151(SCB004)_L (FlyEM-HB:1628973439) PVLP151(SCB004)_L VFB_jrchk4x2 [Entity, Adult, Anatomy, Cell, Cholinergic, In... tracing status-Roughly traced, cropped-False [adult posterior ventrolateral protocerebrum n... [FBbt_20002209] [neuprint_JRC_Hemibrain_1point1] [1628973439] [neuronbridge:1628973439, neuprint_JRC_Hemibra... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
85 PVLP100_R (FlyEM-HB:1375845363) PVLP100_R VFB_jrchk4u3 [Entity, Adult, Anatomy, Cell, GABAergic, Indi... tracing status-Roughly traced, cropped-False [adult posterior ventrolateral protocerebrum n... [FBbt_20002158] [neuprint_JRC_Hemibrain_1point1] [1375845363] [neuronbridge:1375845363, neuprint_JRC_Hemibra... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
86 PVLP094_R (FlyEM-HB:1503733177) PVLP094_R VFB_jrchk4tm [Entity, Adult, Anatomy, Cell, GABAergic, Indi... tracing status-Roughly traced, cropped-False [adult posterior ventrolateral protocerebrum n... [FBbt_20002152] [neuprint_JRC_Hemibrain_1point1] [1503733177] [neuprint_JRC_Hemibrain_1point1:1503733177, ne... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...

87 rows × 13 columns

Let’s try a similar query from one of the LC4 neurons to see what other descending neuron types are downstream of it.

[12]:
vfb.get_neurons_downstream_of('LC4 (FlyEM-HB:1249932198)', classification="'adult descending neuron'", weight = 10)
[12]:
query_neuron_id query_neuron_name weight target_neuron_id target_neuron_name
0 VFB_jrchjy8y LC4 (FlyEM-HB:1249932198) 78 VFB_jrchjtg7 DNp04_R (FlyEM-HB:1405231475)
1 VFB_jrchjy8y LC4 (FlyEM-HB:1249932198) 65 VFB_jrchjtgf DNp11_R (FlyEM-HB:1281324958)
2 VFB_jrchjy8y LC4 (FlyEM-HB:1249932198) 30 VFB_jrchjup1 Giant Fiber_R (FlyEM-HB:2307027729)
3 VFB_jrchjy8y LC4 (FlyEM-HB:1249932198) 11 VFB_jrchjtg6 DNp03_R (FlyEM-HB:1565846637)

More sophisticated connectomics queries require direct queries of connectomics DB APIs

CATMAID connectivity queries

Broadly speaking, using pymaid to query CATMAID servers lets you fetch connectivity data as either lists of up- and downstream partners or as whole adjacency matrices.

These examples use the VFB FAFB server.

[13]:
# Using VFB to get neurons by type
DA1 = vfb.get_instances("'adult antennal lobe projection neuron DA1'", return_dataframe=True, limit=50)
len(DA1)
DA1
Limiting to 50 terms out of 52
Warning: called a non existant id:VFB_00102294
[13]:
label symbol id tags description parents_label parents_id data_source accession xrefs templates dataset license
0 Gad1-F-400088 VFB_00009611 [Entity, Adult, Anatomy, Cell, Chemosensory_sy... OutAge: Adult 5~15 days [expression pattern fragment, adult antennal l... [VFBext_0000004, FBbt_00067372] [FlyCircuit] [Gad1-F-400088] [FlyCircuit:Gad1-F-400088] [JRC2018Unisex, adult brain template JFRC2] [Chiang2010] []
1 Uniglomerular mALT DA1 lPN#L1 (FAFB:4207871) VFB_0010126e [Entity, Adult, Anatomy, Cell, Chemosensory_sy... NaN [adult fruitless aDT-e (female) neuron, adult ... [FBbt_00110423, FBbt_00067363] [catmaid_fafb] [4207871] [catmaid_fafb:4207871] [JRC2018Unisex] [BatesSchlegel2020] [https://creativecommons.org/licenses/by-sa/4....
2 Uniglomerular mALT DA1 lPN#L6 (FAFB:2381753) VFB_0010123b [Entity, Adult, Anatomy, Cell, Chemosensory_sy... NaN [adult antennal lobe projection neuron DA1 lPN... [FBbt_00067363, FBbt_00110423] [catmaid_fafb] [2381753] [catmaid_fafb:2381753] [JRC2018Unisex] [BatesSchlegel2020] [https://creativecommons.org/licenses/by-sa/4....
3 Uniglomerular mALT DA1 lPN#L3 (FAFB:2345089) VFB_0010122p [Entity, Adult, Anatomy, Cell, Chemosensory_sy... NaN [adult fruitless aDT-e (female) neuron, adult ... [FBbt_00110423, FBbt_00067363] [catmaid_fafb] [2345089] [catmaid_fafb:2345089] [JRC2018Unisex] [BatesSchlegel2020] [https://creativecommons.org/licenses/by-sa/4....
4 Uniglomerular mlALT DA1 vPN#L1 (FAFB:2334841) VFB_0010122m [Entity, Adult, Anatomy, Cell, Chemosensory_sy... NaN [adult antennal lobe projection neuron DA1 vPN] [FBbt_00067372] [catmaid_fafb] [2334841] [catmaid_fafb:2334841] [JRC2018Unisex] [BatesSchlegel2020] [https://creativecommons.org/licenses/by-sa/4....
5 Uniglomerular mALT DA1 lPN#L2 (FAFB:2319457) VFB_0010122k [Entity, Adult, Anatomy, Cell, Chemosensory_sy... NaN [adult antennal lobe projection neuron DA1 lPN... [FBbt_00067363, FBbt_00110423] [catmaid_fafb] [2319457] [catmaid_fafb:2319457] [JRC2018Unisex] [BatesSchlegel2020] [https://creativecommons.org/licenses/by-sa/4....
6 Uniglomerular mALT DA1 lPN#L7 (FAFB:3239781) VFB_0010124l [Entity, Adult, Anatomy, Cell, Chemosensory_sy... NaN [adult fruitless aDT-e (female) neuron, adult ... [FBbt_00110423, FBbt_00067363] [catmaid_fafb] [3239781] [catmaid_fafb:3239781] [JRC2018Unisex] [BatesSchlegel2020] [https://creativecommons.org/licenses/by-sa/4....
7 Uniglomerular mALT DA1 lPN#L5 (FAFB:2380564) VFB_0010122z [Entity, Adult, Anatomy, Cell, Chemosensory_sy... NaN [adult antennal lobe projection neuron DA1 lPN... [FBbt_00067363, FBbt_00110423] [catmaid_fafb] [2380564] [catmaid_fafb:2380564] [JRC2018Unisex] [BatesSchlegel2020] [https://creativecommons.org/licenses/by-sa/4....
8 Uniglomerular mlALT DA1 vPN#R1 (FAFB:1811442) VFB_0010121x [Entity, Adult, Anatomy, Cell, Chemosensory_sy... NaN [adult antennal lobe projection neuron DA1 vPN] [FBbt_00067372] [catmaid_fafb] [1811442] [catmaid_fafb:1811442] [JRC2018Unisex] [BatesSchlegel2020] [https://creativecommons.org/licenses/by-sa/4....
9 Uniglomerular mALT DA1 lPN#L4 (FAFB:2379517) VFB_0010122y [Entity, Adult, Anatomy, Cell, Chemosensory_sy... NaN [adult antennal lobe projection neuron DA1 lPN... [FBbt_00067363, FBbt_00110423] [catmaid_fafb] [2379517] [catmaid_fafb:2379517] [JRC2018Unisex] [BatesSchlegel2020] [https://creativecommons.org/licenses/by-sa/4....
10 Uniglomerular mALT DA1 lPN#R4 (FAFB:755022) VFB_00101205 [Entity, Adult, Anatomy, Cell, Chemosensory_sy... NaN [adult antennal lobe projection neuron DA1 lPN] [FBbt_00067363] [catmaid_fafb] [755022] [catmaid_fafb:755022] [JRC2018Unisex] [Zheng2018] [https://creativecommons.org/licenses/by-sa/4....
11 Uniglomerular mALT DA1 lPN#R7 (FAFB:57353) VFB_00101202 [Entity, Adult, Anatomy, Cell, Chemosensory_sy... NaN [adult antennal lobe projection neuron DA1 lPN] [FBbt_00067363] [catmaid_fafb] [57353] [catmaid_fafb:57353] [JRC2018Unisex] [Zheng2018] [https://creativecommons.org/licenses/by-sa/4....
12 Uniglomerular mALT DA1 lPN#R1 (FAFB:57323) VFB_00101201 [Entity, Adult, Anatomy, Cell, Chemosensory_sy... NaN [adult antennal lobe projection neuron DA1 lPN] [FBbt_00067363] [catmaid_fafb] [57323] [catmaid_fafb:57323] [JRC2018Unisex] [Zheng2018] [https://creativecommons.org/licenses/by-sa/4....
13 Uniglomerular mALT DA1 lPN#R3 (FAFB:61221) VFB_00101204 [Entity, Adult, Anatomy, Cell, Chemosensory_sy... NaN [adult antennal lobe projection neuron DA1 lPN] [FBbt_00067363] [catmaid_fafb] [61221] [catmaid_fafb:61221] [JRC2018Unisex] [Zheng2018] [https://creativecommons.org/licenses/by-sa/4....
14 Uniglomerular mALT DA1 lPN#R2 (FAFB:57311) VFB_00101200 [Entity, Adult, Anatomy, Cell, Chemosensory_sy... NaN [adult antennal lobe projection neuron DA1 lPN] [FBbt_00067363] [catmaid_fafb] [57311] [catmaid_fafb:57311] [JRC2018Unisex] [Zheng2018] [https://creativecommons.org/licenses/by-sa/4....
15 Uniglomerular mALT DA1 lPN#R8 (FAFB:57381) VFB_00101203 [Entity, Adult, Anatomy, Cell, Chemosensory_sy... NaN [adult antennal lobe projection neuron DA1 lPN] [FBbt_00067363] [catmaid_fafb] [57381] [catmaid_fafb:57381] [JRC2018Unisex] [Zheng2018] [https://creativecommons.org/licenses/by-sa/4....
16 Multiglomerular mALT lvPN#R45 (FAFB:57035) VFB_001011z3 [Entity, Adult, Anatomy, Cell, Chemosensory_sy... NaN [adult antennal lobe projection neuron DA1 lvPN] [FBbt_20003824] [catmaid_fafb] [57035] [catmaid_fafb:57035] [JRC2018Unisex] [BatesSchlegel2020] [https://creativecommons.org/licenses/by-sa/4....
17 Multiglomerular mALT lvPN#R46 (FAFB:57179) VFB_001011zb [Entity, Adult, Anatomy, Cell, Chemosensory_sy... NaN [adult antennal lobe projection neuron DA1 lvPN] [FBbt_20003824] [catmaid_fafb] [57179] [catmaid_fafb:57179] [JRC2018Unisex] [BatesSchlegel2020] [https://creativecommons.org/licenses/by-sa/4....
18 Multiglomerular mALT lvPN#R44 (FAFB:57158) VFB_001011z9 [Entity, Adult, Anatomy, Cell, Chemosensory_sy... NaN [adult antennal lobe projection neuron DA1 lvPN] [FBbt_20003824] [catmaid_fafb] [57158] [catmaid_fafb:57158] [JRC2018Unisex] [BatesSchlegel2020] [https://creativecommons.org/licenses/by-sa/4....
19 Uniglomerular mALT DA1 lPN#R6 (FAFB:27295) VFB_00101199 [Entity, Adult, Anatomy, Cell, Chemosensory_sy... NaN [adult antennal lobe projection neuron DA1 lPN] [FBbt_00067363] [catmaid_fafb] [27295] [catmaid_fafb:27295] [JRC2018Unisex] [Zheng2018] [https://creativecommons.org/licenses/by-sa/4....
20 Cha-F-300252 VFB_00005625 [Entity, Adult, Anatomy, Cell, Chemosensory_sy... OutAge: Adult 5~15 days [expression pattern fragment, adult ALl1 linea... [VFBext_0000004, FBbt_00050025, FBbt_00067350,... [FlyCircuit] [Cha-F-300252] [FlyCircuit:Cha-F-300252] [adult brain template JFRC2, JRC2018Unisex] [Chiang2010] []
21 VGlut-F-800329 VFB_00005957 [Entity, Adult, Anatomy, Cell, Chemosensory_sy... OutAge: Adult 5~15 days [antennal lobe projection neuron of ALl1 linea... [FBbt_00067362, FBbt_00067350, VFBext_0000004,... [FlyCircuit] [VGlut-F-800329] [FlyCircuit:VGlut-F-800329] [JRC2018Unisex, adult brain template JFRC2] [Chiang2010] []
22 VGlut-F-800317 VFB_00005913 [Entity, Adult, Anatomy, Cell, Chemosensory_sy... OutAge: Adult 5~15 days [antennal lobe projection neuron of ALl1 linea... [FBbt_00067362, VFBext_0000004, FBbt_00050025,... [FlyCircuit] [VGlut-F-800317] [FlyCircuit:VGlut-F-800317] [adult brain template JFRC2, JRC2018Unisex] [Chiang2010] []
23 VGlut-F-000655 VFB_00006552 [Entity, Adult, Anatomy, Cell, Chemosensory_sy... OutAge: Adult 5~15 days [adult antennal lobe projection neuron DA1, ad... [FBbt_00048096, FBbt_00050025, FBbt_00067362, ... [FlyCircuit] [VGlut-F-000655] [FlyCircuit:VGlut-F-000655] [adult brain template JFRC2, JRC2018Unisex] [Chiang2010] []
24 VGlut-F-200574 VFB_00006638 [Entity, Adult, Anatomy, Cell, Chemosensory_sy... OutAge: Adult 5~15 days [medial antennal lobe tract projection neuron,... [FBbt_00067350, VFBext_0000004, FBbt_00048096,... [FlyCircuit] [VGlut-F-200574] [FlyCircuit:VGlut-F-200574] [JRC2018Unisex, adult brain template JFRC2] [Chiang2010] []
25 fru-F-400149 VFB_00006344 [Entity, Adult, Anatomy, Cell, Chemosensory_sy... OutAge: Adult 5~15 days [medial antennal lobe tract projection neuron,... [FBbt_00067350, VFBext_0000004, FBbt_00048096,... [FlyCircuit] [fru-F-400149] [FlyCircuit:fru-F-400149] [JRC2018Unisex, adult brain template JFRC2] [Chiang2010] []
26 M_lvPNm45_R (FlyEM-HB:792023887) M_lvPNm45_R VFB_jrchk0xm [Entity, Adult, Anatomy, Cell, Chemosensory_sy... tracing status-Roughly traced, cropped-False [adult antennal lobe projection neuron DA1 lvPN] [FBbt_20003824] [neuprint_JRC_Hemibrain_1point1] [792023887] [neuronbridge:792023887, neuprint_JRC_Hemibrai... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
27 M_lvPNm45_R (FlyEM-HB:757591093) M_lvPNm45_R VFB_jrchk0xl [Entity, Adult, Anatomy, Cell, Chemosensory_sy... tracing status-Roughly traced, cropped-False [adult antennal lobe projection neuron DA1 lvPN] [FBbt_20003824] [neuprint_JRC_Hemibrain_1point1] [757591093] [neuprint_JRC_Hemibrain_1point1:757591093, neu... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
28 M_lvPNm45_R (FlyEM-HB:757258507) M_lvPNm45_R VFB_jrchk0xk [Entity, Adult, Anatomy, Cell, Chemosensory_sy... tracing status-Roughly traced, cropped-False [adult antennal lobe projection neuron DA1 lvPN] [FBbt_20003824] [neuprint_JRC_Hemibrain_1point1] [757258507] [neuprint_JRC_Hemibrain_1point1:757258507, neu... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
29 Multiglomerular mALT lvPN#L3 (FAFB:4520615) VFB_00102dvz [Entity, Adult, Anatomy, Cell, Chemosensory_sy... Multiglomerular mALT lvPN#L3, FBbt:00049785 [adult antennal lobe projection neuron DA1 lvPN] [FBbt_20003824] [catmaid_fafb] [4520615] [catmaid_fafb:4520615] [JRC2018Unisex] [TaiszGalili2022] [https://creativecommons.org/licenses/by-sa/4....
30 Multiglomerular mALT lvPN#L2 (FAFB:7710838) VFB_00102dw8 [Entity, Adult, Anatomy, Cell, Chemosensory_sy... Multiglomerular mALT lvPN#L2, FBbt:00049785 [adult antennal lobe projection neuron DA1 lvPN] [FBbt_20003824] [catmaid_fafb] [7710838] [catmaid_fafb:7710838] [JRC2018Unisex] [TaiszGalili2022] [https://creativecommons.org/licenses/by-sa/4....
31 Multiglomerular mALT lvPN#L1 (FAFB:4520197) VFB_00102dvy [Entity, Adult, Anatomy, Cell, Chemosensory_sy... Multiglomerular mALT lvPN#L1, FBbt:00049785 [adult antennal lobe projection neuron DA1 lvPN] [FBbt_20003824] [catmaid_fafb] [4520197] [catmaid_fafb:4520197] [JRC2018Unisex] [TaiszGalili2022] [https://creativecommons.org/licenses/by-sa/4....
32 DA1_lPN_R (FlyEM-HB:5813039315) DA1_lPN_R VFB_jrchjtdd [Entity, Adult, Anatomy, Cell, Chemosensory_sy... tracing status-Roughly traced, cropped-False [adult fruitless aDT-e (female) neuron, adult ... [FBbt_00110423, FBbt_00067363] [neuprint_JRC_Hemibrain_1point1] [5813039315] [neuronbridge:5813039315, neuprint_JRC_Hemibra... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
33 DA1_lPN_R (FlyEM-HB:1734350908) DA1_lPN_R VFB_jrchjtdb [Entity, Adult, Anatomy, Cell, Chemosensory_sy... tracing status-Roughly traced, cropped-False [adult antennal lobe projection neuron DA1 lPN... [FBbt_00067363, FBbt_00110423] [neuprint_JRC_Hemibrain_1point1] [1734350908] [neuprint_JRC_Hemibrain_1point1:1734350908, ne... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
34 DA1_lPN_R (FlyEM-HB:754534424) DA1_lPN_R VFB_jrchjtde [Entity, Adult, Anatomy, Cell, Chemosensory_sy... tracing status-Roughly traced, cropped-False [adult antennal lobe projection neuron DA1 lPN... [FBbt_00067363, FBbt_00110423] [neuprint_JRC_Hemibrain_1point1] [754534424] [neuronbridge:754534424, neuprint_JRC_Hemibrai... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
35 DA1_vPN_R (FlyEM-HB:733316908) DA1_vPN_R VFB_jrchjtdh [Entity, Adult, Anatomy, Cell, Chemosensory_sy... tracing status-Roughly traced, cropped-False [adult antennal lobe projection neuron DA1 vPN] [FBbt_00067372] [neuprint_JRC_Hemibrain_1point1] [733316908] [neuronbridge:733316908, neuprint_JRC_Hemibrai... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
36 DA1_lPN_R (FlyEM-HB:1765040289) DA1_lPN_R VFB_jrchjtdc [Entity, Adult, Anatomy, Cell, Chemosensory_sy... tracing status-Roughly traced, cropped-False [adult antennal lobe projection neuron DA1 lPN... [FBbt_00067363, FBbt_00110423] [neuprint_JRC_Hemibrain_1point1] [1765040289] [neuronbridge:1765040289, neuprint_JRC_Hemibra... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
37 DA1_lPN_R (FlyEM-HB:722817260) DA1_lPN_R VFB_jrchjtda [Entity, Adult, Anatomy, Cell, Chemosensory_sy... tracing status-Roughly traced, cropped-False [adult antennal lobe projection neuron DA1 lPN... [FBbt_00067363, FBbt_00110423] [neuprint_JRC_Hemibrain_1point1] [722817260] [neuprint_JRC_Hemibrain_1point1:722817260, neu... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
38 DA1_lPN_R (FlyEM-HB:1734350788) DA1_lPN_R VFB_jrchjtdf [Entity, Adult, Anatomy, Cell, Chemosensory_sy... tracing status-Roughly traced, cropped-False [adult fruitless aDT-e (female) neuron, adult ... [FBbt_00110423, FBbt_00067363] [neuprint_JRC_Hemibrain_1point1] [1734350788] [neuprint_JRC_Hemibrain_1point1:1734350788, ne... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
39 DA1_lPN_R (FlyEM-HB:754538881) DA1_lPN_R VFB_jrchjtdg [Entity, Adult, Anatomy, Cell, Chemosensory_sy... tracing status-Roughly traced, cropped-False [adult fruitless aDT-e (female) neuron, adult ... [FBbt_00110423, FBbt_00067363] [neuprint_JRC_Hemibrain_1point1] [754538881] [neuronbridge:754538881, neuprint_JRC_Hemibrai... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
40 Cha-F-500006 VFB_00010085 [Entity, Adult, Anatomy, Cell, Chemosensory_sy... OutAge: Adult 5~15 days [adult ALl1 lineage neuron, expression pattern... [FBbt_00050025, VFBext_0000004, FBbt_00048096,... [FlyCircuit] [Cha-F-500006] [FlyCircuit:Cha-F-500006] [adult brain template JFRC2, JRC2018Unisex] [Chiang2010] []
41 VGlut-F-000280 VFB_00010758 [Entity, Adult, Anatomy, Cell, Chemosensory_sy... OutAge: Adult 5~15 days [adult antennal lobe projection neuron DA1, me... [FBbt_00048096, FBbt_00067350, FBbt_00067362, ... [FlyCircuit] [VGlut-F-000280] [FlyCircuit:VGlut-F-000280] [adult brain template JFRC2, JRC2018Unisex] [Chiang2010] []
42 VGlut-F-700188 VFB_00010912 [Entity, Adult, Anatomy, Cell, Chemosensory_sy... OutAge: Adult 5~15 days [antennal lobe projection neuron of ALl1 linea... [FBbt_00067362, FBbt_00050025, FBbt_00048096, ... [FlyCircuit] [VGlut-F-700188] [FlyCircuit:VGlut-F-700188] [JRC2018Unisex, adult brain template JFRC2] [Chiang2010] []
43 Gad1-F-200064 VFB_00011249 [Entity, Adult, Anatomy, Cell, Chemosensory_sy... OutAge: Adult 5~15 days [antennal lobe projection neuron of ALl1 linea... [FBbt_00067362, FBbt_00048096, FBbt_00050025, ... [FlyCircuit] [Gad1-F-200064] [FlyCircuit:Gad1-F-200064] [adult brain template JFRC2, JRC2018Unisex] [Chiang2010] []
44 Gad1-F-200010 VFB_00012622 [Entity, Adult, Anatomy, Cell, Chemosensory_sy... OutAge: Adult 5~15 days [adult antennal lobe projection neuron DA1, ad... [FBbt_00048096, FBbt_00050025, FBbt_00067362, ... [FlyCircuit] [Gad1-F-200010] [FlyCircuit:Gad1-F-200010] [adult brain template JFRC2, JRC2018Unisex] [Chiang2010] []
45 VGlut-F-600326 VFB_00012155 [Entity, Adult, Anatomy, Cell, Chemosensory_sy... OutAge: Adult 5~15 days [expression pattern fragment, medial antennal ... [VFBext_0000004, FBbt_00067350, FBbt_00050025,... [FlyCircuit] [VGlut-F-600326] [FlyCircuit:VGlut-F-600326] [JRC2018Unisex, adult brain template JFRC2] [Chiang2010] []
46 VGlut-F-700040 VFB_00013061 [Entity, Adult, Anatomy, Cell, Chemosensory_sy... OutAge: Adult 5~15 days [expression pattern fragment, adult antennal l... [VFBext_0000004, FBbt_00048096, FBbt_00067362,... [FlyCircuit] [VGlut-F-700040] [FlyCircuit:VGlut-F-700040] [adult brain template JFRC2, JRC2018Unisex] [Chiang2010] []
47 fru-M-200319 VFB_00000323 [Entity, Adult, Anatomy, Cell, Chemosensory_sy... OutAge: Adult 5~15 days [antennal lobe projection neuron of ALl1 linea... [FBbt_00067362, FBbt_00067350, VFBext_0000004,... [FlyCircuit] [fru-M-200319] [FlyCircuit:fru-M-200319] [JRC2018Unisex, adult brain template JFRC2] [Chiang2010] []
48 npf-M-300006 VFB_00001755 [Entity, Adult, Anatomy, Cell, Chemosensory_sy... OutAge: Adult 5~15 days [medial antennal lobe tract projection neuron,... [FBbt_00067350, FBbt_00067362, FBbt_00050025, ... [FlyCircuit] [npf-M-300006] [FlyCircuit:npf-M-300006] [JRC2018Unisex, adult brain template JFRC2] [Chiang2010] []
[16]:
# Map neurons to CATMAID Skeleton IDs (skids)

da1_skids = vfb.vfb_id_2_xrefs(DA1['id'], db='catmaid_fafb', reverse_return=True)
da1_skids_int = [int(key.split(':')[1]) for key in da1_skids.keys()]
print(da1_skids_int)

# print is just used so we can see the list as a single line
33mWarning: The following IDs do not match DB &/or id_type constraints: {'VFB_jrchjtdb', 'VFB_00010085', 'VFB_jrchk0xm', 'VFB_00005625', 'VFB_00010912', 'VFB_jrchjtdh', 'VFB_00005913', 'VFB_jrchjtdd', 'VFB_00006344', 'VFB_jrchjtdf', 'VFB_00013061', 'VFB_00012155', 'VFB_00009611', 'VFB_00011249', 'VFB_00006552', 'VFB_jrchjtdg', 'VFB_jrchk0xk', 'VFB_jrchjtda', 'VFB_00006638', 'VFB_00005957', 'VFB_00010758', 'VFB_00000323', 'VFB_jrchjtdc', 'VFB_jrchk0xl', 'VFB_jrchjtde', 'VFB_00012622', 'VFB_00001755'}
No match found for VFB_00009611
No match found for VFB_00005625
No match found for VFB_00005957
No match found for VFB_00005913
No match found for VFB_00006552
No match found for VFB_00006638
No match found for VFB_00006344
No match found for VFB_jrchk0xm
No match found for VFB_jrchk0xl
No match found for VFB_jrchk0xk
No match found for VFB_jrchjtdd
No match found for VFB_jrchjtdb
No match found for VFB_jrchjtde
No match found for VFB_jrchjtdh
No match found for VFB_jrchjtdc
No match found for VFB_jrchjtda
No match found for VFB_jrchjtdf
No match found for VFB_jrchjtdg
No match found for VFB_00010085
No match found for VFB_00010758
No match found for VFB_00010912
No match found for VFB_00011249
No match found for VFB_00012622
No match found for VFB_00012155
No match found for VFB_00013061
No match found for VFB_00000323
No match found for VFB_00001755
[4207871, 2381753, 2345089, 2334841, 2319457, 3239781, 2380564, 1811442, 2379517, 755022, 57353, 57323, 61221, 57311, 57381, 57035, 57179, 57158, 27295, 4520615, 7710838, 4520197]

Generate a connectivity table for neurons downstream of DA1 neurons

[17]:
da1 = pymaid.get_neurons(da1_skids_int)
da1_ds = pymaid.get_partners(da1_skids_int,
                             threshold=3,  # anything with >= 3 synapses
                             directions=['outgoing']  # downstream partners only
                            )

# Result is a pandas DataFrame
da1_ds.head()
Fetch neurons:   0%|          | 0/22 [00:00<?, ?it/s]INFO  : Fetching connectivity table for 22 neurons (pymaid)
INFO  : Done. Found 0 pre-, 273 postsynaptic and 0 gap junction-connected neurons (pymaid)
[17]:
neuron_name skeleton_id num_nodes relation 4207871 2381753 2345089 2334841 2319457 3239781 ... 57311 57381 57035 57179 57158 27295 4520615 7710838 4520197 total
0 Uniglomerular mlALT DA1 vPN mlALTed Milk 23348... 2334841 6362 downstream 17 32 14 0 22 26 ... 0 0 0 0 0 0 0 0 0 139
1 Uniglomerular mlALT DA1 vPN mlALTed Milk 18114... 1811442 11769 downstream 0 0 0 0 0 0 ... 21 4 0 0 1 15 0 0 0 122
2 LHAV2a3#1 1870231 RJVR AJES PS 1870230 14820 downstream 0 0 0 0 0 0 ... 5 28 0 0 0 10 0 0 0 100
3 LHAV4c1#1 488056 downstream DA1 GSXEJ 488055 12137 downstream 0 0 0 0 0 0 ... 17 0 0 13 6 16 0 0 0 96
4 LHAV4a4#1 1911125 FML PS RJVR 1911124 6969 downstream 0 0 0 0 0 0 ... 19 9 0 0 0 5 0 0 0 86

5 rows × 27 columns

[18]:
# Get an adjacency matrix between all Bates, Schlegel et al. neurons
bates = pymaid.find_neurons(annotations='Paper: Bates and Schlegel et al 2020')
adj = pymaid.adjacency_matrix(bates)
adj.head()
INFO  : Found 584 neurons matching the search parameters (pymaid)
[18]:
targets 2863104 57349 57353 16 57361 15738898 57365 4182038 3813399 11524119 ... 57323 4624362 1853423 2842610 57333 4624374 3080183 57337 4624378 57341
sources
2863104 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 ... 2.0 0.0 12.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
57349 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 ... 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
57353 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 ... 0.0 0.0 5.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
16 0.0 0.0 0.0 1.0 0.0 0.0 0.0 0.0 0.0 1.0 ... 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
57361 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 ... 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

5 rows × 584 columns

[19]:
import seaborn as sns

ax = sns.clustermap(adj, vmax=10, cmap='Greys')
# ax = sns.heatmap(adj, vmax=10, cmap='Greys')

/Users/robbiecourt/GIT/VFB_connect/.conda/lib/python3.10/site-packages/seaborn/matrix.py:560: UserWarning: Clustering large matrix with scipy. Installing `fastcluster` may give better performance.
  warnings.warn(msg)
/Users/robbiecourt/GIT/VFB_connect/.conda/lib/python3.10/site-packages/seaborn/matrix.py:560: UserWarning: Clustering large matrix with scipy. Installing `fastcluster` may give better performance.
  warnings.warn(msg)
../_images/tutorials_connectomics_23_1.png
[20]:
# Axo-axonic connections between two different types of DA1 PNs
cn = pymaid.get_connectors_between(2863104, 1811442)
cn.head()
[20]:
connector_id connector_loc node1_id source_neuron confidence1 creator1 node1_loc node2_id target_neuron confidence2 creator2 node2_loc
0 17870563 [363219.0, 169182.0, 153920.0] 6903652 2863104 5 NaN [362894.0, 169511.0, 153920.0] 6546760 1811442 5 NaN [363421.0, 168741.0, 153920.0]
1 6795747 [355030.0, 154048.0, 145800.0] 6795749 2863104 5 NaN [355045.0, 154180.0, 145800.0] 6795745 1811442 5 NaN [355024.0, 153946.0, 145760.0]
2 6826199 [358042.0, 160788.0, 147600.0] 6826200 2863104 5 NaN [355948.0, 160126.0, 147600.0] 6826198 1811442 5 NaN [358194.0, 160883.0, 147600.0]
3 6835037 [354306.0, 154100.0, 152320.0] 6835043 2863104 5 NaN [354088.0, 153842.0, 152320.0] 6835033 1811442 5 NaN [354400.0, 154346.0, 152360.0]
4 7032350 [355192.0, 167586.0, 158320.0] 7032356 2863104 5 NaN [354814.0, 167861.0, 158320.0] 17870268 1811442 5 NaN [356626.0, 167779.0, 158200.0]
[21]:
import numpy as np

points = np.vstack(cn.connector_loc)

navis.plot3d([da1.idx[[1811442, 57353]],  # plot the two neurons
              points],  # plot the points of synaptic contacts as scatter
              scatter_kws=dict(name="synaptic contacts")
              )

Data type cannot be displayed: application/vnd.plotly.v1+json

neuprint connectivity queries

To programmatically interface with neuprint, we will use neuprint-python (link). It requires an API token which you can get via the website and is bound to the Google account that you use to log into neuprint. For this workshop we provide such a token as environment variable but you will need to start using your own token after the workshop is over.

These examples use the hemibrain v1.1 dataset.

neuprint-python

First we have to initialize the connection.

[22]:
!pip install neuprint-python --quiet

import neuprint as neu
client = neu.Client('https://neuprint.janelia.org',
                    dataset='hemibrain:v1.1',
                    token='eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJlbWFpbCI6InZmYndvcmtzaG9wLm5ldXJvZmx5MjAyMEBnbWFpbC5jb20iLCJsZXZlbCI6Im5vYXV0aCIsImltYWdlLXVybCI6Imh0dHBzOi8vbGg2Lmdvb2dsZXVzZXJjb250ZW50LmNvbS8tWXFDN21NRXd3TlEvQUFBQUFBQUFBQUkvQUFBQUFBQUFBQUEvQU1adXVjbU5zaXhXZDRhM0VyTTQ0ODBMa2IzNDdvUlpfUS9zOTYtYy9waG90by5qcGc_c3o9NTA_c3o9NTAiLCJleHAiOjE3OTQwOTE4ODd9.ceg4mrj2o-aOhK0NHNGmBacg8R34PBPoLBwhCo4uOCQ')

Most functions in neuprint-python accept neu.NeuronCriteria which is effectively a filter for body IDs, types, cellbody fibers (~lineages), etc:

[23]:
help(neu.NeuronCriteria)
Help on class NeuronCriteria in module neuprint.queries.neuroncriteria:

class NeuronCriteria(builtins.object)
 |  NeuronCriteria(matchvar='n', *, bodyId=None, type=None, instance=None, regex='guess', status=None, statusLabel=None, rois=None, inputRois=None, outputRois=None, roi_req='all', min_roi_inputs=1, min_roi_outputs=1, group=None, serial=None, cropped=None, birthtime=None, cellBodyFiber=None, class_=None, entryNerve=None, exitNerve=None, hemilineage=None, longTract=None, modality=None, origin=None, predictedNt=None, serialMotif=None, somaNeuromere=None, somaSide=None, subclass=None, synonyms=None, systematicType=None, target=None, label=None, min_pre=0, min_post=0, somaLocation=None, tosomaLocation=None, rootLocation=None, soma=None, client=None)
 |
 |  Neuron selection criteria.
 |
 |  Specifies which fields to filter by when searching for a Neuron (or Segment).
 |  This class does not send queries itself, but you use it to specify search
 |  criteria for various query functions.
 |
 |  Note:
 |      For simple queries involving only particular bodyId(s) or type(s)/instance(s),
 |      you can usually just pass the ``bodyId`` or ``type`` to the query function,
 |      without constructing a full ``NeuronCriteria``.
 |
 |      .. code-block:: python
 |
 |          from neuprint import fetch_neurons, NeuronCriteria as NC
 |
 |          # Equivalent
 |          neuron_df, conn_df = fetch_neurons(NC(bodyId=329566174))
 |          neuron_df, conn_df = fetch_neurons(329566174)
 |
 |          # Equivalent
 |          # (Criteria is satisfied if either type or instance matches.)
 |          neuron_df, conn_df = fetch_neurons(NC(type="OA-VPM3", instance="OA-VPM3"))
 |          neuron_df, conn_df = fetch_neurons("OA-VPM3")
 |
 |  Methods defined here:
 |
 |  __eq__(self, value)
 |      Implement comparison between criteria.
 |      Note: 'matchvar' is not considered during the comparison.
 |
 |  __init__(self, matchvar='n', *, bodyId=None, type=None, instance=None, regex='guess', status=None, statusLabel=None, rois=None, inputRois=None, outputRois=None, roi_req='all', min_roi_inputs=1, min_roi_outputs=1, group=None, serial=None, cropped=None, birthtime=None, cellBodyFiber=None, class_=None, entryNerve=None, exitNerve=None, hemilineage=None, longTract=None, modality=None, origin=None, predictedNt=None, serialMotif=None, somaNeuromere=None, somaSide=None, subclass=None, synonyms=None, systematicType=None, target=None, label=None, min_pre=0, min_post=0, somaLocation=None, tosomaLocation=None, rootLocation=None, soma=None, client=None)
 |      All criteria must be passed as keyword arguments.
 |
 |      .. note::
 |          Only ``bodyId``, ``type``, ``instance``, and ROI-related criteria are
 |          applicable to all datasets.  The applicability of all other criteria depends
 |          on the dataset being accessed (e.g. hemibrain,  manc, etc.).
 |
 |      .. note::
 |
 |          **Options for specifying ROI criteria**
 |
 |          The ``rois`` argument merely matches neurons that intersect the given ROIs at all
 |          (without distinguishing between inputs and outputs).
 |
 |          The ``inputRois`` and ``outputRois`` arguments allow you to put requirements
 |          on whether or not neurons have inputs or outputs in the listed ROIs.
 |          It produces a more expensive query, but it's more selective.
 |          It also enables you to require a minimum number of connections in the given
 |          ``inputRois`` or ``outputRois`` using the ``min_roi_inputs`` and ``min_roi_outputs``
 |          criteria.
 |
 |          In either case, use use ``roi_req`` to specify whether a neuron must match just
 |          one (``any``) of the listed ROIs, or ``all`` of them.
 |
 |      .. note::
 |
 |          **Matching against missing values (NULL)**
 |
 |          To search for neurons which are missing given property entirely,
 |          you can use a list containing ``None``, or the special value ``neuprint.IsNull``.
 |          For example, to find neurons with no `type`, use ``type=[None]`` or ``type=IsNull``.
 |
 |          **Matching against any value (NOT NULL)**
 |
 |          To search for any non-null value, you can use ``neuprint.NotNull``. For
 |          example, to find neurons that have a type (no matter what the
 |          type is), use ``type=NotNull``.
 |
 |      Args:
 |          matchvar (str):
 |              An arbitrary cypher variable name to use when this
 |              ``NeuronCriteria`` is used to construct cypher queries.
 |              Must begin with a lowercase letter.
 |
 |          bodyId (int or list of ints):
 |              List of bodyId values.
 |
 |          type (str or list of str):
 |              Cell type.  Matches depend on the the ``regex`` argument.
 |              If both ``type`` and ``instance`` criteria are supplied, any neuron that
 |              matches EITHER criteria will match the overall criteria.
 |
 |          instance (str or list of str):
 |              Cell instance (specific cell name).  Matches depend on the the ``regex`` argument.
 |              If both ``type`` and ``instance`` criteria are supplied, any neuron that
 |              matches EITHER criteria will match the overall criteria.
 |
 |          regex (bool):
 |              If ``True``, the ``instance`` and ``type`` arguments will be interpreted as
 |              regular expressions, rather than exact match strings.
 |              If ``False``, only exact matches will be found.
 |              By default, the matching method will be automatically chosen by inspecting the
 |              ``type`` and ``instance`` strings.  If they contain regex-like characters,
 |              then we assume you intend regex matching. (You can see which method was chosen by
 |              checking the ``regex`` field after the ``NeuronCriteria`` is constructed.)
 |
 |          status (str or list of str):
 |              Indicates the status of the neuron's reconstruction quality.
 |              Typically, named/annotated neurons have ``Traced`` status,
 |              the best quality.
 |          statusLabel (str or list of str):
 |             ``statusLabel`` is typically more fine-grained than ``status``,
 |             and mostly of interest during the construction of the connectome,
 |             not for end-users.  The possible values of ``statusLabel`` do not
 |             correspond one-to-one to those of ``status``.
 |
 |          rois (str or list of str):
 |              ROIs that merely intersect the neuron, without specifying whether
 |              they're intersected by input or output synapses.
 |              If not provided, will be auto-set from ``inputRois`` and ``outputRois``.
 |
 |          inputRois (str or list of str):
 |              Only Neurons which have inputs in EVERY one of the given ROIs will be matched.
 |              ``regex`` does not apply to this parameter.
 |
 |          outputRois (str or list of str):
 |              Only Neurons which have outputs in EVERY one of the given ROIs will be matched.
 |              ``regex`` does not apply to this parameter.
 |
 |          min_roi_inputs (int):
 |              How many input (post) synapses a neuron must have in each ROI to satisfy the
 |              ``inputRois`` criteria.  Can only be used if you provided ``inputRois``.
 |
 |          min_roi_outputs (int):
 |              How many output (pre) synapses a neuron must have in each ROI to satisfy the
 |              ``outputRois`` criteria.   Can only be used if you provided ``outputRois``.
 |
 |          roi_req (Either ``'any'`` or ``'all'``):
 |              Whether a neuron must intersect all of the listed input/output ROIs, or any of the listed input/output ROIs.
 |              When using 'any', each neuron must still match at least one input AND at least one output ROI.
 |
 |          group (int or list of int)
 |              In some datasets, the ``group`` ID is used to associate neurons morphological type,
 |              including left-right homologues. Neurons with the same group ID have matching morphology.
 |
 |          serial (int or list of int)
 |              Similar to ``group``, but used for associating neurons across segmental neuropils in the nerve cord.
 |              Neurons with the same ``serial`` ID are analogous to one another, but in different leg segments.
 |
 |          cropped (bool):
 |              If given, restrict results to neurons that are cropped or not.
 |
 |          birthtime (str or list of str):
 |          cellBodyFiber (str or list of str):
 |          class\_ (str or list of str):
 |              Matches for the neuron ``class`` field.
 |          entryNerve (str or list of str):
 |          exitNerve (str or list of str):
 |          hemilineage (str or list of str):
 |          longTract (str or list of str):
 |          modality (str or list of str):
 |          origin (str or list of str):
 |          predictedNt (str or list of str):
 |          serialMotif (str or list of str):
 |          somaNeuromere (str or list of str):
 |          somaSide  (str or list of str):
 |              Valid choices are 'RHS', 'LHS', 'Midline'
 |          subclass (str or list of str):
 |          synonyms (str or list of str):
 |          systematicType (str or list of str):
 |          target (str or list of str):
 |
 |          label (Either ``'Neuron'`` or ``'Segment'``):
 |              Which node label to match with.
 |              (In neuprint, all ``Neuron`` nodes are also ``Segment`` nodes.)
 |              By default, ``'Neuron'`` is used, unless you provided a non-empty ``bodyId`` list.
 |              In that case, ``'Segment'`` is the default. (It's assumed you're really interested
 |              in the bodies you explicitly listed, whether or not they have the ``'Neuron'`` label.)
 |
 |          min_pre (int):
 |              Exclude neurons that don't have at least this many t-bars (outputs) overall,
 |              regardless of how many t-bars exist in any particular ROI.
 |
 |          min_post (int):
 |              Exclude neurons that don't have at least this many PSDs (inputs) overall,
 |              regardless of how many PSDs exist in any particular ROI.
 |
 |          somaLocation:
 |              The ``somaLocation`` property of ``:Neuron`` objects contains
 |              the ``[X,Y,Z]`` coordinate (in voxels) of the cell body.
 |              ``NeuronCriteria`` does not allow you to match a specific coordinate,
 |              but you may set this argument to ``NotNull` (or ```IsNull``) to
 |              search for cells with (or without) a recorded cell body.
 |
 |          tosomaLocation:
 |              Neurons which could not be successfully attached to their cell body do not have
 |              a recorded ``somaLocation``.  Instead, they have an annotaiton on the cell body
 |              fiber, on the severed end extending out toward the cell body.
 |              Like ``somaLocation``, you can't match a specific coordinate using ``NeuronCriteria``,
 |              but you can use ``NotNull``/``IsNull``.
 |
 |          rootLocation:
 |              Some (but not all) Neurons which have no soma in the tissue sample are tagged with
 |              a ``rootLocation``, indicating where they enter/exit the sample.
 |              Like ``somaLocation``, you can't match a specific coordinate using ``NeuronCriteria``,
 |              but you can use ``NotNull``/``IsNull``.
 |
 |          soma (Either ``True``, ``False``, or ``None``)
 |              DEPRECATED.  Use ``somaLocation=NotNull`` or ``somaLocation=IsNull``.
 |
 |          client (:py:class:`neuprint.client.Client`):
 |              Used to validate ROI names.
 |              If not provided, the global default ``Client`` will be used.
 |
 |  __repr__(self)
 |      Return repr(self).
 |
 |  all_conditions(self, *vars, prefix=0, comments=True)
 |
 |  basic_conditions(self, prefix=0, comments=True)
 |      Construct a WHERE clause based on the basic conditions
 |      in this criteria (i.e. everything except for the "directed ROI" conditions.)
 |
 |  basic_exprs(self)
 |      Return the list of expressions that correspond
 |      to the members in this NeuronCriteria object.
 |      They're intended be combined (via 'AND') in
 |      the WHERE clause of a cypher query.
 |
 |  directed_rois_condition(self, *vars, prefix=0, comments=True)
 |      Construct the ```WITH...WHERE``` statements that apply the "directed ROI"
 |      conditions specified by this criteria's ``inputRois`` and ``outputRois``
 |      members.
 |
 |      These conditions are expensive to evaluate, so it's usually a good
 |      idea to position them LAST in your cypher query, once the result set
 |      has already been narrowed down by eariler filters.
 |
 |  global_vars(self)
 |
 |  global_with(self, *vars, prefix=0)
 |
 |  rois_expr(self)
 |
 |  typeinst_expr(self)
 |      Unlike all other fields, type and instance OR'd together.
 |      Either match satisfies the criteria.
 |
 |  ----------------------------------------------------------------------
 |  Class methods defined here:
 |
 |  combined_conditions(neuron_conditions, vars=[], prefix=0, comments=True) from builtins.type
 |      Combine the conditions from multiple NeuronCriteria into a single string,
 |      putting the "cheap" conditions first and the "expensive" conditions last.
 |      (That is, basic conditions first and the directed ROI conditions last.)
 |
 |  combined_global_with(neuron_conditions, vars=[], prefix=0) from builtins.type
 |
 |  ----------------------------------------------------------------------
 |  Data descriptors defined here:
 |
 |  __dict__
 |      dictionary for instance variables (if defined)
 |
 |  __weakref__
 |      list of weak references to the object (if defined)
 |
 |  ----------------------------------------------------------------------
 |  Data and other attributes defined here:
 |
 |  MAX_LITERAL_LENGTH = 3
 |
 |  __hash__ = None

Fetching neurons

Let’s say we want to find all antennnal lobe projection neurons (PNs). Their type nomenclature adheres to {glomerulus}_{lineage}PN (e.g. DA1_lPN)for uniglomerular PNs and a M_{lineage}PN{tract}{type} (e.g. M_vPNml50 = “multiglomerular ventral lineage PN mediolateral tract type 50) for multiglomerular PNs.

To get them all, we need to use regex patterns (see this cheatsheet):

[24]:
# Define the filter criteria
nc = neu.NeuronCriteria(type='.*?_.*?PN.*?', regex=True)

# Get general info for these neurons
pns, roi_info = neu.fetch_neurons(nc)

print(f'{pns.shape[0]} PNs found.')

pns.head()
/Users/robbiecourt/GIT/VFB_connect/.conda/lib/python3.10/site-packages/neuprint/client.py:609: FutureWarning:

Series.__getitem__ treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use `ser.iloc[pos]`

337 PNs found.
[24]:
bodyId instance type pre post downstream upstream size status cropped statusLabel cellBodyFiber somaRadius somaLocation roiInfo notes inputRois outputRois
0 294792184 M_vPNml53_R M_vPNml53 92 344 730 344 420662445 Traced False Roughly traced AVM04 336.5 [18923, 34319, 35424] {'SNP(R)': {'pre': 70, 'post': 155, 'downstrea... None [AL(R), AL-D(R), AL-DA2(R), AL-DA4m(R), AL-DC1... [AL(R), AL-DC1(R), LH(R), PLP(R), SIP(R), SLP(...
1 329599710 M_lvPNm32_R M_lvPNm32 247 285 2052 285 343478957 Traced False Roughly traced AVM06 NaN None {'SNP(R)': {'pre': 180, 'post': 93, 'downstrea... None [AL(R), AL-DC4(R), AL-DL2v(R), AL-DM1(R), AL-D... [AL(R), AL-DL2v(R), AL-DM1(R), AL-DM4(R), AL-D...
2 417199910 M_lvPNm36_R M_lvPNm36 162 347 1590 347 387058559 Traced False Roughly traced AVM06 351.5 [13823, 33925, 34176] {'SNP(R)': {'pre': 156, 'post': 95, 'downstrea... None [AL(R), AL-DL5(R), AL-DM4(R), AL-DP1m(R), AL-V... [AL(R), AL-DL5(R), AL-DM4(R), AL-VP1d(R), AL-V...
3 480927537 M_vPNml70_R M_vPNml70 82 276 692 276 240153322 Traced False Roughly traced AVM04 NaN None {'SNP(R)': {'pre': 15, 'post': 18, 'downstream... None [AL(R), AL-DA2(R), AL-DA4l(R), AL-DA4m(R), AL-... [LH(R), SLP(R), SNP(R)]
4 481268653 M_vPNml89_R M_vPNml89 146 58 1614 58 265085609 Traced False Roughly traced AVM04 NaN None {'SNP(R)': {'pre': 10, 'post': 2, 'downstream'... None [AL(R), AL-VC3l(R), AL-VC4(R), AL-VP1m(R), LH(... [LH(R), SLP(R), SNP(R)]
[25]:
# Check that the regex did not have any accidental by-catch
pns['type'].unique()
[25]:
array(['M_vPNml53', 'M_lvPNm32', 'M_lvPNm36', 'M_vPNml70', 'M_vPNml89',
       'VP1l+_lvPN', 'M_vPNml69', 'DM1_lPN', 'DM4_vPN', 'M_vPNml79',
       'VP4+_vPN', 'DA4l_adPN', 'M_vPNml87', 'DM4_adPN', 'M_vPNml83',
       'VA5_lPN', 'DA4m_adPN', 'M_lvPNm24', 'M_vPNml85', 'VP1l+VP3_ilPN',
       'M_vPNml77', 'M_vPNml84', 'VC1_lPN', 'M_lvPNm39', 'M_vPNml50',
       'DM2_lPN', 'VC5_lvPN', 'M_vPNml88', 'M_vPNml58', 'VP4_vPN',
       'DP1m_vPN', 'DP1m_adPN', 'DM5_lPN', 'VC5_adPN', 'M_vPNml80',
       'M_lvPNm25', 'VC3m_lvPN', 'VP3+_vPN', 'VP1m+_lvPN', 'DA3_adPN',
       'V_l2PN', 'M_vPNml56', 'VC3l_adPN', 'VM7v_adPN', 'DL5_adPN',
       'VM4_adPN', 'VM2_adPN', 'M_lvPNm40', 'DC4_vPN', 'V_ilPN',
       'M_vPNml74', 'Z_lvPNm1', 'DA1_lPN', 'DP1l_adPN', 'VM4_lvPN',
       'M_vPNml71', 'DP1l_vPN', 'M_lvPNm41', 'M_spPN5t10', 'DA1_vPN',
       'VC4_adPN', 'DM3_adPN', 'M_lvPNm45', 'VL1_vPN', 'M_lvPNm44',
       'M_vPNml78', 'M_vPNml67', 'M_adPNm5', 'M_smPNm1', 'DM6_adPN',
       'DL2d_adPN', 'M_adPNm6', 'M_adPNm8', 'M_lvPNm43', 'Z_vPNml1',
       'M_vPNml59', 'DA2_lPN', 'M_lPNm11A', 'M_vPNml52', 'DL2d_vPN',
       'VL2p_vPN', 'VA1d_adPN', 'M_lPNm11B', 'M_lvPNm48', 'M_lPNm11C',
       'M_lvPNm42', 'VA1v_vPN', 'M_vPNml68', 'M_vPNml55', 'M_vPNml62',
       'VL2a_vPN', 'M_vPNml60', 'M_vPNml65', 'VM5d_adPN', 'M_l2PNm16',
       'M_vPNml61', 'M_vPNml57', 'M_vPNml64', 'M_lv2PN9t49',
       'VP2+VC5_l2PN', 'M_spPN4t9', 'M_vPNml66', 'M_vPNml75', 'M_vPNml63',
       'M_vPNml72', 'M_lvPNm38', 'D_adPN', 'M_vPNml76', 'M_vPNml54',
       'DM3_vPN', 'M_vPNml86', 'DL3_lPN', 'VA4_lPN', 'VP1d_il2PN',
       'DC1_adPN', 'M_l2PN3t18', 'M_lvPNm35', 'DL4_adPN', 'M_lvPNm28',
       'M_lvPNm27', 'M_ilPNm90', 'M_l2PNl20', 'M_lvPNm29', 'VA7l_adPN',
       'M_lPNm13', 'M_l2PNl21', 'DL1_adPN', 'M_imPNl92', 'M_vPNml73',
       'M_ilPN8t91', 'M_l2PNm14', 'VP1d+VP4_l2PN1', 'M_lvPNm26',
       'DL2v_adPN', 'VP3+VP1l_ivPN', 'M_lvPNm33', 'VA1v_adPN',
       'VP3+_l2PN', 'M_l2PN10t19', 'VP4+VL1_l2PN', 'M_l2PNl22',
       'M_l2PNm15', 'M_lPNm11D', 'MZ_lv2PN', 'DC2_adPN', 'M_lvPNm46',
       'VC2_lPN', 'VM1_lPN', 'VM3_adPN', 'VM7d_adPN', 'M_lvPNm47',
       'M_lPNm12', 'DC3_adPN', 'VP2+_adPN', 'VP1m+VP2_lvPN2',
       'VP1m+VP2_lvPN1', 'VA6_adPN', 'VA7m_lPN', 'M_adPNm7', 'M_adPNm4',
       'VA1d_vPN', 'VA3_adPN', 'VL1_ilPN', 'M_l2PNl23', 'M_lvPNm31',
       'VP1m+VP5_ilPN', 'VL2p_adPN', 'MZ_lvPN', 'VP2_adPN', 'VA2_adPN',
       'VM5v_adPN', 'VP5+VP2_l2PN', 'VP5+VP3_l2PN', 'VP5+_l2PN',
       'M_vPNml51', 'M_smPN6t2', 'M_lvPNm37', 'M_vPNml82', 'M_adPNm3',
       'VP1m_l2PN', 'DC4_adPN', 'VP5+Z_adPN', 'VL2a_adPN', 'VP2_l2PN',
       'M_lvPNm34', 'VP2+Z_lvPN', 'M_lvPNm30', 'M_l2PNm17', 'M_vPNml81',
       'VP1d+VP4_l2PN2'], dtype=object)

We can find the same neuron types using VFB instead. This allows curated neuron classes to be used and doesn’t depend on knowing naming conventions and using potentially error prone regex pattern matching.

[26]:
#This will get all ALPNs from ALL datasets on VFB
ALPNs = vfb.get_instances("'adult antennal lobe projection neuron'", return_dataframe=True, limit=50)
# Explode the lists in the 'data_source' column into separate rows as each image can potentialy have multiple data sources. Note this can be done for any column with lists
exploded_ALPNs = ALPNs.explode('data_source')
#Select only rows from Hemibrain1.1 dataset
ALPNs=exploded_ALPNs[exploded_ALPNs['data_source'] == 'neuprint_JRC_Hemibrain_1point1']
ALPNs
Limiting to 50 terms out of 1667
[26]:
label symbol id tags description parents_label parents_id data_source accession xrefs templates dataset license
13 M_vPNml84_R (FlyEM-HB:791298858) M_vPNml84_R VFB_jrchk0zp [Entity, Adult, Anatomy, Cell, GABAergic, Indi... tracing status-Roughly traced, cropped-False [adult multiglomerular antennal lobe projectio... [FBbt_20003859] neuprint_JRC_Hemibrain_1point1 [791298858] [neuprint_JRC_Hemibrain_1point1:791298858, neu... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
14 M_vPNml85_R (FlyEM-HB:635407942) M_vPNml85_R VFB_jrchk0zt [Entity, Adult, Anatomy, Cell, GABAergic, Indi... tracing status-Roughly traced, cropped-False [adult multiglomerular antennal lobe projectio... [FBbt_20003860, FBbt_00058207] neuprint_JRC_Hemibrain_1point1 [635407942] [neuronbridge:635407942, neuprint_JRC_Hemibrai... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
15 M_vPNml83_R (FlyEM-HB:697145036) M_vPNml83_R VFB_jrchk0zn [Entity, Adult, Anatomy, Cell, GABAergic, Indi... tracing status-Roughly traced, cropped-False [adult GABAergic neuron, adult multiglomerular... [FBbt_00058207, FBbt_20003858] neuprint_JRC_Hemibrain_1point1 [697145036] [neuronbridge:697145036, neuprint_JRC_Hemibrai... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
16 M_vPNml84_R (FlyEM-HB:760250272) M_vPNml84_R VFB_jrchk0zq [Entity, Adult, Anatomy, Cell, GABAergic, Indi... tracing status-Roughly traced, cropped-False [adult multiglomerular antennal lobe projectio... [FBbt_20003859] neuprint_JRC_Hemibrain_1point1 [760250272] [neuprint_JRC_Hemibrain_1point1:760250272, neu... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
17 M_adPNm8_R (FlyEM-HB:1693827279) M_adPNm8_R VFB_jrchk0vq [Entity, Adult, Anatomy, Cell, Cholinergic, In... tracing status-Roughly traced, cropped-False [adult multiglomerular antennal lobe projectio... [FBbt_20003794] neuprint_JRC_Hemibrain_1point1 [1693827279] [neuronbridge:1693827279, neuprint_JRC_Hemibra... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
18 M_lvPNm35_R (FlyEM-HB:1670597454) M_lvPNm35_R VFB_jrchk0x3 [Entity, Adult, Anatomy, Cell, Cholinergic, In... tracing status-Roughly traced, cropped-False [adult multiglomerular antennal lobe projectio... [FBbt_20003816] neuprint_JRC_Hemibrain_1point1 [1670597454] [neuronbridge:1670597454, neuprint_JRC_Hemibra... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
19 M_vPNml84_R (FlyEM-HB:729544359) M_vPNml84_R VFB_jrchk0zr [Entity, Adult, Anatomy, Cell, GABAergic, Indi... tracing status-Roughly traced, cropped-False [adult multiglomerular antennal lobe projectio... [FBbt_20003859] neuprint_JRC_Hemibrain_1point1 [729544359] [neuprint_JRC_Hemibrain_1point1:729544359, neu... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
20 M_vPNml85_R (FlyEM-HB:603349484) M_vPNml85_R VFB_jrchk0zs [Entity, Adult, Anatomy, Cell, GABAergic, Indi... tracing status-Roughly traced, cropped-False [adult GABAergic neuron, adult multiglomerular... [FBbt_00058207, FBbt_20003860] neuprint_JRC_Hemibrain_1point1 [603349484] [neuronbridge:603349484, neuprint_JRC_Hemibrai... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
21 M_vPNml84_R (FlyEM-HB:605050789) M_vPNml84_R VFB_jrchk0zo [Entity, Adult, Anatomy, Cell, GABAergic, Indi... tracing status-Roughly traced, cropped-False [adult multiglomerular antennal lobe projectio... [FBbt_20003859] neuprint_JRC_Hemibrain_1point1 [605050789] [neuronbridge:605050789, neuprint_JRC_Hemibrai... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
22 M_adPNm5_R (FlyEM-HB:762982753) M_adPNm5_R VFB_jrchk0vl [Entity, Adult, Anatomy, Cell, Cholinergic, In... tracing status-Roughly traced, cropped-False [adult cholinergic neuron, adult multiglomerul... [FBbt_00058205, FBbt_20003791] neuprint_JRC_Hemibrain_1point1 [762982753] [neuprint_JRC_Hemibrain_1point1:762982753, neu... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
23 M_adPNm4_R (FlyEM-HB:1887872301) M_adPNm4_R VFB_jrchk0vj [Entity, Adult, Anatomy, Cell, Cholinergic, In... tracing status-Roughly traced, cropped-False [adult cholinergic neuron, adult multiglomerul... [FBbt_00058205, FBbt_20003790] neuprint_JRC_Hemibrain_1point1 [1887872301] [neuronbridge:1887872301, neuprint_JRC_Hemibra... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
24 M_adPNm4_R (FlyEM-HB:1888213190) M_adPNm4_R VFB_jrchk0vk [Entity, Adult, Anatomy, Cell, Cholinergic, In... tracing status-Roughly traced, cropped-False [adult multiglomerular antennal lobe projectio... [FBbt_20003790, FBbt_00058205] neuprint_JRC_Hemibrain_1point1 [1888213190] [neuronbridge:1888213190, neuprint_JRC_Hemibra... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
25 M_adPNm6_R (FlyEM-HB:788940872) M_adPNm6_R VFB_jrchk0vo [Entity, Adult, Anatomy, Cell, Cholinergic, In... tracing status-Roughly traced, cropped-False [adult multiglomerular antennal lobe projectio... [FBbt_20003792] neuprint_JRC_Hemibrain_1point1 [788940872] [neuprint_JRC_Hemibrain_1point1:788940872, neu... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
26 M_lvPNm33_R (FlyEM-HB:1759999022) M_lvPNm33_R VFB_jrchk0x1 [Entity, Adult, Anatomy, Cell, Cholinergic, In... tracing status-Roughly traced, cropped-False [adult cholinergic neuron, adult multiglomerul... [FBbt_00058205, FBbt_20003814] neuprint_JRC_Hemibrain_1point1 [1759999022] [neuprint_JRC_Hemibrain_1point1:1759999022, ne... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
27 M_adPNm5_R (FlyEM-HB:2040344064) M_adPNm5_R VFB_jrchk0vn [Entity, Adult, Anatomy, Cell, Cholinergic, In... tracing status-Roughly traced, cropped-False [adult cholinergic neuron, adult multiglomerul... [FBbt_00058205, FBbt_20003791] neuprint_JRC_Hemibrain_1point1 [2040344064] [neuprint_JRC_Hemibrain_1point1:2040344064, ne... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
28 M_lvPNm32_R (FlyEM-HB:329599710) M_lvPNm32_R VFB_jrchk0x0 [Entity, Adult, Anatomy, Cell, Cholinergic, In... tracing status-Roughly traced, cropped-False [adult multiglomerular antennal lobe projectio... [FBbt_20003813, FBbt_00058205] neuprint_JRC_Hemibrain_1point1 [329599710] [neuronbridge:329599710, neuprint_JRC_Hemibrai... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
29 M_adPNm7_R (FlyEM-HB:1886132855) M_adPNm7_R VFB_jrchk0vp [Entity, Adult, Anatomy, Cell, Cholinergic, In... tracing status-Roughly traced, cropped-False [adult multiglomerular antennal lobe projectio... [FBbt_20003793] neuprint_JRC_Hemibrain_1point1 [1886132855] [neuprint_JRC_Hemibrain_1point1:1886132855, ne... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
30 M_lvPNm34_R (FlyEM-HB:5813069532) M_lvPNm34_R VFB_jrchk0x2 [Entity, Adult, Anatomy, Cell, Cholinergic, In... tracing status-Roughly traced, cropped-False [adult multiglomerular antennal lobe projectio... [FBbt_20003815, FBbt_00058205] neuprint_JRC_Hemibrain_1point1 [5813069532] [neuronbridge:5813069532, neuprint_JRC_Hemibra... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
31 M_adPNm5_R (FlyEM-HB:1916528384) M_adPNm5_R VFB_jrchk0vm [Entity, Adult, Anatomy, Cell, Cholinergic, In... tracing status-Roughly traced, cropped-False [adult multiglomerular antennal lobe projectio... [FBbt_20003791, FBbt_00058205] neuprint_JRC_Hemibrain_1point1 [1916528384] [neuronbridge:1916528384, neuprint_JRC_Hemibra... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
32 M_vPNml86_R (FlyEM-HB:1571025824) M_vPNml86_R VFB_jrchk0zv [Entity, Adult, Anatomy, Cell, GABAergic, Indi... tracing status-Roughly traced, cropped-False [adult multiglomerular antennal lobe projectio... [FBbt_20003861, FBbt_00058207] neuprint_JRC_Hemibrain_1point1 [1571025824] [neuprint_JRC_Hemibrain_1point1:1571025824, ne... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
33 M_vPNml89_R (FlyEM-HB:481268653) M_vPNml89_R VFB_jrchk0zz [Entity, Adult, Anatomy, Cell, GABAergic, Indi... tracing status-Roughly traced, cropped-False [adult multiglomerular antennal lobe projectio... [FBbt_20003864, FBbt_00058207] neuprint_JRC_Hemibrain_1point1 [481268653] [neuronbridge:481268653, neuprint_JRC_Hemibrai... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
34 M_vPNml87_R (FlyEM-HB:572663539) M_vPNml87_R VFB_jrchk0zw [Entity, Adult, Anatomy, Cell, GABAergic, Indi... tracing status-Roughly traced, cropped-False [adult multiglomerular antennal lobe projectio... [FBbt_20003862, FBbt_00058207] neuprint_JRC_Hemibrain_1point1 [572663539] [neuronbridge:572663539, neuprint_JRC_Hemibrai... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
35 M_vPNml86_R (FlyEM-HB:5813045696) M_vPNml86_R VFB_jrchk0zu [Entity, Adult, Anatomy, Cell, Individual, Ner... tracing status-Roughly traced, cropped-False [adult multiglomerular antennal lobe projectio... [FBbt_20003861] neuprint_JRC_Hemibrain_1point1 [5813045696] [neuprint_JRC_Hemibrain_1point1:5813045696, ne... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
36 M_vPNml88_R (FlyEM-HB:634379734) M_vPNml88_R VFB_jrchk0zy [Entity, Adult, Anatomy, Cell, GABAergic, Indi... tracing status-Roughly traced, cropped-False [adult GABAergic neuron, adult multiglomerular... [FBbt_00058207, FBbt_20003863] neuprint_JRC_Hemibrain_1point1 [634379734] [neuronbridge:634379734, neuprint_JRC_Hemibrai... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...
37 M_vPNml87_R (FlyEM-HB:5813013823) M_vPNml87_R VFB_jrchk0zx [Entity, Adult, Anatomy, Cell, GABAergic, Indi... tracing status-Roughly traced, cropped-False [adult multiglomerular antennal lobe projectio... [FBbt_20003862, FBbt_00058207] neuprint_JRC_Hemibrain_1point1 [5813013823] [neuprint_JRC_Hemibrain_1point1:5813013823, ne... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l...

Fetching synaptic partners

Looks good! Next: What’s downstream of those PNs?

[27]:
exploded_ALPNs = ALPNs.explode('accession')
ds = neu.fetch_simple_connections(upstream_criteria=list(map(int, exploded_ALPNs['accession'])))
#using hemibrain regex
#ds = neu.fetch_simple_connections(upstream_criteria=neu.NeuronCriteria(bodyId=pns.bodyId.values))
ds
[27]:
bodyId_pre bodyId_post weight type_pre type_post instance_pre instance_post conn_roiInfo
0 791298858 510317265 50 M_vPNml84 LHPD4d1 M_vPNml84_R LHPD4d1_R {'LH(R)': {'pre': 50, 'post': 50}}
1 329599710 330268940 45 M_lvPNm32 LHCENT9 M_lvPNm32_R LHCENT9_R {'SNP(R)': {'pre': 45, 'post': 45}, 'SLP(R)': ...
2 5813069532 1667251683 42 M_lvPNm34 lLN2T_d M_lvPNm34_R lLN2T_d(Tortuous)_R {'AL(R)': {'pre': 42, 'post': 42}, 'AL-DM1(R)'...
3 329599710 1669924220 37 M_lvPNm32 lLN2T_d M_lvPNm32_R lLN2T_d(Tortuous)_R {'AL(R)': {'pre': 37, 'post': 37}, 'AL-DP1l(R)...
4 760250272 510317265 36 M_vPNml84 LHPD4d1 M_vPNml84_R LHPD4d1_R {'LH(R)': {'pre': 36, 'post': 36}}
... ... ... ... ... ... ... ... ...
3851 5813069532 5813088801 1 M_lvPNm34 SLP405_c M_lvPNm34_R SLP405_c_R {'SNP(R)': {'pre': 1, 'post': 1}, 'SLP(R)': {'...
3852 5813069532 5901196806 1 M_lvPNm34 v2LN3A M_lvPNm34_R v2LN3a_R {'AL(R)': {'pre': 1, 'post': 1}, 'AL-DM1(R)': ...
3853 5813069532 5901205793 1 M_lvPNm34 SLP464 M_lvPNm34_R SLP464(SCB068)_R {'SNP(R)': {'pre': 1, 'post': 1}, 'SLP(R)': {'...
3854 5813069532 5901206553 1 M_lvPNm34 il3LN6 M_lvPNm34_R il3LN6_L {'AL(R)': {'pre': 1, 'post': 1}, 'AL-DP1m(R)':...
3855 5813069532 5901219179 1 M_lvPNm34 LHAV3c4 M_lvPNm34_R LHAV3c4_R {'SNP(R)': {'pre': 1, 'post': 1}, 'SLP(R)': {'...

3856 rows × 8 columns

Each row is now a connections from a single up- to a single downstream neuron. The “weight” is the number of synapses between the pre- and the postsynaptic neuron. Let’s simplify by grouping by type:

[28]:
by_type = ds.groupby(['type_pre', 'type_post'], as_index=False).weight.sum()
by_type.sort_values('weight', ascending=False, inplace=True)
by_type.reset_index(drop=True, inplace=True)
by_type
[28]:
type_pre type_post weight
0 M_adPNm4 KCg-m 252
1 M_adPNm4 KCab-m 235
2 M_vPNml84 LHPD4d1 145
3 M_adPNm4 KCa'b'-m 106
4 M_adPNm4 KCab-c 103
... ... ... ...
2174 M_lvPNm33 SLP192 1
2175 M_lvPNm33 SLP191 1
2176 M_lvPNm33 SLP135 1
2177 M_lvPNm33 SLP105 1
2178 M_vPNml89 SMP010 1

2179 rows × 3 columns

The strongest connections are between PNs and Kenyon Cells (KCs). That’s not much of a surprise since there are thousands of KCs. For the sake of the argument let’s say we want to know where these connections occur:

[29]:
#First find KCs in VFB
KCs = vfb.get_instances("'adult Kenyon cell'", return_dataframe=True, limit=300)
#Select only rows from Hemibrain1.1 dataset
exploded_KCs = KCs.explode('data_source')
KCs=exploded_KCs[exploded_KCs['data_source'] == 'neuprint_JRC_Hemibrain_1point1']
KCs
Limiting to 300 terms out of 5118
[29]:
label symbol id tags parents_label parents_id data_source accession xrefs templates dataset license description
53 KCab-c_R (FlyEM-HB:877974490) KCab-c_R VFB_jrchjvcj [Entity, Adult, Anatomy, Cell, Cholinergic, Do... [adult dopaminergic neuron, alpha/beta core Ke... [FBbt_00058206, FBbt_00110929, FBbt_00048138] neuprint_JRC_Hemibrain_1point1 [877974490] [neuprint_JRC_Hemibrain_1point1:877974490, neu... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False
54 KCab-c_R (FlyEM-HB:5813021316) KCab-c_R VFB_jrchjvha [Entity, Adult, Anatomy, Cell, Cholinergic, Do... [adult dopaminergic neuron, mushroom body dopa... [FBbt_00058206, FBbt_00048138, FBbt_00110929] neuprint_JRC_Hemibrain_1point1 [5813021316] [neuprint_JRC_Hemibrain_1point1:5813021316, ne... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False
55 KCab-c_R (FlyEM-HB:363375247) KCab-c_R VFB_jrchjvdk [Entity, Adult, Anatomy, Cell, Cholinergic, Do... [alpha/beta core Kenyon cell, mushroom body do... [FBbt_00110929, FBbt_00048138, FBbt_00058206] neuprint_JRC_Hemibrain_1point1 [363375247] [neuronbridge:363375247, neuprint_JRC_Hemibrai... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False
56 KCab-c_R (FlyEM-HB:569334986) KCab-c_R VFB_jrchjvck [Entity, Adult, Anatomy, Cell, Cholinergic, Do... [mushroom body dopaminergic neuron, alpha/beta... [FBbt_00048138, FBbt_00110929, FBbt_00058206] neuprint_JRC_Hemibrain_1point1 [569334986] [neuprint_JRC_Hemibrain_1point1:569334986, neu... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False
57 KCab-c_R (FlyEM-HB:923018247) KCab-c_R VFB_jrchjvds [Entity, Adult, Anatomy, Cell, Cholinergic, Do... [mushroom body dopaminergic neuron, alpha/beta... [FBbt_00048138, FBbt_00110929, FBbt_00058206] neuprint_JRC_Hemibrain_1point1 [923018247] [neuprint_JRC_Hemibrain_1point1:923018247, neu... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False
... ... ... ... ... ... ... ... ... ... ... ... ... ...
291 KCab-c_R (FlyEM-HB:5813027747) KCab-c_R VFB_jrchjvgx [Entity, Adult, Anatomy, Cell, Cholinergic, Do... [alpha/beta core Kenyon cell, adult dopaminerg... [FBbt_00110929, FBbt_00058206, FBbt_00048138] neuprint_JRC_Hemibrain_1point1 [5813027747] [neuronbridge:5813027747, neuprint_JRC_Hemibra... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False
292 KCab-c_R (FlyEM-HB:692792746) KCab-c_R VFB_jrchjvgy [Entity, Adult, Anatomy, Cell, Cholinergic, Do... [alpha/beta core Kenyon cell, adult dopaminerg... [FBbt_00110929, FBbt_00058206, FBbt_00048138] neuprint_JRC_Hemibrain_1point1 [692792746] [neuronbridge:692792746, neuprint_JRC_Hemibrai... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False
293 KCab-m_R (FlyEM-HB:642681035) KCab-m_R VFB_jrchjvhn [Entity, Adult, Anatomy, Cell, Cholinergic, Do... [alpha/beta Kenyon cell, mushroom body dopamin... [FBbt_00100248, FBbt_00048138, FBbt_00058206] neuprint_JRC_Hemibrain_1point1 [642681035] [neuprint_JRC_Hemibrain_1point1:642681035, neu... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False
294 KCab-m_R (FlyEM-HB:940084060) KCab-m_R VFB_jrchjvj0 [Entity, Adult, Anatomy, Cell, Cholinergic, Do... [adult dopaminergic neuron, mushroom body dopa... [FBbt_00058206, FBbt_00048138, FBbt_00100248] neuprint_JRC_Hemibrain_1point1 [940084060] [neuprint_JRC_Hemibrain_1point1:940084060, neu... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False
295 KCab-m_R (FlyEM-HB:363038831) KCab-m_R VFB_jrchjvjd [Entity, Adult, Anatomy, Cell, Cholinergic, Do... [mushroom body dopaminergic neuron, adult dopa... [FBbt_00048138, FBbt_00058206, FBbt_00100248] neuprint_JRC_Hemibrain_1point1 [363038831] [neuprint_JRC_Hemibrain_1point1:363038831, neu... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False

243 rows × 13 columns

[30]:
exploded_KCs = KCs.explode('accession')
adj, roi_info2 = neu.fetch_adjacencies(sources=list(map(int, exploded_ALPNs['accession'][:300])), targets=list(map(int, exploded_KCs['accession'][:300])))
roi_info2.head()
[30]:
bodyId_pre bodyId_post roi weight
0 1887872301 331999156 CA(R) 14
1 1887872301 394755742 CA(R) 5
2 1887872301 425445301 CA(R) 1
3 1887872301 673715784 CA(R) 10
4 1887872301 753489892 CA(R) 1
[31]:
# Group by region of interest (ROI)
by_roi = roi_info2.groupby('roi').weight.sum()
by_roi.head()
[31]:
roi
CA(R)    121
Name: weight, dtype: int64
[32]:
ax = by_roi.plot.bar()
ax.set_xlabel('')
ax.set_ylabel('PN to KC synapses')
[32]:
Text(0, 0.5, 'PN to KC synapses')
../_images/tutorials_connectomics_45_1.png
[33]:

adj = roi_info2[roi_info2.roi == 'CA(R)'].pivot(columns="bodyId_pre", index="bodyId_post", values="weight").fillna(0)
[34]:
sns.clustermap(adj, cmap='Greys')
[34]:
<seaborn.matrix.ClusterGrid at 0x7f80614a3a30>
../_images/tutorials_connectomics_47_1.png

Querying paths

Let’s say we want to find out how to go from a PN (second order olfactory neurons) all the way to a descending neuron (presumably leading to motor neurons in the VNC).

[35]:
#First find DNs in VFB
DNs = vfb.get_instances("'adult descending neuron'", limit=50)
#Select only rows from Hemibrain1.1 dataset
exploded_DNs = DNs.explode('data_source')
DNs=exploded_DNs[exploded_DNs['data_source'] == 'neuprint_JRC_Hemibrain_1point1']
DNs
Limiting to 50 terms out of 297
[35]:
label symbol id tags parents_label parents_id data_source accession xrefs templates dataset license description
1 IB111_R (FlyEM-HB:853173648) IB111_R VFB_jrchjuxu [Entity, Adult, Anatomy, Cell, Cholinergic, In... [adult inferior bridge neuron 111] [FBbt_20001288] neuprint_JRC_Hemibrain_1point1 [853173648] [neuprint_JRC_Hemibrain_1point1:853173648, neu... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False
2 LAL041_R (FlyEM-HB:1603757560) LAL041_R VFB_jrchjwkv [Entity, Adult, Anatomy, Cell, Cholinergic, In... [adult lateral accessory lobe neuron 041] [FBbt_20001337] neuprint_JRC_Hemibrain_1point1 [1603757560] [neuprint_JRC_Hemibrain_1point1:1603757560, ne... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False
3 LAL041_R (FlyEM-HB:5813075030) LAL041_R VFB_jrchjwkw [Entity, Adult, Anatomy, Cell, Cholinergic, In... [adult lateral accessory lobe neuron 041] [FBbt_20001337] neuprint_JRC_Hemibrain_1point1 [5813075030] [neuronbridge:5813075030, neuprint_JRC_Hemibra... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False
4 CL320_R (FlyEM-HB:1258631261) CL320_R VFB_jrchjt1g [Entity, Adult, Anatomy, Cell, Cholinergic, In... [adult clamp neuron 320] [FBbt_20001025] neuprint_JRC_Hemibrain_1point1 [1258631261] [neuronbridge:1258631261, neuprint_JRC_Hemibra... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False
5 CL325_R (FlyEM-HB:1318986524) CL325_R VFB_jrchjt1n [Entity, Adult, Anatomy, Cell, Cholinergic, In... [adult clamp neuron 325] [FBbt_20001030] neuprint_JRC_Hemibrain_1point1 [1318986524] [neuronbridge:1318986524, neuprint_JRC_Hemibra... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False
6 CL324_R (FlyEM-HB:915857055) CL324_R VFB_jrchjt1l [Entity, Adult, Anatomy, Cell, Cholinergic, In... [adult clamp neuron 324] [FBbt_20001029] neuprint_JRC_Hemibrain_1point1 [915857055] [neuprint_JRC_Hemibrain_1point1:915857055, neu... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False
7 CL341_R (FlyEM-HB:982684196) CL341_R VFB_jrchjt2b [Entity, Adult, Anatomy, Cell, Cholinergic, In... [adult clamp neuron 341] [FBbt_20001046] neuprint_JRC_Hemibrain_1point1 [982684196] [neuprint_JRC_Hemibrain_1point1:982684196, neu... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False
8 CL342_R (FlyEM-HB:1044403618) CL342_R VFB_jrchjt2c [Entity, Adult, Anatomy, Cell, Glutamatergic, ... [adult clamp neuron 342] [FBbt_20001047] neuprint_JRC_Hemibrain_1point1 [1044403618] [neuronbridge:1044403618, neuprint_JRC_Hemibra... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False
9 CL332_R (FlyEM-HB:1134107162) CL332_R VFB_jrchjt1y [Entity, Adult, Anatomy, Cell, Cholinergic, In... [adult clamp neuron 332] [FBbt_20001037] neuprint_JRC_Hemibrain_1point1 [1134107162] [neuprint_JRC_Hemibrain_1point1:1134107162, ne... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False
10 CL324(PVM02)_L (FlyEM-HB:852906243) CL324(PVM02)_L VFB_jrchjt1m [Entity, Adult, Anatomy, Cell, Cholinergic, In... [adult clamp neuron 324] [FBbt_20001029] neuprint_JRC_Hemibrain_1point1 [852906243] [neuprint_JRC_Hemibrain_1point1:852906243, neu... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False
11 CL342_R (FlyEM-HB:953013850) CL342_R VFB_jrchjt2d [Entity, Adult, Anatomy, Cell, Glutamatergic, ... [adult clamp neuron 342] [FBbt_20001047] neuprint_JRC_Hemibrain_1point1 [953013850] [neuronbridge:953013850, neuprint_JRC_Hemibrai... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False
12 CL330_R (FlyEM-HB:823062947) CL330_R VFB_jrchjt1w [Entity, Adult, Anatomy, Cell, Cholinergic, In... [adult clamp neuron 330] [FBbt_20001035] neuprint_JRC_Hemibrain_1point1 [823062947] [neuprint_JRC_Hemibrain_1point1:823062947, neu... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False
13 AVLP499_R (FlyEM-HB:1134456668) AVLP499_R VFB_jrchjse8 [Entity, Adult, Anatomy, Cell, Cholinergic, In... [adult anterior ventrolateral protocerebrum ne... [FBbt_20000608] neuprint_JRC_Hemibrain_1point1 [1134456668] [neuronbridge:1134456668, neuprint_JRC_Hemibra... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False
14 CL124(AVM19)_R (FlyEM-HB:1252833634) CL124(AVM19)_R VFB_jrchjsqv [Entity, Adult, Anatomy, Cell, Cholinergic, In... [adult clamp neuron 124] [FBbt_20000829] neuprint_JRC_Hemibrain_1point1 [1252833634] [neuprint_JRC_Hemibrain_1point1:1252833634, ne... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False
15 CL139_R (FlyEM-HB:5812983561) CL139_R VFB_jrchjsrk [Entity, Adult, Anatomy, Cell, Cholinergic, In... [adult clamp neuron 139] [FBbt_20000844] neuprint_JRC_Hemibrain_1point1 [5812983561] [neuprint_JRC_Hemibrain_1point1:5812983561, ne... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False
16 CL138_R (FlyEM-HB:707190304) CL138_R VFB_jrchjsri [Entity, Adult, Anatomy, Cell, Cholinergic, In... [adult clamp neuron 138] [FBbt_20000843] neuprint_JRC_Hemibrain_1point1 [707190304] [neuronbridge:707190304, neuprint_JRC_Hemibrai... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False
17 CL207_R (FlyEM-HB:604476368) CL207_R VFB_jrchjsv1 [Entity, Adult, Anatomy, Cell, Cholinergic, In... [adult clamp neuron 207] [FBbt_20000912] neuprint_JRC_Hemibrain_1point1 [604476368] [neuprint_JRC_Hemibrain_1point1:604476368, neu... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False
18 CL139_R (FlyEM-HB:800920725) CL139_R VFB_jrchjsrj [Entity, Adult, Anatomy, Cell, Cholinergic, In... [adult clamp neuron 139] [FBbt_20000844] neuprint_JRC_Hemibrain_1point1 [800920725] [neuprint_JRC_Hemibrain_1point1:800920725, neu... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False
19 CL137_R (FlyEM-HB:1067240551) CL137_R VFB_jrchjsrh [Entity, Adult, Anatomy, Cell, Cholinergic, In... [adult clamp neuron 137] [FBbt_20000842] neuprint_JRC_Hemibrain_1point1 [1067240551] [neuronbridge:1067240551, neuprint_JRC_Hemibra... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False
20 CRE101_R (FlyEM-HB:985835016) CRE101_R VFB_jrchjtco [Entity, Adult, Anatomy, Cell, Cholinergic, In... [adult crepine neuron 101] [FBbt_20001170] neuprint_JRC_Hemibrain_1point1 [985835016] [neuprint_JRC_Hemibrain_1point1:985835016, neu... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False
21 CL206_R (FlyEM-HB:634884062) CL206_R VFB_jrchjsv0 [Entity, Adult, Anatomy, Cell, Cholinergic, In... [adult clamp neuron 206] [FBbt_20000911] neuprint_JRC_Hemibrain_1point1 [634884062] [neuprint_JRC_Hemibrain_1point1:634884062, neu... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False
22 CRE101(PDM27)_L (FlyEM-HB:5813021985) CRE101(PDM27)_L VFB_jrchjtcn [Entity, Adult, Anatomy, Cell, Cholinergic, In... [adult crepine neuron 101] [FBbt_20001170] neuprint_JRC_Hemibrain_1point1 [5813021985] [neuronbridge:5813021985, neuprint_JRC_Hemibra... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False
23 DNp02_R (FlyEM-HB:5813024015) DNp02_R VFB_jrchjtg5 [Entity, Adult, Anatomy, Cell, Cholinergic, In... [descending neuron of the posterior brain DNp0... [FBbt_00047635, FBbt_00049526] neuprint_JRC_Hemibrain_1point1 [5813024015] [neuronbridge:5813024015, neuprint_JRC_Hemibra... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False
24 DNd01_L (FlyEM-HB:5813026404) DNd01_L VFB_jrchjtg3 [Entity, Adult, Anatomy, Cell, Individual, Ner... [descending neuron of the anterior brain DNd01] [FBbt_00047590] neuprint_JRC_Hemibrain_1point1 [5813026404] [neuronbridge:5813026404, neuprint_JRC_Hemibra... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False
25 DNp05_R (FlyEM-HB:1466998977) DNp05_R VFB_jrchjtg8 [Entity, Adult, Anatomy, Cell, Cholinergic, In... [descending neuron of the posterior brain DNp05] [FBbt_00047638] neuprint_JRC_Hemibrain_1point1 [1466998977] [neuronbridge:1466998977, neuprint_JRC_Hemibra... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False
26 DNd01_R (FlyEM-HB:5813020864) DNd01_R VFB_jrchjtg0 [Entity, Adult, Anatomy, Cell, Individual, Ner... [descending neuron of the anterior brain DNd01] [FBbt_00047590] neuprint_JRC_Hemibrain_1point1 [5813020864] [neuronbridge:5813020864, neuprint_JRC_Hemibra... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False
27 DNg30_R (FlyEM-HB:571346836) DNg30_R VFB_jrchjtg4 [Entity, Adult, Anatomy, Cell, Individual, Ner... [descending neuron of the gnathal ganglion DNg... [FBbt_00047622, FBbt_00058203] neuprint_JRC_Hemibrain_1point1 [571346836] [neuronbridge:571346836, neuprint_JRC_Hemibrai... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False
28 DNp06_R (FlyEM-HB:5813023322) DNp06_R VFB_jrchjtg9 [Entity, Adult, Anatomy, Cell, Cholinergic, In... [descending neuron of the posterior brain DNp06] [FBbt_00047639] neuprint_JRC_Hemibrain_1point1 [5813023322] [neuronbridge:5813023322, neuprint_JRC_Hemibra... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False
29 DNp03_R (FlyEM-HB:1565846637) DNp03_R VFB_jrchjtg6 [Entity, Adult, Anatomy, Cell, Cholinergic, In... [descending neuron of the posterior brain DNp0... [FBbt_00047636, FBbt_00058205] neuprint_JRC_Hemibrain_1point1 [1565846637] [neuronbridge:1565846637, neuprint_JRC_Hemibra... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False
30 DNd01_R (FlyEM-HB:5813012529) DNd01_R VFB_jrchjtg2 [Entity, Adult, Anatomy, Cell, Individual, Ner... [descending neuron of the anterior brain DNd01] [FBbt_00047590] neuprint_JRC_Hemibrain_1point1 [5813012529] [neuronbridge:5813012529, neuprint_JRC_Hemibra... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False
31 DNp04_R (FlyEM-HB:1405231475) DNp04_R VFB_jrchjtg7 [Entity, Adult, Anatomy, Cell, Cholinergic, In... [descending neuron of the posterior brain DNp04] [FBbt_00047637] neuprint_JRC_Hemibrain_1point1 [1405231475] [neuprint_JRC_Hemibrain_1point1:1405231475, ne... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False
32 DNd01_L (FlyEM-HB:5813077405) DNd01_L VFB_jrchjtg1 [Entity, Adult, Anatomy, Cell, Individual, Ner... [descending neuron of the anterior brain DNd01] [FBbt_00047590] neuprint_JRC_Hemibrain_1point1 [5813077405] [neuprint_JRC_Hemibrain_1point1:5813077405, ne... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False
33 SAD095_R (FlyEM-HB:2305628261) SAD095_R VFB_jrchk53s [Entity, Adult, Anatomy, Cell, Cholinergic, In... [adult saddle neuron 095] [FBbt_20002304] neuprint_JRC_Hemibrain_1point1 [2305628261] [neuprint_JRC_Hemibrain_1point1:2305628261, ne... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False
34 PS133_R (FlyEM-HB:1313261883) PS133_R VFB_jrchk4ea [Entity, Adult, Anatomy, Cell, Cholinergic, In... [adult posterior slope neuron 133] [FBbt_20001888] neuprint_JRC_Hemibrain_1point1 [1313261883] [neuronbridge:1313261883, neuprint_JRC_Hemibra... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False
35 PS113(PDM12)_L (FlyEM-HB:1133593331) PS113(PDM12)_L VFB_jrchk4cz [Entity, Adult, Anatomy, Cell, Cholinergic, In... [adult posterior slope neuron 113] [FBbt_20001868] neuprint_JRC_Hemibrain_1point1 [1133593331] [neuronbridge:1133593331, neuprint_JRC_Hemibra... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False
36 PS103_R (FlyEM-HB:5812989815) PS103_R VFB_jrchk4cb [Entity, Adult, Anatomy, Cell, Cholinergic, In... [adult posterior slope neuron 103] [FBbt_20001858] neuprint_JRC_Hemibrain_1point1 [5812989815] [neuronbridge:5812989815, neuprint_JRC_Hemibra... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False
37 PS133_R (FlyEM-HB:5813078352) PS133_R VFB_jrchk4eb [Entity, Adult, Anatomy, Cell, Cholinergic, In... [adult posterior slope neuron 133] [FBbt_20001888] neuprint_JRC_Hemibrain_1point1 [5813078352] [neuronbridge:5813078352, neuprint_JRC_Hemibra... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False
38 PS113_R (FlyEM-HB:727652372) PS113_R VFB_jrchk4cy [Entity, Adult, Anatomy, Cell, Cholinergic, In... [adult posterior slope neuron 113] [FBbt_20001868] neuprint_JRC_Hemibrain_1point1 [727652372] [neuronbridge:727652372, neuprint_JRC_Hemibrai... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False
39 PVLP116_R (FlyEM-HB:1475482533) PVLP116_R VFB_jrchk4v3 [Entity, Adult, Anatomy, Cell, Glutamatergic, ... [adult posterior ventrolateral protocerebrum n... [FBbt_20002174] neuprint_JRC_Hemibrain_1point1 [1475482533] [neuprint_JRC_Hemibrain_1point1:1475482533, ne... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False
40 PVLP119_R (FlyEM-HB:5813021112) PVLP119_R VFB_jrchk4v7 [Entity, Adult, Anatomy, Cell, Cholinergic, In... [adult posterior ventrolateral protocerebrum n... [FBbt_20002177] neuprint_JRC_Hemibrain_1point1 [5813021112] [neuronbridge:5813021112, neuprint_JRC_Hemibra... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False
41 PVLP117_R (FlyEM-HB:1196526636) PVLP117_R VFB_jrchk4v4 [Entity, Adult, Anatomy, Cell, Cholinergic, In... [adult posterior ventrolateral protocerebrum n... [FBbt_20002175] neuprint_JRC_Hemibrain_1point1 [1196526636] [neuronbridge:1196526636, neuprint_JRC_Hemibra... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False
42 PVLP116_R (FlyEM-HB:5813071292) PVLP116_R VFB_jrchk4v2 [Entity, Adult, Anatomy, Cell, Glutamatergic, ... [adult posterior ventrolateral protocerebrum n... [FBbt_20002174] neuprint_JRC_Hemibrain_1point1 [5813071292] [neuprint_JRC_Hemibrain_1point1:5813071292, ne... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False
43 SMP585_R (FlyEM-HB:5813078074) SMP585_R VFB_jrchk792 [Entity, Adult, Anatomy, Cell, Cholinergic, In... [adult superior medial protocerebrum neuron 585] [FBbt_20003447] neuprint_JRC_Hemibrain_1point1 [5813078074] [neuronbridge:5813078074, neuprint_JRC_Hemibra... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False
44 VES082(SCB034)_R (FlyEM-HB:1785926866) VES082(SCB034)_R VFB_jrchk7hs [Entity, Adult, Anatomy, Cell, Cholinergic, In... [adult vest neuron 082] [FBbt_20003548] neuprint_JRC_Hemibrain_1point1 [1785926866] [neuronbridge:1785926866, neuprint_JRC_Hemibra... [JRC_FlyEM_Hemibrain, JRC2018Unisex] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False
45 VES081_R (FlyEM-HB:5813096489) VES081_R VFB_jrchk7hr [Entity, Adult, Anatomy, Cell, Cholinergic, In... [adult vest neuron 081] [FBbt_20003547] neuprint_JRC_Hemibrain_1point1 [5813096489] [neuprint_JRC_Hemibrain_1point1:5813096489, ne... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False
46 VES083(SCB035)_R (FlyEM-HB:5813055134) VES083(SCB035)_R VFB_jrchk7ht [Entity, Adult, Anatomy, Cell, Cholinergic, In... [adult vest neuron 083] [FBbt_20003549] neuprint_JRC_Hemibrain_1point1 [5813055134] [neuprint_JRC_Hemibrain_1point1:5813055134, ne... [JRC2018Unisex, JRC_FlyEM_Hemibrain] [Xu2020NeuronsV1point1] [https://creativecommons.org/licenses/by/4.0/l... tracing status-Roughly traced, cropped-False
[36]:
# First fetch the DNs
exploded_DNs = DNs.explode('accession')
dns, _ = neu.fetch_neurons(list(map(int, exploded_DNs['accession'])))
#with regex
#dns, _ = neu.fetch_neurons(neu.NeuronCriteria(type='(.*DN[^1]{0,}.*|Giant Fiber)', regex=True))
dns
[36]:
bodyId instance type pre post downstream upstream size status cropped statusLabel cellBodyFiber somaRadius somaLocation roiInfo notes inputRois outputRois
0 571346836 DNg30_R DNg30 325 1335 1164 1335 1733411550 Traced False Roughly traced None NaN None {'SNP(R)': {'pre': 28, 'post': 217, 'downstrea... None [AVLP(R), ICL(R), INP, LH(R), MB(+ACA)(R), MB(... [AVLP(R), ICL(R), INP, LH(R), MB(+ACA)(R), PEN...
1 604476368 CL207_R CL207 138 1189 749 1189 1848207477 Traced False Roughly traced PDM12 339.0 [22006, 19354, 5824] {'SNP(R)': {'pre': 38, 'post': 379, 'downstrea... None [AOTU(R), ATL(R), AVLP(R), CX, EPA(R), FB, FBl... [AVLP(R), EPA(R), GOR(R), IB, ICL(R), INP, SCL...
2 634884062 CL206_R CL206 159 623 932 623 870179749 Traced False Roughly traced PDM12 304.5 [22379, 22533, 4744] {'SNP(R)': {'pre': 46, 'post': 211, 'downstrea... None [AOTU(R), EPA(R), GOR(R), ICL(R), INP, LAL(-GA... [AOTU(R), EPA(R), GOR(R), ICL(R), INP, LAL(-GA...
3 707190304 CL138_R CL138 11 3572 32 3572 2354061292 Traced False Roughly traced PDL18 346.0 [7511, 13006, 15184] {'SNP(R)': {'pre': 3, 'post': 1988, 'downstrea... None [CAN(R), CRE(-ROB,-RUB)(R), CRE(R), FLA(R), GO... [ICL(R), INP, SCL(R), SMP(R), SNP(R), SPS(R), ...
4 727652372 PS113_R PS113 11 2504 33 2504 2661988321 Traced False Roughly traced PDM12 434.0 [23181, 19780, 7208] {'SNP(R)': {'post': 124, 'upstream': 124}, 'SI... None [AOTU(R), ATL(R), CAN(R), EPA(R), GNG, GOR(R),... [INP, LAL(-GA)(R), LAL(R), LX(R), SCL(R), SPS(...
5 800920725 CL139_R CL139 11 641 52 641 1258365481 Traced False Roughly traced PDL18 321.0 [11155, 11964, 17208] {'SNP(R)': {'pre': 1, 'post': 83, 'downstream'... pMP12 candidates [AOTU(R), EPA(R), GOR(R), IB, ICL(R), INP, PVL... [EPA(R), GOR(R), ICL(R), INP, SCL(R), SIP(R), ...
6 823062947 CL330_R CL330 65 533 342 533 1526201562 Traced False Roughly traced PVM08 356.0 [13464, 10201, 17312] {'INP': {'pre': 5, 'post': 232, 'downstream': ... pIP16c candidates [AVLP(R), IB, ICL(R), INP, LH(R), PENP, PLP(R)... [ICL(R), INP, PENP, PLP(R), SAD, SAD(-AMMC), S...
7 852906243 CL324(PVM02)_L CL324 15 2289 51 2289 1525345473 Traced False Roughly traced None 470.0 [30578, 9780, 20784] {'SNP(L)': {'pre': 4, 'post': 437, 'downstream... None [ATL(L), GC, GOR(L), IB, ICL(L), INP, SCL(L), ... [GC, IB, INP, SMP(L), SNP(L), SPS(L), VMNP]
8 853173648 IB111_R IB111 609 3540 4225 3540 2227642144 Traced False Roughly traced PVM15 321.0 [11495, 9940, 18560] {'SNP(R)': {'pre': 12, 'post': 420, 'downstrea... None [ATL(L), ATL(R), GNG, GOR(R), IB, INP, IPS(R),... [ATL(L), ATL(R), GNG, GOR(R), IB, INP, IPS(R),...
9 915857055 CL324_R CL324 13 3473 48 3473 1859345530 Traced False Roughly traced PVM02 376.0 [25929, 10630, 19680] {'SNP(R)': {'pre': 2, 'post': 694, 'downstream... None [ATL(R), GOR(R), IB, ICL(R), INP, IPS(R), PLP(... [IB, ICL(R), INP, SCL(R), SMP(R), SNP(R), SPS(...
10 953013850 CL342_R CL342 77 1200 461 1200 719504713 Traced False Roughly traced PVM09 281.0 [16009, 11078, 15800] {'VLNP(R)': {'pre': 28, 'post': 416, 'downstre... pIP9 candidates [AOTU(R), AVLP(R), CX, EPA(R), GC, GOR(R), ICL... [AOTU(R), AVLP(R), EPA(R), GC, GOR(R), ICL(R),...
11 982684196 CL341_R CL341 34 1756 179 1756 1761436814 Traced False Roughly traced PVM09 421.0 [16659, 12205, 16464] {'SNP(R)': {'post': 19, 'upstream': 19}, 'SIP(... pIP9 candidates [AVLP(R), CX, EPA(R), FB, FBl6, GC, GOR(R), IC... [AVLP(R), CX, EPA(R), FB, FBl6, GC, ICL(R), IN...
12 985835016 CRE101_R CRE101 7 939 35 939 867118151 Traced False Roughly traced PDM27 361.0 [23119, 19137, 8608] {'SNP(R)': {'pre': 1, 'post': 31, 'downstream'... None [CRE(-ROB,-RUB)(R), CRE(R), EPA(R), GOR(R), IN... [CRE(-ROB,-RUB)(R), CRE(R), INP, SMP(R), SNP(R...
13 1044403618 CL342_R CL342 174 488 1173 488 762426453 Traced False Roughly traced PVM09 281.0 [15238, 10519, 16448] {'SNP(R)': {'pre': 20, 'post': 58, 'downstream... pIP9 candidates [AOTU(R), AVLP(R), EPA(R), GOR(R), ICL(R), INP... [AOTU(R), AVLP(R), EPA(L), EPA(R), ICL(R), INP...
14 1067240551 CL137_R CL137 159 2188 1212 2188 2420069857 Traced False Roughly traced PDL18 361.0 [8238, 12302, 15200] {'SNP(R)': {'pre': 109, 'post': 59, 'downstrea... None [AVLP(R), CRE(-ROB,-RUB)(R), CRE(R), EPA(R), G... [AVLP(R), CRE(-ROB,-RUB)(R), CRE(R), ICL(R), I...
15 1133593331 PS113(PDM12)_L PS113 4 866 10 866 1780695634 Traced False Roughly traced None 326.0 [27541, 20185, 8496] {'INP': {'pre': 1, 'post': 102, 'downstream': ... None [GOR(L), IB, ICL(L), INP, IPS(R), SCL(L), SMP(... [ICL(L), INP, SPS(L), SPS(R), VMNP]
16 1134107162 CL332_R CL332 65 3462 242 3462 2843145939 Traced False Roughly traced PVM09 490.5 [15255, 8180, 23744] {'SNP(R)': {'pre': 4, 'post': 350, 'downstream... None [AMMC, AVLP(R), EPA(R), GC, GOR(L), GOR(R), IB... [AVLP(R), EPA(R), GC, GOR(R), ICL(R), INP, PVL...
17 1134456668 AVLP499_R AVLP499 19 1522 80 1522 1818898408 Traced False Roughly traced PVL05 NaN None {'INP': {'pre': 2, 'post': 378, 'downstream': ... None [AVLP(R), EPA(R), GC, GOR(R), ICL(R), INP, PLP... [AVLP(R), EPA(R), GC, ICL(R), INP, PVLP(R), SC...
18 1196526636 PVLP117_R PVLP117 37 1561 253 1561 1796498938 Traced False Roughly traced PVL04 526.5 [10472, 10676, 21136] {'INP': {'pre': 4, 'post': 537, 'downstream': ... None [AVLP(R), EPA(R), GOR(R), IB, ICL(R), INP, PLP... [EPA(R), ICL(R), INP, LAL(-GA)(R), LAL(R), LX(...
19 1252833634 CL124(AVM19)_R CL124 0 1639 0 1639 2004860450 Traced False Roughly traced None 521.5 [25362, 32537, 22288] {'SNP(R)': {'post': 47}, 'SMP(R)': {'post': 47... None [ATL(R), EPA(R), FLA(R), GOR(R), IB, ICL(R), I... []
20 1258631261 CL320_R CL320 259 1573 1714 1573 1078331220 Traced False Roughly traced PVM01 365.0 [15937, 8384, 22640] {'INP': {'pre': 68, 'post': 525, 'downstream':... None [AVLP(R), EPA(R), GOR(R), IB, ICL(R), INP, LAL... [AVLP(R), EPA(R), GOR(R), IB, ICL(R), INP, LAL...
21 1313261883 PS133_R PS133 83 945 512 945 1740613822 Traced False Roughly traced PDM17 411.0 [25681, 16704, 11120] {'INP': {'pre': 2, 'post': 254, 'downstream': ... None [EPA(L), EPA(R), GNG, GOR(L), GOR(R), IB, ICL(... [GNG, GOR(L), GOR(R), IB, ICL(R), INP, IPS(R),...
22 1318986524 CL325_R CL325 4 1166 19 1166 1287591710 Traced False Roughly traced PVM02 321.5 [25440, 10435, 18728] {'INP': {'pre': 2, 'post': 298, 'downstream': ... None [AVLP(R), EPA(R), GC, GOR(R), IB, ICL(R), INP,... [ICL(R), INP, PLP(R), VLNP(R)]
23 1405231475 DNp04_R DNp04 1295 7221 9456 7221 2933704323 Traced False Roughly traced PVL15 687.5 [12895, 10321, 20416] {'INP': {'pre': 22, 'post': 16, 'downstream': ... None [EPA(R), GC, GF(R), ICL(R), INP, PLP(R), PVLP(... [EPA(R), GC, ICL(R), INP, PENP, PLP(R), PVLP(R...
24 1466998977 DNp05_R DNp05 73 3517 226 3517 2361393183 Traced False Roughly traced PVM01 511.0 [15133, 9204, 20512] {'VMNP': {'pre': 7, 'post': 847, 'downstream':... None [EPA(R), GC, GOR(R), IB, INP, PENP, PLP(R), PV... [EPA(R), GC, PLP(R), PVLP(R), SPS(R), VES(R), ...
25 1475482533 PVLP116_R PVLP116 319 2016 2303 2016 1615571952 Traced False Roughly traced PVL04 500.0 [9817, 10980, 23392] {'INP': {'pre': 46, 'post': 405, 'downstream':... None [AVLP(R), EPA(R), GOR(R), ICL(R), INP, LAL(-GA... [AVLP(R), EPA(R), GOR(R), ICL(R), INP, LAL(-GA...
26 1565846637 DNp03_R DNp03 116 6460 411 6460 2539709294 Traced False Roughly traced None 346.0 [19014, 16285, 12928] {'INP': {'pre': 4, 'post': 5, 'downstream': 5,... None [EPA(R), IB, INP, PLP(R), PVLP(R), SPS(R), VLN... [IB, INP, PLP(R), PVLP(R), SPS(R), VLNP(R), VM...
27 1603757560 LAL041_R LAL041 166 6559 936 6559 2522236842 Traced False Roughly traced ADM06 349.0 [13299, 32464, 17536] {'MB(R)': {'post': 1, 'upstream': 1}, 'aL(R)':... aSP3 candidates [EPA(R), GNG, IPS(R), LAL(-GA)(R), LAL(R), LX(... [IPS(R), LAL(-GA)(R), LAL(R), LX(R), SPS(R), V...
28 1785926866 VES082(SCB034)_R VES082 12 3385 44 3385 1368392579 Traced False Roughly traced None 441.5 [13561, 31420, 27976] {'VMNP': {'pre': 6, 'post': 2432, 'downstream'... None [AVLP(R), IPS(R), LAL(-GA)(R), LAL(R), LX(R), ... [AL(R), AL-VL2p(R), LAL(-GA)(R), LAL(R), LX(R)...
29 2305628261 SAD095_R SAD095 14 1480 40 1480 2168145446 Traced False Roughly traced PVM15 471.0 [17021, 10666, 19472] {'VMNP': {'pre': 2, 'post': 15, 'downstream': ... None [AMMC, GNG, IPS(R), PENP, SAD, SAD(-AMMC), SPS... [AMMC, GNG, IPS(R), PENP, SAD, SAD(-AMMC), VLN...
30 5812983561 CL139_R CL139 11 713 37 713 1380453305 Traced False Roughly traced PDL18 356.0 [11431, 13013, 16056] {'SNP(R)': {'post': 12, 'upstream': 12}, 'SIP(... pMP12 candidates [EPA(L), EPA(R), GOR(L), GOR(R), IB, ICL(L), I... [EPA(R), ICL(R), INP, VES(R), VMNP]
31 5812989815 PS103_R PS103 35 7364 125 7364 2331049566 Traced False Roughly traced AVM22 NaN None {'INP': {'pre': 1, 'post': 54, 'downstream': 3... None [AMMC, CAN(R), EPA(R), GC, GNG, IB, ICL(R), IN... [EPA(R), IB, INP, IPS(R), PLP(R), SPS(R), VLNP...
32 5813012529 DNd01_R DNd01 53 1501 261 1501 858717733 Traced False Roughly traced None 343.5 [25432, 30434, 12496] {'SNP(R)': {'pre': 6, 'post': 1205, 'downstrea... None [SMP(L), SMP(R), SNP(L), SNP(R)] [SMP(L), SMP(R), SNP(L), SNP(R)]
33 5813020864 DNd01_R DNd01 1 1245 1 1245 740943094 Traced False Roughly traced None 331.0 [25315, 32128, 15280] {'SNP(R)': {'post': 985}, 'SMP(R)': {'post': 9... None [SMP(L), SMP(R), SNP(L), SNP(R)] []
34 5813021112 PVLP119_R PVLP119 490 12798 1636 12798 5048827044 Traced False Roughly traced PVL05 500.0 [10773, 10457, 23200] {'INP': {'pre': 76, 'post': 2850, 'downstream'... None [AMMC, AVLP(R), EPA(R), GC, GF(R), GOR(R), IB,... [AMMC, AVLP(R), EPA(R), GC, GF(R), GOR(R), IB,...
35 5813021985 CRE101(PDM27)_L CRE101 30 572 208 572 813988632 Traced False Roughly traced None 351.0 [27605, 20057, 9840] {'SNP(L)': {'pre': 5, 'post': 42, 'downstream'... None [CRE(-RUB)(L), CRE(L), INP, LAL(L), LX(L), MB(... [CRE(-RUB)(L), CRE(L), INP, LAL(L), LX(L), SMP...
36 5813023322 DNp06_R DNp06 143 12661 489 12661 3778739918 Traced False Roughly traced PVL15 366.0 [12622, 10767, 19712] {'VLNP(R)': {'pre': 119, 'post': 11532, 'downs... AMMC-Di6 (Matsuo et al. JCN 2016) [AMMC, AVLP(R), EPA(R), GC, GF(R), GOR(R), ICL... [AMMC, AVLP(R), GF(R), GOR(R), ICL(R), INP, IP...
37 5813024015 DNp02_R DNp02 122 6624 334 6624 3506481413 Traced False Roughly traced PVL15 516.5 [14066, 11012, 20712] {'INP': {'pre': 2, 'downstream': 4}, 'ICL(R)':... AMMC-D1 (Matsuo et al. JCN 2016) [AMMC, EPA(R), GF(R), PENP, PLP(R), PVLP(R), S... [AMMC, EPA(R), ICL(R), INP, PENP, PLP(R), PVLP...
38 5813026404 DNd01_L DNd01 2 651 8 651 693369642 Traced False Roughly traced None 292.5 [25144, 32778, 14648] {'SNP(L)': {'pre': 2, 'post': 604, 'downstream... None [SMP(L), SMP(R), SNP(L), SNP(R)] [SMP(L), SNP(L)]
39 5813055134 VES083(SCB035)_R VES083 5 3332 19 3332 1272176729 Traced False Roughly traced None 581.5 [15998, 28584, 29984] {'VMNP': {'pre': 3, 'post': 2458, 'downstream'... None [GNG, IPS(R), LAL(-GA)(R), LAL(R), LX(R), PENP... [GNG, VES(R), VLNP(R), VMNP, WED(R)]
40 5813071292 PVLP116_R PVLP116 361 2278 2697 2278 1673517104 Traced False Roughly traced PVL04 565.5 [10021, 11033, 22256] {'INP': {'pre': 42, 'post': 586, 'downstream':... None [AVLP(R), EPA(R), GOR(R), ICL(R), INP, LAL(-GA... [AVLP(R), EPA(R), GOR(R), ICL(R), INP, LAL(-GA...
41 5813075030 LAL041_R LAL041 142 6443 808 6443 2364051413 Traced False Roughly traced ADM06 401.5 [13459, 33330, 17912] {'LX(R)': {'pre': 66, 'post': 3141, 'downstrea... aSP3 candidates [EPA(R), GNG, GOR(R), IPS(R), LAL(-GA)(R), LAL... [EPA(R), GNG, IPS(R), LAL(-GA)(R), LAL(R), LX(...
42 5813077405 DNd01_L DNd01 21 731 101 731 738596888 Traced False Roughly traced None 342.0 [25173, 33207, 14176] {'SNP(L)': {'pre': 13, 'post': 675, 'downstrea... None [SMP(L), SMP(R), SNP(L), SNP(R)] [SMP(L), SMP(R), SNP(L), SNP(R)]
43 5813078074 SMP585_R SMP585 10 1369 40 1369 3156737135 Traced False Roughly traced PVM08 476.0 [15811, 11922, 16464] {'SNP(R)': {'pre': 2, 'post': 817, 'downstream... None [CRE(-ROB,-RUB)(R), CRE(R), FLA(R), GNG, GOR(L... [GNG, GOR(R), IPS(R), SMP(R), SNP(R), VES(R), ...
44 5813078352 PS133_R PS133 9 1041 30 1041 1572727885 Traced False Roughly traced PDM17 351.0 [26154, 14795, 14256] {'INP': {'post': 252, 'upstream': 252}, 'SCL(R... None [CAN(R), EPA(L), EPA(R), GNG, GOR(L), GOR(R), ... [CAN(R), GOR(R), IPS(R), PENP, SPS(L), SPS(R),...
45 5813096489 VES081_R VES081 14 1321 71 1321 928031787 Traced False Roughly traced PVM15 451.0 [15106, 10109, 20144] {'VMNP': {'pre': 5, 'post': 1190, 'downstream'... None [AL(R), GNG, IPS(R), LAL(-GA)(R), LAL(R), LX(R... [GNG, VES(R), VMNP]

Neuprint lets you query paths from a single source to a single target. For multi-source or -target queries, your best bet is to download the entire graph and run the queries locally using networkx or igraph.

[37]:
# Find all paths from A PN to A DNs
paths = neu.fetch_shortest_paths(upstream_bodyId=list(map(int, exploded_ALPNs['accession']))[0],
                                 downstream_bodyId=list(map(int, exploded_DNs['accession']))[0],
                                 min_weight=10)
paths
[37]:
path bodyId type weight
0 0 791298858 M_vPNml84 0
1 0 424716408 LHAV3k1 10
2 0 545444996 SMP038 17
3 0 1037750917 IB009 15
4 0 853173648 IB111 173
5 1 791298858 M_vPNml84 0
6 1 424716408 LHAV3k1 10
7 1 298258611 SLP388 15
8 1 5813056054 SMP050 19
9 1 853173648 IB111 10
10 2 791298858 M_vPNml84 0
11 2 424716408 LHAV3k1 10
12 2 5813055800 LHPD5d1 21
13 2 5813056054 SMP050 11
14 2 853173648 IB111 10
15 3 791298858 M_vPNml84 0
16 3 424716408 LHAV3k1 10
17 3 360236724 LHAV4l1 44
18 3 5813011660 aMe24 13
19 3 853173648 IB111 10
20 4 791298858 M_vPNml84 0
21 4 510317265 LHPD4d1 50
22 4 327933008 LHPD5b1 19
23 4 578621125 SMP470 34
24 4 853173648 IB111 47

So it looks like there are three separate 7-hop paths to go from M_vPNml53 to DN1a. Let’s visualize the neurons involved!

Fetching meshes & skeletons

You can fetch skeletons as SWCs directly via neuprint-python. For visualization however it’s easiest to load neuron morphologies via navis. For that navis wraps neuprint-python and adds some convenience functions (see also the tutorial):

[38]:
# Import the wrapped neuprint-python
# -> this exposes ALL base functions plus a couple navis-specific extras
import navis
import navis.interfaces.neuprint as neu

#client = neu.Client('https://neuprint.janelia.org', dataset='hemibrain:v1.1')

# Fetch neurons in the first path
bodyIDS = paths.loc[(paths.path == 0), 'bodyId']
# nl = neu.fetch_skeletons(paths.loc[(paths.path == 0), 'bodyId'])
# nl

xrefs = ['neuprint_JRC_Hemibrain_1point1:' + str(id) for id in bodyIDS]

nl_terms = vfb.terms(xrefs)
nl = [term.skeleton for term in nl_terms]
nl_terms.summary
Warning: No results returned for query: MATCH (s:Individual)<-[r:database_cross_reference]-(i:Entity) WHERE r.accession[0] in [] AND s.short_form = 'neuprint_JRC_Hemibrain_1point1' RETURN r.accession[0] as key, collect({ db: s.short_form, vfb_id: i.short_form }) as mapping -> [{'columns': ['key', 'mapping'], 'data': []}] -> []
Error: Unrecognized value: neuprint_JRC_Hemibrain_1point1:791298858
Warning: No results returned for query: MATCH (s:Individual)<-[r:database_cross_reference]-(i:Entity) WHERE r.accession[0] in [] AND s.short_form = 'neuprint_JRC_Hemibrain_1point1' RETURN r.accession[0] as key, collect({ db: s.short_form, vfb_id: i.short_form }) as mapping -> [{'columns': ['key', 'mapping'], 'data': []}] -> []
Error: Unrecognized value: neuprint_JRC_Hemibrain_1point1:424716408
Warning: No results returned for query: MATCH (s:Individual)<-[r:database_cross_reference]-(i:Entity) WHERE r.accession[0] in [] AND s.short_form = 'neuprint_JRC_Hemibrain_1point1' RETURN r.accession[0] as key, collect({ db: s.short_form, vfb_id: i.short_form }) as mapping -> [{'columns': ['key', 'mapping'], 'data': []}] -> []
Error: Unrecognized value: neuprint_JRC_Hemibrain_1point1:545444996
Warning: No results returned for query: MATCH (s:Individual)<-[r:database_cross_reference]-(i:Entity) WHERE r.accession[0] in [] AND s.short_form = 'neuprint_JRC_Hemibrain_1point1' RETURN r.accession[0] as key, collect({ db: s.short_form, vfb_id: i.short_form }) as mapping -> [{'columns': ['key', 'mapping'], 'data': []}] -> []
Error: Unrecognized value: neuprint_JRC_Hemibrain_1point1:1037750917
Warning: No results returned for query: MATCH (s:Individual)<-[r:database_cross_reference]-(i:Entity) WHERE r.accession[0] in [] AND s.short_form = 'neuprint_JRC_Hemibrain_1point1' RETURN r.accession[0] as key, collect({ db: s.short_form, vfb_id: i.short_form }) as mapping -> [{'columns': ['key', 'mapping'], 'data': []}] -> []
Error: Unrecognized value: neuprint_JRC_Hemibrain_1point1:853173648
Pulling 5 terms from VFB...
Error: No key provided.
Error: No key provided.
Error: No key provided.
Error: No key provided.
Error: No key provided.
Warning: called a non existant id:
Some terms not found in cache. Falling back to slower Neo4j queries.
Error: No key provided.
Error: No key provided.
Error: No key provided.
Error: No key provided.
Error: No key provided.
Warning: No results returned for query: MATCH (e:Entity) WHERE e.short_form in ['', '', '', '', ''] RETURN e.short_form as short_form, labels(e) as labs  -> [{'columns': ['short_form', 'labs'], 'data': []}] -> []
Failed to load 5 terms: ['', '', '', '', '']
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Cell In[38], line 17
     15 nl_terms = vfb.terms(xrefs)
     16 nl = [term.skeleton for term in nl_terms]
---> 17 nl_terms.summary

File ~/GIT/VFB_connect/.conda/lib/python3.10/site-packages/vfb_connect/schema/vfb_term.py:3071, in VFBTerms.summary(self)
   3067 """
   3068 Get the summary of the term.
   3069 """
   3070 if self._summary is None:
-> 3071     self._summary = self.get_summaries()
   3072 return self._summary

File ~/GIT/VFB_connect/.conda/lib/python3.10/site-packages/vfb_connect/schema/vfb_term.py:3913, in VFBTerms.get_summaries(self, return_dataframe, verbose, limit)
   3910             break
   3912 if return_dataframe:
-> 3913     return pandas.concat(summaries, ignore_index=True)
   3914 return summaries

File ~/GIT/VFB_connect/.conda/lib/python3.10/site-packages/pandas/core/reshape/concat.py:382, in concat(objs, axis, join, ignore_index, keys, levels, names, verify_integrity, sort, copy)
    379 elif copy and using_copy_on_write():
    380     copy = False
--> 382 op = _Concatenator(
    383     objs,
    384     axis=axis,
    385     ignore_index=ignore_index,
    386     join=join,
    387     keys=keys,
    388     levels=levels,
    389     names=names,
    390     verify_integrity=verify_integrity,
    391     copy=copy,
    392     sort=sort,
    393 )
    395 return op.get_result()

File ~/GIT/VFB_connect/.conda/lib/python3.10/site-packages/pandas/core/reshape/concat.py:445, in _Concatenator.__init__(self, objs, axis, join, keys, levels, names, ignore_index, verify_integrity, copy, sort)
    442 self.verify_integrity = verify_integrity
    443 self.copy = copy
--> 445 objs, keys = self._clean_keys_and_objs(objs, keys)
    447 # figure out what our result ndim is going to be
    448 ndims = self._get_ndims(objs)

File ~/GIT/VFB_connect/.conda/lib/python3.10/site-packages/pandas/core/reshape/concat.py:507, in _Concatenator._clean_keys_and_objs(self, objs, keys)
    504     objs_list = list(objs)
    506 if len(objs_list) == 0:
--> 507     raise ValueError("No objects to concatenate")
    509 if keys is None:
    510     objs_list = list(com.not_none(*objs_list))

ValueError: No objects to concatenate
[ ]:
# Let's also get some ROI meshes

# al = neu.fetch_roi('AL(R)')
# lh = neu.fetch_roi('LH(R)')
# ca = neu.fetch_roi('CA(R)')

# If the neuprint server fails to return the meshes (often due to capacity issues), we can use the VFB API to get the meshes instead
[al,lh,ca] = [term.mesh for term in vfb.terms(['AL(R) on JRC_FlyEM_Hemibrain','LH(R) on JRC_FlyEM_Hemibrain','CA(R) on JRC_FlyEM_Hemibrain'])]

[ ]:
# Plot
navis.plot3d([nl, lh, al, ca])

Data type cannot be displayed: application/vnd.plotly.v1+json

Plotting graphs

There are various ways of plotting static graphs. In theory Jupyter notebooks lend themselves to interactive graphs too but unfortunately DeepNote does not yet support the required libraries (e.g. ipywidgets). That being said: if you want to run this locally or on Google colab, check out ipycytoscape.

There are numerous options to do this but we will use networkx to plot a static graph:

[ ]:
import networkx as nx
import numpy as np

# Initialize the graph
G = nx.DiGraph()

# Generate edges from the paths
edges = []
for p in paths.path.unique():
    this_path = paths.loc[(paths.path == p)]
    this_edges = list(zip(this_path.values[:-1], this_path.values[1:]))

    for i in range(this_path.shape[0] - 1):
        edges.append([this_path.bodyId.values[i], this_path.bodyId.values[i + 1], this_path.weight.values[i + 1]])

# Add the edges
G.add_weighted_edges_from(edges)

# Add some names to the nodes
nx.set_node_attributes(G, paths.set_index('bodyId')['type'].to_dict(), name='name')
[ ]:
import matplotlib.pyplot as plt

# Draw using a simple force-directed layout
pos = nx.kamada_kawai_layout(G)

# We could draw everything in one step but this way we have more control over the plot
fig, ax = plt.subplots(figsize=(10, 10))

# Draw nodes
nx.draw_networkx_nodes(G, pos=pos, ax=ax)

# Draw edges
weights = np.array([e[2]['weight'] for e in G.edges(data=True)])
nx.draw_networkx_edges(G, pos=pos, width=(weights / 12).tolist())

# Add node labels
nx.draw_networkx_labels(G, pos=pos, labels=dict(G.nodes('name')), font_size=14)

# Turn axes of
ax.set_axis_off()
../_images/tutorials_connectomics_59_0.png

In general, I recommend exporting your graph to e.g. graphml and importing it into e.g. cytoscape if you want to explore an interactive network graph. see nx.write_gml