Discovery
Required packages: vfb-connect and python-catmaid (pymaid & navis)
[1]:
!pip install ../../../
!pip install python-catmaid --upgrade
Processing /Users/robbiecourt/GIT/VFB_connect
Preparing metadata (setup.py) ... done
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ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
gensim 4.3.0 requires FuzzyTM>=0.4.0, which is not installed.
scipy 1.10.0 requires numpy<1.27.0,>=1.19.5, but you have numpy 2.0.1 which is incompatible.
numba 0.56.4 requires numpy<1.24,>=1.18, but you have numpy 2.0.1 which is incompatible.
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Successfully installed certifi-2024.7.4 charset-normalizer-3.3.2 decorator-5.1.1 idna-3.7 jsonpath_rw-1.4.0 numpy-2.0.1 pandas-2.2.2 ply-3.11 python-dateutil-2.9.0.post0 pytz-2024.1 requests-2.32.3 six-1.16.0 tzdata-2024.1 urllib3-2.2.2 vfb-connect-1.2.20.dev7+f222e3e.dirty
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Installing collected packages: numpy
Attempting uninstall: numpy
Found existing installation: numpy 2.0.1
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ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
gensim 4.3.0 requires FuzzyTM>=0.4.0, which is not installed.
numba 0.56.4 requires numpy<1.24,>=1.18, but you have numpy 1.26.4 which is incompatible.
Successfully installed numpy-1.26.4
How to find neurons across datasets
VirtualFlyBrain integrates images and connectomics profiles of neurons from many sources. It classifies and records their properties using a standard, queryable classification (The Drosophila Anatomy Ontology). This standardises the names of neuron types across sources, so you don’t need to worry about differences in nomenclature uses and supports queries for neurons by their classification.
[2]:
# Import libs and initialise API objects
from vfb_connect.cross_server_tools import VfbConnect
import pandas as pd
vc = VfbConnect()
import pymaid
import navis
navis.set_pbars(jupyter=False)
pymaid.set_pbars(jupyter=False)
# Connect to the VFB CATMAID server hosting the FAFB data
rm = pymaid.connect_catmaid(server="https://fafb.catmaid.virtualflybrain.org/", api_token=None, max_threads=10)
# Test call to see if connection works
print(f'Server is running CATMAID version {rm.catmaid_version}')
/usr/local/anaconda3/lib/python3.10/site-packages/pandas/core/arrays/masked.py:60: UserWarning: Pandas requires version '1.3.6' or newer of 'bottleneck' (version '1.3.5' currently installed).
from pandas.core import (
INFO : Global CATMAID instance set. Caching is ON. (pymaid)
Server is running CATMAID version 2020.02.15-102-gce1dee4
Finds neurons by type (classification) across datasets
We can use the vc.get_instances method in combination with the name of a neuron type on VFB to find individual neurons from multiple sources.
Use the search tool on VFB to find neuron types by name or synonym:
|b07465fb7d014292affcae78a7f768b2| |6413bf0548d748d7aa847dec71ec77a3|
Use either the full name or the Symbol to query for neurons:
[3]:
DA3adPN = vc.get_instances("adult Drosulfakinin neuron", summary=True)
pd.DataFrame.from_records(DA3adPN)
[3]:
| label | symbol | id | tags | parents_label | parents_id | data_source | accession | templates | dataset | license | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | DSKMP1A_R | DSKMP1A_R | VFB_jrchjti2 | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult octopaminergic neuron|adult Drosulfakini... | FBbt_00058203|FBbt_00051433 | neuprint_JRC_Hemibrain_1point1 | 1135837629 | JRC2018Unisex|JRC_FlyEM_Hemibrain | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 1 | DSKMP1A(PVM02)_L | DSKMP1A(PVM02)_L | VFB_jrchjti3 | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult Drosulfakinin MP1a neuron|adult octopami... | FBbt_00051433|FBbt_00058203 | neuprint_JRC_Hemibrain_1point1 | 1260833150 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 2 | DSKMP1B_R | DSKMP1B_R | VFB_jrchjti4 | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult octopaminergic neuron|adult Drosulfakini... | FBbt_00058203|FBbt_00051434 | neuprint_JRC_Hemibrain_1point1 | 1352077058 | JRC2018Unisex|JRC_FlyEM_Hemibrain | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 3 | DSKMP1B(PVM02)_L | DSKMP1B(PVM02)_L | VFB_jrchjti5 | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult Drosulfakinin MP1b neuron|adult octopami... | FBbt_00051434|FBbt_00058203 | neuprint_JRC_Hemibrain_1point1 | 1011184205 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 4 | DSKMP3_R | DSKMP3_R | VFB_jrchjti7 | Entity|Adult|Anatomy|Cell|Cholinergic|Individu... | adult cholinergic neuron|adult Drosulfakinin M... | FBbt_00058205|FBbt_00051432 | neuprint_JRC_Hemibrain_1point1 | 328559607 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 5 | DSKMP3_R | DSKMP3_R | VFB_jrchjti6 | Entity|Adult|Anatomy|Cell|Cholinergic|Individu... | adult cholinergic neuron|adult Drosulfakinin M... | FBbt_00058205|FBbt_00051432 | neuprint_JRC_Hemibrain_1point1 | 327937328 | JRC2018Unisex|JRC_FlyEM_Hemibrain | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
Find neurons by location
We can use the same method to search for neurons by location, using simple queries.
[4]:
# Find neurons by location. The following query works across multiple data sources and both sides of the brain.
# Results may be incomplete & may include minor overlap inferred from low synapse counts
neurons_in_DA3 = vc.get_instances("'neuron' that 'overlaps' some 'antennal lobe glomerulus DA3'", summary=True)
neurons_in_DA3_tab = pd.DataFrame.from_records(neurons_in_DA3)
neurons_in_DA3_tab[0:5]
Running query: FBbt:00005106 that RO:0002131 some FBbt:00003934
Query URL: http://owl.virtualflybrain.org/kbs/vfb/instances?object=FBbt%3A00005106+that+RO%3A0002131+some+FBbt%3A00003934&prefixes=%7B%22FBbt%22%3A+%22http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FFBbt_%22%2C+%22RO%22%3A+%22http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FRO_%22%2C+%22BFO%22%3A+%22http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBFO_%22%7D&direct=False
Query results: 158
[4]:
| label | symbol | id | tags | parents_label | parents_id | data_source | accession | templates | dataset | license | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | ORN_DA1_R | ORN_DA1_R | VFB_jrchk15e | Entity|Adult|Anatomy|Cell|Chemosensory_system|... | adult olfactory receptor neuron Or67d | FBbt_00067031 | neuprint_JRC_Hemibrain_1point1 | 1703682799 | JRC2018Unisex|JRC_FlyEM_Hemibrain | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 1 | ORN_DL4_R | ORN_DL4_R | VFB_jrchk1km | Entity|Adult|Anatomy|Cell|Chemosensory_system|... | adult olfactory receptor neuron Or49a/85f | FBbt_00067055 | neuprint_JRC_Hemibrain_1point1 | 1671271059 | JRC2018Unisex|JRC_FlyEM_Hemibrain | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 2 | ORN_DA1_R | ORN_DA1_R | VFB_jrchk13v | Entity|Adult|Anatomy|Cell|Chemosensory_system|... | adult olfactory receptor neuron Or67d | FBbt_00067031 | neuprint_JRC_Hemibrain_1point1 | 1735054607 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 3 | v2LN35_R | v2LN35_R | VFB_jrchk8ew | Entity|Adult|Anatomy|Cell|Cholinergic|Individu... | cholinergic local interneuron of the adult ant... | FBbt_00007403|FBbt_20003766 | neuprint_JRC_Hemibrain_1point1 | 1733056086 | JRC2018Unisex|JRC_FlyEM_Hemibrain | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 4 | lLN2T_a(Tortuous)_R | lLN2T_a(Tortuous)_R | VFB_jrchk8bd | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN2T|adult s... | FBbt_00049816|FBbt_00049526 | neuprint_JRC_Hemibrain_1point1 | 5813032595 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
[5]:
# Find local interneurons (intrinsic neurons) of the AL, overlapping DA3:
local_in_DA3 = vc.get_instances("'local interneuron of adult antennal lobe' that 'overlaps' some 'antennal lobe glomerulus DA3'")
local_in_DA3_tab = pd.DataFrame.from_records(local_in_DA3)
local_in_DA3_tab
Running query: FBbt:00007390 that RO:0002131 some FBbt:00003934
Query URL: http://owl.virtualflybrain.org/kbs/vfb/instances?object=FBbt%3A00007390+that+RO%3A0002131+some+FBbt%3A00003934&prefixes=%7B%22FBbt%22%3A+%22http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FFBbt_%22%2C+%22RO%22%3A+%22http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FRO_%22%2C+%22BFO%22%3A+%22http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBFO_%22%7D&direct=False
Query results: 53
[5]:
| label | symbol | id | tags | parents_label | parents_id | data_source | accession | templates | dataset | license | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | v2LN35_R | v2LN35_R | VFB_jrchk8ew | Entity|Adult|Anatomy|Cell|Cholinergic|Individu... | cholinergic local interneuron of the adult ant... | FBbt_00007403|FBbt_20003766 | neuprint_JRC_Hemibrain_1point1 | 1733056086 | JRC2018Unisex|JRC_FlyEM_Hemibrain | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 1 | lLN2T_a(Tortuous)_R | lLN2T_a(Tortuous)_R | VFB_jrchk8bd | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN2T|adult s... | FBbt_00049816|FBbt_00049526 | neuprint_JRC_Hemibrain_1point1 | 5813032595 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 2 | lLN2T_d(Tortuous)_R | lLN2T_d(Tortuous)_R | VFB_jrchk8bp | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN2T|adult s... | FBbt_00049816|FBbt_00049526 | neuprint_JRC_Hemibrain_1point1 | 1667251683 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 3 | lLN2P_b(Patchy)_R | lLN2P_b(Patchy)_R | VFB_jrchk8au | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult local interneuron of the lateral ALl1 ne... | FBbt_00007394|FBbt_00049813|FBbt_00049526 | neuprint_JRC_Hemibrain_1point1 | 1946178096 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 4 | lLN2T_a(Tortuous)_R | lLN2T_a(Tortuous)_R | VFB_jrchk8bg | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN2T|adult s... | FBbt_00049816|FBbt_00049526 | neuprint_JRC_Hemibrain_1point1 | 1762354941 | JRC2018Unisex|JRC_FlyEM_Hemibrain | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 5 | lLN1_c_R | lLN1_c_R | VFB_jrchk8ai | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult serotonergic neuron|adult antennal lobe ... | FBbt_00049526|FBbt_00007395 | neuprint_JRC_Hemibrain_1point1 | 1547454812 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 6 | lLN1_b_R | lLN1_b_R | VFB_jrchk8a8 | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN1|adult se... | FBbt_00007395|FBbt_00049526 | neuprint_JRC_Hemibrain_1point1 | 5813054622 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 7 | lLN2T_a(Tortuous)_R | lLN2T_a(Tortuous)_R | VFB_jrchk8bi | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN2T|adult s... | FBbt_00049816|FBbt_00049526 | neuprint_JRC_Hemibrain_1point1 | 5813056598 | JRC2018Unisex|JRC_FlyEM_Hemibrain | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 8 | lLN16b_R | lLN16b_R | VFB_jrchk89w | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN16B | FBbt_20003752 | neuprint_JRC_Hemibrain_1point1 | 1887168462 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 9 | lLN2T_e(Tortuous)_R | lLN2T_e(Tortuous)_R | VFB_jrchk8bs | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult serotonergic neuron|adult antennal lobe ... | FBbt_00049526|FBbt_00049816 | neuprint_JRC_Hemibrain_1point1 | 1640922516 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 10 | lLN1_b_R | lLN1_b_R | VFB_jrchk8ad | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN1|adult se... | FBbt_00007395|FBbt_00049526 | neuprint_JRC_Hemibrain_1point1 | 1642623277 | JRC2018Unisex|JRC_FlyEM_Hemibrain | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 11 | lLN1_c_R | lLN1_c_R | VFB_jrchk8aj | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN1|adult se... | FBbt_00007395|FBbt_00049526 | neuprint_JRC_Hemibrain_1point1 | 1702651358 | JRC2018Unisex|JRC_FlyEM_Hemibrain | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 12 | lLN2F_a(Full)_R | lLN2F_a(Full)_R | VFB_jrchk8al | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult local interneuron of the lateral ALl1 ne... | FBbt_00007394|FBbt_00049812|FBbt_00049526 | neuprint_JRC_Hemibrain_1point1 | 1670287030 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 13 | lLN1_a_R | lLN1_a_R | VFB_jrchk8a4 | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult serotonergic neuron|adult antennal lobe ... | FBbt_00049526|FBbt_00007395 | neuprint_JRC_Hemibrain_1point1 | 5813130064 | JRC2018Unisex|JRC_FlyEM_Hemibrain | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 14 | lLN1_b_R | lLN1_b_R | VFB_jrchk8aa | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult serotonergic neuron|adult antennal lobe ... | FBbt_00049526|FBbt_00007395 | neuprint_JRC_Hemibrain_1point1 | 5813069055 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 15 | lLN2S(Star)_R | lLN2S(Star)_R | VFB_jrchk8bc | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult local interneuron of the lateral ALl1 ne... | FBbt_00007394|FBbt_00049526|FBbt_00049815 | neuprint_JRC_Hemibrain_1point1 | 1762359683 | JRC2018Unisex|JRC_FlyEM_Hemibrain | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 16 | lLN1_c_R | lLN1_c_R | VFB_jrchk8ah | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN1|adult se... | FBbt_00007395|FBbt_00049526 | neuprint_JRC_Hemibrain_1point1 | 1578826464 | JRC2018Unisex|JRC_FlyEM_Hemibrain | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 17 | lLN2F_b(Full)_R | lLN2F_b(Full)_R | VFB_jrchk8an | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN2F|adult l... | FBbt_00049812|FBbt_00007394 | neuprint_JRC_Hemibrain_1point1 | 5813024698 | JRC2018Unisex|JRC_FlyEM_Hemibrain | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 18 | lLN2R_b(Regional)_R | lLN2R_b(Regional)_R | VFB_jrchk8b6 | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult serotonergic neuron|adult local interneu... | FBbt_00049526|FBbt_00007394|FBbt_00049814 | neuprint_JRC_Hemibrain_1point1 | 5813076969 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 19 | lLN1_b_R | lLN1_b_R | VFB_jrchk8a9 | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN1|adult se... | FBbt_00007395|FBbt_00049526 | neuprint_JRC_Hemibrain_1point1 | 5813054777 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 20 | lLN2T_b(Tortuous)_R | lLN2T_b(Tortuous)_R | VFB_jrchk8bl | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN2T|adult s... | FBbt_00049816|FBbt_00049526 | neuprint_JRC_Hemibrain_1point1 | 1640572741 | JRC2018Unisex|JRC_FlyEM_Hemibrain | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 21 | lLN1_c_R | lLN1_c_R | VFB_jrchk8af | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult serotonergic neuron|adult antennal lobe ... | FBbt_00049526|FBbt_00007395 | neuprint_JRC_Hemibrain_1point1 | 5813062199 | JRC2018Unisex|JRC_FlyEM_Hemibrain | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 22 | lLN16a_R | lLN16a_R | VFB_jrchk89t | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN16A | FBbt_20003751 | neuprint_JRC_Hemibrain_1point1 | 1702318692 | JRC2018Unisex|JRC_FlyEM_Hemibrain | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 23 | lLN12a_R | lLN12a_R | VFB_jrchk89g | Entity|Adult|Anatomy|Cell|Cholinergic|Individu... | cholinergic local interneuron of the adult ant... | FBbt_00007403|FBbt_20003746 | neuprint_JRC_Hemibrain_1point1 | 1826445251 | JRC2018Unisex|JRC_FlyEM_Hemibrain | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 24 | lLN1_c_R | lLN1_c_R | VFB_jrchk8ae | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult serotonergic neuron|adult antennal lobe ... | FBbt_00049526|FBbt_00007395 | neuprint_JRC_Hemibrain_1point1 | 5813047691 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 25 | lLN2T_a(Tortuous)_R | lLN2T_a(Tortuous)_R | VFB_jrchk8bh | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult serotonergic neuron|adult antennal lobe ... | FBbt_00049526|FBbt_00049816 | neuprint_JRC_Hemibrain_1point1 | 5813054726 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 26 | lLN2S(Star)_R | lLN2S(Star)_R | VFB_jrchk8bb | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN2S|adult s... | FBbt_00049815|FBbt_00049526|FBbt_00007394 | neuprint_JRC_Hemibrain_1point1 | 1670627928 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 27 | lLN1_b_R | lLN1_b_R | VFB_jrchk8a7 | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult serotonergic neuron|adult antennal lobe ... | FBbt_00049526|FBbt_00007395 | neuprint_JRC_Hemibrain_1point1 | 5813078440 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 28 | lLN2R_b(Regional)_R | lLN2R_b(Regional)_R | VFB_jrchk8b5 | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult serotonergic neuron|adult antennal lobe ... | FBbt_00049526|FBbt_00049814|FBbt_00007394 | neuprint_JRC_Hemibrain_1point1 | 1702305987 | JRC2018Unisex|JRC_FlyEM_Hemibrain | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 29 | lLN1_b_R | lLN1_b_R | VFB_jrchk8ab | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN1|adult se... | FBbt_00007395|FBbt_00049526 | neuprint_JRC_Hemibrain_1point1 | 5813054725 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 30 | lLN2S(Star)_R | lLN2S(Star)_R | VFB_jrchk8ba | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN2S|adult s... | FBbt_00049815|FBbt_00049526|FBbt_00007394 | neuprint_JRC_Hemibrain_1point1 | 1732995501 | JRC2018Unisex|JRC_FlyEM_Hemibrain | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 31 | lLN1_b_R | lLN1_b_R | VFB_jrchk8a6 | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult serotonergic neuron|adult antennal lobe ... | FBbt_00049526|FBbt_00007395 | neuprint_JRC_Hemibrain_1point1 | 1640887603 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 32 | lLN2P_a(Patchy)_R | lLN2P_a(Patchy)_R | VFB_jrchk8ao | Entity|Adult|Anatomy|Cell|GABAergic|Individual... | adult local interneuron of the lateral ALl1 ne... | FBbt_00007394|FBbt_00007402|FBbt_00049813 | neuprint_JRC_Hemibrain_1point1 | 2041621893 | JRC2018Unisex|JRC_FlyEM_Hemibrain | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 33 | lLN2S(Star)_R | lLN2S(Star)_R | VFB_jrchk8b7 | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult serotonergic neuron|adult local interneu... | FBbt_00049526|FBbt_00007394|FBbt_00049815 | neuprint_JRC_Hemibrain_1point1 | 1702306037 | JRC2018Unisex|JRC_FlyEM_Hemibrain | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 34 | v2LN30_R | v2LN30_R | VFB_jrchk8e8 | Entity|Adult|Anatomy|Cell|GABAergic|Individual... | adult antennal lobe local neuron v2LN30|GABAer... | FBbt_20003756|FBbt_00007402 | neuprint_JRC_Hemibrain_1point1 | 1671620613 | JRC2018Unisex|JRC_FlyEM_Hemibrain | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 35 | lLN11_R | lLN11_R | VFB_jrchk89d | Entity|Adult|Anatomy|Cell|Cholinergic|Individu... | cholinergic local interneuron of the adult ant... | FBbt_00007403|FBbt_20003745 | neuprint_JRC_Hemibrain_1point1 | 2040301572 | JRC2018Unisex|JRC_FlyEM_Hemibrain | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 36 | lLN1_c_R | lLN1_c_R | VFB_jrchk8ag | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult serotonergic neuron|adult antennal lobe ... | FBbt_00049526|FBbt_00007395 | neuprint_JRC_Hemibrain_1point1 | 1824101645 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 37 | lLN2S(Star)_R | lLN2S(Star)_R | VFB_jrchk8b8 | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN2S|adult l... | FBbt_00049815|FBbt_00007394|FBbt_00049526 | neuprint_JRC_Hemibrain_1point1 | 1640922754 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 38 | lLN2S(Star)_R | lLN2S(Star)_R | VFB_jrchk8b9 | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult serotonergic neuron|adult antennal lobe ... | FBbt_00049526|FBbt_00049815|FBbt_00007394 | neuprint_JRC_Hemibrain_1point1 | 5813069085 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 39 | lLN2P_c(Patchy)_R | lLN2P_c(Patchy)_R | VFB_jrchk8b0 | Entity|Adult|Anatomy|Cell|GABAergic|Individual... | adult local interneuron of the lateral ALl1 ne... | FBbt_00007394|FBbt_00049813|FBbt_00007402 | neuprint_JRC_Hemibrain_1point1 | 2105086391 | JRC2018Unisex|JRC_FlyEM_Hemibrain | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 40 | lLN1_b_R | lLN1_b_R | VFB_jrchk8ac | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult serotonergic neuron|adult antennal lobe ... | FBbt_00049526|FBbt_00007395 | neuprint_JRC_Hemibrain_1point1 | 1610530558 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 41 | lLN2T_e(Tortuous)_R | lLN2T_e(Tortuous)_R | VFB_jrchk8br | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN2T|adult s... | FBbt_00049816|FBbt_00049526 | neuprint_JRC_Hemibrain_1point1 | 1699974843 | JRC2018Unisex|JRC_FlyEM_Hemibrain | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 42 | lLN2T_a(Tortuous)_R | lLN2T_a(Tortuous)_R | VFB_jrchk8bf | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN2T|adult s... | FBbt_00049816|FBbt_00049526 | neuprint_JRC_Hemibrain_1point1 | 5813055277 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 43 | lLN2F_a(Full)_R | lLN2F_a(Full)_R | VFB_jrchk8ak | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult local interneuron of the lateral ALl1 ne... | FBbt_00007394|FBbt_00049526|FBbt_00049812 | neuprint_JRC_Hemibrain_1point1 | 5901218894 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 44 | il3LN6_R | il3LN6_R | VFB_jrchk88v | Entity|Adult|Anatomy|Cell|GABAergic|Individual... | adult serotonergic SE neuron|antennal lobe loc... | FBbt_00047319|FBbt_00047710 | neuprint_JRC_Hemibrain_1point1 | 5813018460 | JRC2018Unisex|JRC_FlyEM_Hemibrain | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 45 | lLN2T_c(Tortuous)_R | lLN2T_c(Tortuous)_R | VFB_jrchk8bo | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN2T | FBbt_00049816 | neuprint_JRC_Hemibrain_1point1 | 1671292719 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 46 | lLN2T_b(Tortuous)_R | lLN2T_b(Tortuous)_R | VFB_jrchk8bm | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult serotonergic neuron|adult antennal lobe ... | FBbt_00049526|FBbt_00049816 | neuprint_JRC_Hemibrain_1point1 | 5813034493 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 47 | l2LN18_R | l2LN18_R | VFB_jrchk891 | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult serotonergic neuron|adult antennal lobe ... | FBbt_00049526|FBbt_20003734 | neuprint_JRC_Hemibrain_1point1 | 5813054773 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 48 | lLN10_R | lLN10_R | VFB_jrchk89b | Entity|Adult|Anatomy|Cell|GABAergic|Individual... | GABAergic local interneuron of the adult anten... | FBbt_00007402|FBbt_20003744 | neuprint_JRC_Hemibrain_1point1 | 1825789179 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 49 | v2LN3b_R | v2LN3b_R | VFB_jrchk8fg | Entity|Adult|Anatomy|Cell|Cholinergic|Individu... | adult antennal lobe local neuron v2LN3B|cholin... | FBbt_20003755|FBbt_00007403 | neuprint_JRC_Hemibrain_1point1 | 1888199872 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 50 | v2LN3b_R | v2LN3b_R | VFB_jrchk8ff | Entity|Adult|Anatomy|Cell|Cholinergic|Individu... | cholinergic local interneuron of the adult ant... | FBbt_00007403|FBbt_20003755 | neuprint_JRC_Hemibrain_1point1 | 5813034455 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 51 | lLN2F_b(Full)_R | lLN2F_b(Full)_R | VFB_jrchk8am | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN2F|adult l... | FBbt_00049812|FBbt_00007394 | neuprint_JRC_Hemibrain_1point1 | 1640909284 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 52 | lLN11_R | lLN11_R | VFB_jrchk89e | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN11 | FBbt_20003745 | neuprint_JRC_Hemibrain_1point1 | 1670278227 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
[6]:
# Find neurons by dataset/paper - on CATMAID
bates = pymaid.find_neurons(annotations='Paper: Bates and Schlegel et al 2020')
bates
INFO : Found 584 neurons matching the search parameters (pymaid)
[6]:
<class 'pymaid.core.CatmaidNeuronList'> containing 584 neurons (0.0B)
| type | name | skeleton_id | n_nodes | n_connectors | n_branches | n_leafs | cable_length | soma | units | |
|---|---|---|---|---|---|---|---|---|---|---|
| 0 | CatmaidNeuron | Uniglomerular mALT DA1 lPN 57316 2863105 ML | 2863104 | NA | NA | NA | NA | NA | NA | 1 nanometer |
| 1 | CatmaidNeuron | Uniglomerular mALT DA3 adPN 57350 HG | 57349 | NA | NA | NA | NA | NA | NA | 1 nanometer |
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
| 582 | CatmaidNeuron | Multiglomerular mlALT vPN VM7d+VM5d+DC4+6 LTS ... | 4624378 | NA | NA | NA | NA | NA | NA | 1 nanometer |
| 583 | CatmaidNeuron | Uniglomerular mALT DL2d adPN 57342 ML | 57341 | NA | NA | NA | NA | NA | NA | 1 nanometer |
[7]:
# Inspect what datasets are available on VFB
ds = vc.neo_query_wrapper.get_datasets(summary=True)
ds_tab = pd.DataFrame.from_records(ds)
ds_tab.sort_values(by=['id'])
[7]:
| label | symbol | id | tags | description | miniref | FlyBase | PMID | DOI | |
|---|---|---|---|---|---|---|---|---|---|
| 76 | EM L1 Andrade et al. 2019 | Andrade2019 | Entity|DataSet|Individual|has_image|L1EM | [L1 EM reconstructed neurons from Andrade et a... | Andrade et al., 2019, Curr. Biol. 29(3): 412--... | FBrf0241389 | 30661802 | 10.1016/j.cub.2018.12.012 | |
| 30 | MBONs and split-GAL4 lines that target them (A... | Aso2014 | Entity|DataSet|Individual|has_image | [] | Aso et al., 2014, eLife 3: e04577 | FBrf0227179 | 25535793 | 10.7554/eLife.04577 | |
| 72 | split-GAL4 lines for dopaminergic neurons (Aso... | AsoRubin2016 | Entity|DataSet|Individual|has_image | [For comparison of the properties of memories ... | Aso and Rubin, 2016, eLife 5: e16135 | FBrf0233230 | 27441388 | 10.7554/eLife.16135 | |
| 165 | EM FAFB Baltruschat et al 2021 | Baltruschat2021 | Entity|DataSet|Individual|has_image|FAFB | [FAFB EM reconstructed neurons from Baltruscha... | Baltruschat et al., 2021, Cell Rep. 34(11): 10... | FBrf0248487 | 33730583 | 10.1016/j.celrep.2021.108871 | |
| 29 | EM L1 Barnes et al., 2022 | Barnes2022 | Entity|DataSet|Individual|L1EM | [L1 EM reconstructed neurons from Barnes et al... | Barnes et al., 2022, PLoS ONE 17(4): e0266064 | FBrf0253082 | 35377898 | 10.1371/journal.pone.0266064 | |
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
| 95 | EM L1 Zarin, Mark et al. 2019 | Zarin2019 | Entity|DataSet|Individual|has_image|L1EM | [L1 EM reconstructed neurons from Zarin, Mark ... | Zarin, Mark et al., 2019 | 10.1101/617977 | |||
| 93 | EM FAFB Zhao et al., 2023 | Zhao2023 | Entity|DataSet|Individual|has_image|FAFB | [FAFB EM reconstructed neurons from Zhao et al... | Zhao et al., 2023 | 10.1101/2022.12.14.520178 | |||
| 47 | EM FAFB Zheng et al 2018 | Zheng2018 | Entity|DataSet|Individual|has_image|FAFB | [FAFB EM reconstructed neurons from Zheng et a... | Zheng et al., 2018, Cell 174(3): 730--743.e22 | FBrf0239557 | 30033368 | 10.1016/j.cell.2018.06.019 | |
| 48 | EM FAFB Zheng et al 2020 (published 2022) | Zheng2020 | Entity|DataSet|Individual|has_image|FAFB | [FAFB EM reconstructed neurons from Zheng et a... | Zheng et al., 2022, Curr. Biol. 32(15): 3334--... | FBrf0254218 | 35797998 | 10.1016/j.cub.2022.06.031 | |
| 83 | Larval motor circuit neurons (Zwart2016) | Zwart2016 | Entity|DataSet|Individual|has_image|L1EM | [Zwart et al. 2016] | Zwart et al., 2016, Neuron 91(3): 615--628 | FBrf0233076 | 27427461 | 10.1016/j.neuron.2016.06.031 |
166 rows × 9 columns
[8]:
sayin_tab = pd.DataFrame.from_records(vc.get_instances_by_dataset('Sayin2019', summary=True))
sayin_tab
[8]:
| label | symbol | id | tags | parents_label | parents_id | data_source | accession | templates | dataset | license | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | OA-VPM3 (FAFB:1329078) | VFB_001001dr | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | octopaminergic VPM3 neuron | FBbt_00110151 | catmaid_fafb | 1329078 | JRC2018Unisex | Sayin2019 | https://creativecommons.org/licenses/by-sa/4.0... | |
| 1 | OA-VPM4 (FAFB:1191261) | VFB_001001dq | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | octopaminergic VPM4 neuron | FBbt_00110152 | catmaid_fafb | 1191261 | JRC2018Unisex | Sayin2019 | https://creativecommons.org/licenses/by-sa/4.0... |
[9]:
vc.get_connected_neurons_by_type(upstream_type='LNd', downstream_type='adult descending neuron', weight=20)
[9]:
| upstream_neuron_id | upstream_neuron_name | weight | downstream_neuron_id | downstream_neuron_name | upstream_class | downstream_class | up_data_source | up_accession | down_source | down_accession | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | VFB_jrchjzxx | LNd_R (FlyEM-HB:5813021192) | 25 | VFB_jrchjthm | DNp27_R (FlyEM-HB:1072063538) | LNd neuron | descending neuron of the posterior brain DNp27... | None | None | None | None |
[10]:
# Intra pacemaker neuron neuron connections
vc.get_connected_neurons_by_type(upstream_type='pacemaker neuron', downstream_type='pacemaker neuron', weight=20)
[10]:
| upstream_neuron_id | upstream_neuron_name | weight | downstream_neuron_id | downstream_neuron_name | upstream_class | downstream_class | up_data_source | up_accession | down_source | down_accession | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | VFB_jrchk8e0 | 5th s-LNv (FlyEM-HB:511051477) | 25 | VFB_jrchjzxx | LNd_R (FlyEM-HB:5813021192) | adult cholinergic neuron|adult s-LNv neuron | LNd neuron | None | None | None | None |
| 1 | VFB_jrchjzxy | LNd_R (FlyEM-HB:5813069648) | 21 | VFB_jrchjzxx | LNd_R (FlyEM-HB:5813021192) | adult cholinergic neuron|LNd neuron | LNd neuron | None | None | None | None |
| 2 | VFB_jrchjtf3 | DN1pA_R (FlyEM-HB:387166379) | 30 | VFB_jrchjzxy | LNd_R (FlyEM-HB:5813069648) | ventro-contralateral-projecting DN1p neuron|ad... | adult cholinergic neuron|LNd neuron | None | None | None | None |
| 3 | VFB_jrchjtex | DN1a_R (FlyEM-HB:264083994) | 79 | VFB_jrchjzxy | LNd_R (FlyEM-HB:5813069648) | DN1a neuron | adult cholinergic neuron|LNd neuron | None | None | None | None |
| 4 | VFB_jrchjtf1 | DN1pA_R (FlyEM-HB:325529237) | 30 | VFB_jrchjzxy | LNd_R (FlyEM-HB:5813069648) | adult glutamatergic neuron|ventro-contralatera... | adult cholinergic neuron|LNd neuron | None | None | None | None |
| 5 | VFB_jrchjtey | DN1a_R (FlyEM-HB:5813022274) | 75 | VFB_jrchjzxy | LNd_R (FlyEM-HB:5813069648) | DN1a neuron | adult cholinergic neuron|LNd neuron | None | None | None | None |
| 6 | VFB_jrchk8e0 | 5th s-LNv (FlyEM-HB:511051477) | 40 | VFB_jrchjzxy | LNd_R (FlyEM-HB:5813069648) | adult cholinergic neuron|adult s-LNv neuron | adult cholinergic neuron|LNd neuron | None | None | None | None |
| 7 | VFB_jrchjtf2 | DN1pA_R (FlyEM-HB:387944118) | 34 | VFB_jrchjzxy | LNd_R (FlyEM-HB:5813069648) | adult glutamatergic neuron|ventro-contralatera... | adult cholinergic neuron|LNd neuron | None | None | None | None |
| 8 | VFB_jrchjtf0 | DN1pA_R (FlyEM-HB:324846570) | 37 | VFB_jrchjzxy | LNd_R (FlyEM-HB:5813069648) | ventro-contralateral-projecting DN1p neuron|ad... | adult cholinergic neuron|LNd neuron | None | None | None | None |
| 9 | VFB_jrchjzxy | LNd_R (FlyEM-HB:5813069648) | 29 | VFB_jrchjzxw | LNd_R (FlyEM-HB:5813056917) | adult cholinergic neuron|LNd neuron | adult cholinergic neuron|LNd neuron | None | None | None | None |
| 10 | VFB_jrchjtf0 | DN1pA_R (FlyEM-HB:324846570) | 25 | VFB_jrchk8e0 | 5th s-LNv (FlyEM-HB:511051477) | ventro-contralateral-projecting DN1p neuron|ad... | adult cholinergic neuron|adult s-LNv neuron | None | None | None | None |
| 11 | VFB_jrchjtf2 | DN1pA_R (FlyEM-HB:387944118) | 22 | VFB_jrchk8e0 | 5th s-LNv (FlyEM-HB:511051477) | adult glutamatergic neuron|ventro-contralatera... | adult cholinergic neuron|adult s-LNv neuron | None | None | None | None |
| 12 | VFB_jrchjzxy | LNd_R (FlyEM-HB:5813069648) | 37 | VFB_jrchk8e0 | 5th s-LNv (FlyEM-HB:511051477) | adult cholinergic neuron|LNd neuron | adult cholinergic neuron|adult s-LNv neuron | None | None | None | None |
| 13 | VFB_jrchjtey | DN1a_R (FlyEM-HB:5813022274) | 63 | VFB_jrchk8e0 | 5th s-LNv (FlyEM-HB:511051477) | DN1a neuron | adult cholinergic neuron|adult s-LNv neuron | None | None | None | None |
| 14 | VFB_jrchjtf1 | DN1pA_R (FlyEM-HB:325529237) | 33 | VFB_jrchk8e0 | 5th s-LNv (FlyEM-HB:511051477) | adult glutamatergic neuron|ventro-contralatera... | adult cholinergic neuron|adult s-LNv neuron | None | None | None | None |
| 15 | VFB_jrchjtez | DN1pA_R (FlyEM-HB:5813010153) | 25 | VFB_jrchk8e0 | 5th s-LNv (FlyEM-HB:511051477) | adult glutamatergic neuron|ventro-contralatera... | adult cholinergic neuron|adult s-LNv neuron | None | None | None | None |
| 16 | VFB_jrchjtex | DN1a_R (FlyEM-HB:264083994) | 55 | VFB_jrchk8e0 | 5th s-LNv (FlyEM-HB:511051477) | DN1a neuron | adult cholinergic neuron|adult s-LNv neuron | None | None | None | None |
| 17 | VFB_jrchjtf3 | DN1pA_R (FlyEM-HB:387166379) | 25 | VFB_jrchk8e0 | 5th s-LNv (FlyEM-HB:511051477) | ventro-contralateral-projecting DN1p neuron|ad... | adult cholinergic neuron|adult s-LNv neuron | None | None | None | None |
| 18 | VFB_jrchk089 | LPN_R (FlyEM-HB:480029788) | 43 | VFB_jrchk08a | LPN_R (FlyEM-HB:450034902) | adult LP neuron|adult dopaminergic neuron | adult LP neuron | None | None | None | None |
| 19 | VFB_jrchk08a | LPN_R (FlyEM-HB:450034902) | 30 | VFB_jrchk089 | LPN_R (FlyEM-HB:480029788) | adult LP neuron | adult LP neuron|adult dopaminergic neuron | None | None | None | None |
[11]:
vc.get_connected_neurons_by_type(upstream_type='adult neuron', downstream_type='adult Drosulfakinin neuron', weight=20)
[11]:
| upstream_neuron_id | upstream_neuron_name | weight | downstream_neuron_id | downstream_neuron_name | upstream_class | downstream_class | up_data_source | up_accession | down_source | down_accession | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | VFB_jrchjrmu | AVLP053_R (FlyEM-HB:5813021533) | 124 | VFB_jrchjti2 | DSKMP1A_R (FlyEM-HB:1135837629) | adult anterior ventrolateral protocerebrum neu... | adult octopaminergic neuron|adult Drosulfakini... | None | None | None | None |
| 1 | VFB_jrchjs4y | AVLP340_R (FlyEM-HB:1260949492) | 29 | VFB_jrchjti2 | DSKMP1A_R (FlyEM-HB:1135837629) | adult anterior ventrolateral protocerebrum neu... | adult octopaminergic neuron|adult Drosulfakini... | None | None | None | None |
| 2 | VFB_jrchk5in | SLP130_R (FlyEM-HB:456847100) | 94 | VFB_jrchjti2 | DSKMP1A_R (FlyEM-HB:1135837629) | adult superior lateral protocerebrum neuron 130 | adult octopaminergic neuron|adult Drosulfakini... | None | None | None | None |
| 3 | VFB_jrchjsi7 | AVLP580_L (FlyEM-HB:1097642017) | 91 | VFB_jrchjti2 | DSKMP1A_R (FlyEM-HB:1135837629) | adult glutamatergic neuron|adult anterior vent... | adult octopaminergic neuron|adult Drosulfakini... | None | None | None | None |
| 4 | VFB_jrchjsi9 | AVLP580_L (FlyEM-HB:5812991151) | 64 | VFB_jrchjti2 | DSKMP1A_R (FlyEM-HB:1135837629) | adult anterior ventrolateral protocerebrum neu... | adult octopaminergic neuron|adult Drosulfakini... | None | None | None | None |
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
| 56 | VFB_jrchk5zh | SLP384_R (FlyEM-HB:482702027) | 20 | VFB_jrchjti6 | DSKMP3_R (FlyEM-HB:327937328) | adult superior lateral protocerebrum neuron 384 | adult cholinergic neuron|adult Drosulfakinin M... | None | None | None | None |
| 57 | VFB_jrchk5ch | SLP031_R (FlyEM-HB:5813026615) | 59 | VFB_jrchjti6 | DSKMP3_R (FlyEM-HB:327937328) | adult superior lateral protocerebrum neuron 031 | adult cholinergic neuron|adult Drosulfakinin M... | None | None | None | None |
| 58 | VFB_jrchk0fd | MBON23(a2sp)_R (FlyEM-HB:423382015) | 21 | VFB_jrchjti6 | DSKMP3_R (FlyEM-HB:327937328) | mushroom body output neuron 23|adult cholinerg... | adult cholinergic neuron|adult Drosulfakinin M... | None | None | None | None |
| 59 | VFB_jrchjz3e | LHAV6h1_R (FlyEM-HB:672960748) | 27 | VFB_jrchjti6 | DSKMP3_R (FlyEM-HB:327937328) | adult glutamatergic neuron|adult lateral horn ... | adult cholinergic neuron|adult Drosulfakinin M... | None | None | None | None |
| 60 | VFB_jrchjyu7 | LHAV3j1_R (FlyEM-HB:297851977) | 24 | VFB_jrchjti6 | DSKMP3_R (FlyEM-HB:327937328) | adult lateral horn AV3j1 neuron|adult choliner... | adult cholinergic neuron|adult Drosulfakinin M... | None | None | None | None |
61 rows × 11 columns
Transcriptomics Queries
Finding single cell transcriptomics data for a given cell type
[12]:
profile = vc.get_transcriptomic_profile(cell_type = 'adult olfactory receptor neuron')
print(profile.head())
cell_type cell_type_id sample_sex \
0 adult antennal olfactory receptor neuron FBbt_00007352 female organism
1 adult antennal olfactory receptor neuron FBbt_00007352 male organism
2 adult antennal olfactory receptor neuron FBbt_00007352 None
3 adult antennal olfactory receptor neuron FBbt_00007352 female organism
4 adult antennal olfactory receptor neuron FBbt_00007352 male organism
sample_tissue \
0 [antenna, adult corpus cardiacum, antenna, adu...
1 [wing, haltere, adult, adult pars intercerebra...
2 [antenna, proboscis, male reproductive system,...
3 [antenna, adult corpus cardiacum, antenna, adu...
4 [wing, haltere, adult, adult pars intercerebra...
ref gene gene_id \
0 Li et al., 2022, Science 375(6584): eabk2432 14-3-3ε FBgn0020238
1 Li et al., 2022, Science 375(6584): eabk2432 14-3-3ε FBgn0020238
2 Li et al., 2022, Science 375(6584): eabk2432 14-3-3ε FBgn0020238
3 Li et al., 2022, Science 375(6584): eabk2432 14-3-3ζ FBgn0004907
4 Li et al., 2022, Science 375(6584): eabk2432 14-3-3ζ FBgn0004907
function extent level
0 [] 0.609756 1395.2687
1 [] 0.625000 1317.0752
2 [] 0.618605 1340.0747
3 [] 0.725610 1721.6161
4 [] 0.640625 1561.3594
These results can be filtered by gene function - first find available gene functions
[13]:
functions = vc.get_gene_function_filters()
print(functions)
['Acetylcholine_receptor', 'Calcium_binding', 'Carbohydrate_binding', 'Chaperone', 'Cytoskeleton_binding', 'DNA_binding', 'Dopamine_receptor', 'Enzyme', 'GABA_receptor', 'GPCR', 'Glutamate_receptor', 'Gustatory_receptor', 'Histamine_receptor', 'Hormone', 'Ion_channel', 'Ligand', 'Lipid_binding', 'Mechanosensory_ion_channel', 'Metal_ion_binding', 'Neuropeptide', 'Neurotransmitter_receptor', 'Octopamine_receptor', 'Odorant_binding', 'Olfactory_receptor', 'Peptide_or_protein_hormone_receptor', 'Photoreceptor', 'RNA_binding', 'Receptor', 'Regulator', 'Serotonin_receptor', 'Small_molecule_binding', 'Structural_molecule', 'Thermosensory_ion_channel', 'Transcription_factor', 'Transporter', 'Tyramine_receptor']
Then run transcriptomics query speicfying a gene function to filter on
[14]:
filtered_profile = vc.get_transcriptomic_profile(cell_type = 'adult olfactory receptor neuron', gene_type='Olfactory_receptor')
print(filtered_profile.head())
cell_type cell_type_id sample_sex \
0 adult antennal olfactory receptor neuron FBbt_00007352 female organism
1 adult antennal olfactory receptor neuron FBbt_00007352 male organism
2 adult antennal olfactory receptor neuron FBbt_00007352 None
3 adult olfactory receptor neuron FBbt_00007386 female organism
4 adult olfactory receptor neuron FBbt_00007386 male organism
sample_tissue \
0 [antenna, adult corpus cardiacum, antenna, adu...
1 [wing, haltere, adult, adult pars intercerebra...
2 [antenna, proboscis, male reproductive system,...
3 [adult head]
4 [adult head]
ref gene gene_id \
0 Li et al., 2022, Science 375(6584): eabk2432 Orco FBgn0037324
1 Li et al., 2022, Science 375(6584): eabk2432 Orco FBgn0037324
2 Li et al., 2022, Science 375(6584): eabk2432 Orco FBgn0037324
3 Li et al., 2022, Science 375(6584): eabk2432 CG42260 FBgn0259145
4 Li et al., 2022, Science 375(6584): eabk2432 CG42260 FBgn0259145
function extent level
0 [Olfactory_receptor, Receptor, Ion_channel, Od... 0.469512 1800.4366
1 [Olfactory_receptor, Receptor, Ion_channel, Od... 0.432292 1710.8816
2 [Olfactory_receptor, Receptor, Ion_channel, Od... 0.479070 1633.1283
3 [Small_molecule_binding, Olfactory_receptor, R... 0.201531 1282.2848
4 [Small_molecule_binding, Olfactory_receptor, R... 0.201299 1171.4191