Discovery
Required packages: vfb-connect and python-catmaid (pymaid & navis)
[1]:
!pip install vfb-connect --upgrade
!pip install python-catmaid --upgrade
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Collecting navis>=1.0.0 (from python-catmaid)
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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}')
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:
|85d9019ddd3443169b3090388f2825a3| |44de8341f35640d383557750be8534a1|
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(PVM02)_L (FlyEM-HB:1260833150) | 1260833150 | VFB_jrchjti3 | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult Drosulfakinin neuron | FBbt_00048999 | neuprint_JRC_Hemibrain_1point1 | 1260833150 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 1 | DSKMP3_R (FlyEM-HB:327937328) | 327937328 | VFB_jrchjti6 | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult Drosulfakinin neuron | FBbt_00048999 | neuprint_JRC_Hemibrain_1point1 | 327937328 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 2 | DSKMP3_R (FlyEM-HB:328559607) | 328559607 | VFB_jrchjti7 | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult Drosulfakinin neuron | FBbt_00048999 | neuprint_JRC_Hemibrain_1point1 | 328559607 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 3 | DSKMP1A_R (FlyEM-HB:1135837629) | 1135837629 | VFB_jrchjti2 | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult Drosulfakinin neuron | FBbt_00048999 | neuprint_JRC_Hemibrain_1point1 | 1135837629 | JRC2018Unisex|JRC_FlyEM_Hemibrain | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 4 | DSKMP1B_R (FlyEM-HB:1352077058) | 1352077058 | VFB_jrchjti4 | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult Drosulfakinin neuron | FBbt_00048999 | neuprint_JRC_Hemibrain_1point1 | 1352077058 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 5 | DSKMP1B(PVM02)_L (FlyEM-HB:1011184205) | 1011184205 | VFB_jrchjti5 | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult Drosulfakinin neuron | FBbt_00048999 | neuprint_JRC_Hemibrain_1point1 | 1011184205 | JRC_FlyEM_Hemibrain|JRC2018Unisex | 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: 159
[4]:
| label | symbol | id | tags | parents_label | parents_id | data_source | accession | templates | dataset | license | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | ORN_DA1_R (FlyEM-HB:1703682799) | 1703682799 | VFB_jrchk15e | Entity|Adult|Anatomy|Cell|Chemosensory_system|... | adult olfactory receptor neuron Or67d | FBbt_00067031 | neuprint_JRC_Hemibrain_1point1 | 1703682799 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 1 | ORN_DL4_R (FlyEM-HB:1671271059) | 1671271059 | VFB_jrchk1km | Entity|Adult|Anatomy|Cell|Chemosensory_system|... | adult olfactory receptor neuron Or49a/85f | FBbt_00067055 | neuprint_JRC_Hemibrain_1point1 | 1671271059 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 2 | ORN_DA1_R (FlyEM-HB:1735054607) | 1735054607 | VFB_jrchk13v | Entity|Adult|Anatomy|Cell|Chemosensory_system|... | adult olfactory receptor neuron Or67d | FBbt_00067031 | neuprint_JRC_Hemibrain_1point1 | 1735054607 | JRC2018Unisex|JRC_FlyEM_Hemibrain | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 3 | v2LN35_R (FlyEM-HB:1733056086) | 1733056086 | VFB_jrchk8ew | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron v2LN35 | 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 (FlyEM-HB:5813032595) | 5813032595 | VFB_jrchk8bd | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN2T | FBbt_00049816 | neuprint_JRC_Hemibrain_1point1 | 5813032595 | JRC2018Unisex|JRC_FlyEM_Hemibrain | 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'",
summary=True)
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 (FlyEM-HB:1733056086) | 1733056086 | VFB_jrchk8ew | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron v2LN35 | 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 (FlyEM-HB:5813032595) | 5813032595 | VFB_jrchk8bd | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN2T | FBbt_00049816 | neuprint_JRC_Hemibrain_1point1 | 5813032595 | JRC2018Unisex|JRC_FlyEM_Hemibrain | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 2 | lLN2T_d(Tortuous)_R (FlyEM-HB:1667251683) | 1667251683 | VFB_jrchk8bp | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN2T | FBbt_00049816 | neuprint_JRC_Hemibrain_1point1 | 1667251683 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 3 | lLN2P_b(Patchy)_R (FlyEM-HB:1946178096) | 1946178096 | VFB_jrchk8au | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN2P | FBbt_00049813 | neuprint_JRC_Hemibrain_1point1 | 1946178096 | JRC2018Unisex|JRC_FlyEM_Hemibrain | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 4 | lLN2T_a(Tortuous)_R (FlyEM-HB:1762354941) | 1762354941 | VFB_jrchk8bg | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN2T | FBbt_00049816 | neuprint_JRC_Hemibrain_1point1 | 1762354941 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 5 | lLN1_c_R (FlyEM-HB:1547454812) | 1547454812 | VFB_jrchk8ai | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN1 | FBbt_00007395 | neuprint_JRC_Hemibrain_1point1 | 1547454812 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 6 | lLN1_b_R (FlyEM-HB:5813054622) | 5813054622 | VFB_jrchk8a8 | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN1 | FBbt_00007395 | neuprint_JRC_Hemibrain_1point1 | 5813054622 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 7 | lLN2T_a(Tortuous)_R (FlyEM-HB:5813056598) | 5813056598 | VFB_jrchk8bi | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN2T | FBbt_00049816 | neuprint_JRC_Hemibrain_1point1 | 5813056598 | JRC2018Unisex|JRC_FlyEM_Hemibrain | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 8 | lLN16b_R (FlyEM-HB:1887168462) | 1887168462 | VFB_jrchk89w | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN16B | FBbt_20003752 | neuprint_JRC_Hemibrain_1point1 | 1887168462 | JRC2018Unisex|JRC_FlyEM_Hemibrain | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 9 | lLN2T_e(Tortuous)_R (FlyEM-HB:1640922516) | 1640922516 | VFB_jrchk8bs | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN2T | FBbt_00049816 | neuprint_JRC_Hemibrain_1point1 | 1640922516 | JRC2018Unisex|JRC_FlyEM_Hemibrain | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 10 | lLN1_b_R (FlyEM-HB:1642623277) | 1642623277 | VFB_jrchk8ad | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN1 | FBbt_00007395 | neuprint_JRC_Hemibrain_1point1 | 1642623277 | JRC2018Unisex|JRC_FlyEM_Hemibrain | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 11 | lLN1_c_R (FlyEM-HB:1702651358) | 1702651358 | VFB_jrchk8aj | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN1 | FBbt_00007395 | neuprint_JRC_Hemibrain_1point1 | 1702651358 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 12 | lLN2F_a(Full)_R (FlyEM-HB:1670287030) | 1670287030 | VFB_jrchk8al | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN2F | FBbt_00049812 | neuprint_JRC_Hemibrain_1point1 | 1670287030 | JRC2018Unisex|JRC_FlyEM_Hemibrain | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 13 | lLN1_a_R (FlyEM-HB:5813130064) | 5813130064 | VFB_jrchk8a4 | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN1 | FBbt_00007395 | neuprint_JRC_Hemibrain_1point1 | 5813130064 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 14 | lLN1_b_R (FlyEM-HB:5813069055) | 5813069055 | VFB_jrchk8aa | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN1 | FBbt_00007395 | neuprint_JRC_Hemibrain_1point1 | 5813069055 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 15 | lLN2S(Star)_R (FlyEM-HB:1762359683) | 1762359683 | VFB_jrchk8bc | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN2S | FBbt_00049815 | neuprint_JRC_Hemibrain_1point1 | 1762359683 | JRC2018Unisex|JRC_FlyEM_Hemibrain | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 16 | lLN1_c_R (FlyEM-HB:1578826464) | 1578826464 | VFB_jrchk8ah | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN1 | FBbt_00007395 | neuprint_JRC_Hemibrain_1point1 | 1578826464 | JRC2018Unisex|JRC_FlyEM_Hemibrain | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 17 | lLN2F_b(Full)_R (FlyEM-HB:5813024698) | 5813024698 | VFB_jrchk8an | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN2F | FBbt_00049812 | neuprint_JRC_Hemibrain_1point1 | 5813024698 | JRC2018Unisex|JRC_FlyEM_Hemibrain | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 18 | lLN2R_b(Regional)_R (FlyEM-HB:5813076969) | 5813076969 | VFB_jrchk8b6 | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN2R | FBbt_00049814 | neuprint_JRC_Hemibrain_1point1 | 5813076969 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 19 | lLN1_b_R (FlyEM-HB:5813054777) | 5813054777 | VFB_jrchk8a9 | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN1 | FBbt_00007395 | neuprint_JRC_Hemibrain_1point1 | 5813054777 | JRC2018Unisex|JRC_FlyEM_Hemibrain | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 20 | lLN2T_b(Tortuous)_R (FlyEM-HB:1640572741) | 1640572741 | VFB_jrchk8bl | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN2T | FBbt_00049816 | neuprint_JRC_Hemibrain_1point1 | 1640572741 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 21 | lLN1_c_R (FlyEM-HB:5813062199) | 5813062199 | VFB_jrchk8af | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN1 | FBbt_00007395 | neuprint_JRC_Hemibrain_1point1 | 5813062199 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 22 | lLN16a_R (FlyEM-HB:1702318692) | 1702318692 | VFB_jrchk89t | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN16A | FBbt_20003751 | neuprint_JRC_Hemibrain_1point1 | 1702318692 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 23 | lLN12a_R (FlyEM-HB:1826445251) | 1826445251 | VFB_jrchk89g | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN12A | FBbt_20003746 | neuprint_JRC_Hemibrain_1point1 | 1826445251 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 24 | lLN1_c_R (FlyEM-HB:5813047691) | 5813047691 | VFB_jrchk8ae | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN1 | 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 (FlyEM-HB:5813054726) | 5813054726 | VFB_jrchk8bh | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN2T | FBbt_00049816 | neuprint_JRC_Hemibrain_1point1 | 5813054726 | JRC2018Unisex|JRC_FlyEM_Hemibrain | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 26 | lLN2S(Star)_R (FlyEM-HB:1670627928) | 1670627928 | VFB_jrchk8bb | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN2S | FBbt_00049815 | neuprint_JRC_Hemibrain_1point1 | 1670627928 | JRC2018Unisex|JRC_FlyEM_Hemibrain | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 27 | lLN1_b_R (FlyEM-HB:5813078440) | 5813078440 | VFB_jrchk8a7 | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN1 | 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 (FlyEM-HB:1702305987) | 1702305987 | VFB_jrchk8b5 | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN2R | FBbt_00049814 | neuprint_JRC_Hemibrain_1point1 | 1702305987 | JRC2018Unisex|JRC_FlyEM_Hemibrain | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 29 | lLN1_b_R (FlyEM-HB:5813054725) | 5813054725 | VFB_jrchk8ab | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN1 | FBbt_00007395 | neuprint_JRC_Hemibrain_1point1 | 5813054725 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 30 | lLN2S(Star)_R (FlyEM-HB:1732995501) | 1732995501 | VFB_jrchk8ba | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN2S | FBbt_00049815 | neuprint_JRC_Hemibrain_1point1 | 1732995501 | JRC2018Unisex|JRC_FlyEM_Hemibrain | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 31 | lLN1_b_R (FlyEM-HB:1640887603) | 1640887603 | VFB_jrchk8a6 | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN1 | 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 (FlyEM-HB:2041621893) | 2041621893 | VFB_jrchk8ao | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN2P | FBbt_00049813 | neuprint_JRC_Hemibrain_1point1 | 2041621893 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 33 | lLN2S(Star)_R (FlyEM-HB:1702306037) | 1702306037 | VFB_jrchk8b7 | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN2S | FBbt_00049815 | neuprint_JRC_Hemibrain_1point1 | 1702306037 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 34 | v2LN30_R (FlyEM-HB:1671620613) | 1671620613 | VFB_jrchk8e8 | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron v2LN30 | FBbt_20003756 | neuprint_JRC_Hemibrain_1point1 | 1671620613 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 35 | lLN11_R (FlyEM-HB:2040301572) | 2040301572 | VFB_jrchk89d | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN11 | FBbt_20003745 | neuprint_JRC_Hemibrain_1point1 | 2040301572 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 36 | lLN1_c_R (FlyEM-HB:1824101645) | 1824101645 | VFB_jrchk8ag | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN1 | FBbt_00007395 | neuprint_JRC_Hemibrain_1point1 | 1824101645 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 37 | lLN2S(Star)_R (FlyEM-HB:1640922754) | 1640922754 | VFB_jrchk8b8 | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN2S | FBbt_00049815 | neuprint_JRC_Hemibrain_1point1 | 1640922754 | JRC2018Unisex|JRC_FlyEM_Hemibrain | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 38 | lLN2S(Star)_R (FlyEM-HB:5813069085) | 5813069085 | VFB_jrchk8b9 | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN2S | FBbt_00049815 | neuprint_JRC_Hemibrain_1point1 | 5813069085 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 39 | lLN2P_c(Patchy)_R (FlyEM-HB:2105086391) | 2105086391 | VFB_jrchk8b0 | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN2P | FBbt_00049813 | neuprint_JRC_Hemibrain_1point1 | 2105086391 | JRC2018Unisex|JRC_FlyEM_Hemibrain | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 40 | lLN1_b_R (FlyEM-HB:1610530558) | 1610530558 | VFB_jrchk8ac | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN1 | 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 (FlyEM-HB:1699974843) | 1699974843 | VFB_jrchk8br | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN2T | FBbt_00049816 | neuprint_JRC_Hemibrain_1point1 | 1699974843 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 42 | lLN2T_a(Tortuous)_R (FlyEM-HB:5813055277) | 5813055277 | VFB_jrchk8bf | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN2T | FBbt_00049816 | neuprint_JRC_Hemibrain_1point1 | 5813055277 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 43 | lLN2F_a(Full)_R (FlyEM-HB:5901218894) | 5901218894 | VFB_jrchk8ak | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN2F | FBbt_00049812 | neuprint_JRC_Hemibrain_1point1 | 5901218894 | JRC2018Unisex|JRC_FlyEM_Hemibrain | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 44 | il3LN6_R (FlyEM-HB:5813018460) | 5813018460 | VFB_jrchk88v | Entity|Adult|Anatomy|Cell|GABAergic|Individual... | antennal lobe local neuron 6 | FBbt_00047710 | neuprint_JRC_Hemibrain_1point1 | 5813018460 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 45 | lLN2T_c(Tortuous)_R (FlyEM-HB:1671292719) | 1671292719 | VFB_jrchk8bo | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN2T | FBbt_00049816 | neuprint_JRC_Hemibrain_1point1 | 1671292719 | JRC2018Unisex|JRC_FlyEM_Hemibrain | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 46 | lLN2T_b(Tortuous)_R (FlyEM-HB:5813034493) | 5813034493 | VFB_jrchk8bm | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN2T | FBbt_00049816 | neuprint_JRC_Hemibrain_1point1 | 5813034493 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 47 | l2LN18_R (FlyEM-HB:5813054773) | 5813054773 | VFB_jrchk891 | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron l2LN18 | FBbt_20003734 | neuprint_JRC_Hemibrain_1point1 | 5813054773 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 48 | lLN10_R (FlyEM-HB:1825789179) | 1825789179 | VFB_jrchk89b | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN10 | FBbt_20003744 | neuprint_JRC_Hemibrain_1point1 | 1825789179 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 49 | v2LN3b_R (FlyEM-HB:1888199872) | 1888199872 | VFB_jrchk8fg | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron v2LN3B | FBbt_20003755 | neuprint_JRC_Hemibrain_1point1 | 1888199872 | JRC2018Unisex|JRC_FlyEM_Hemibrain | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 50 | v2LN3b_R (FlyEM-HB:5813034455) | 5813034455 | VFB_jrchk8ff | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron v2LN3B | FBbt_20003755 | neuprint_JRC_Hemibrain_1point1 | 5813034455 | JRC2018Unisex|JRC_FlyEM_Hemibrain | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 51 | lLN2F_b(Full)_R (FlyEM-HB:1640909284) | 1640909284 | VFB_jrchk8am | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN2F | FBbt_00049812 | neuprint_JRC_Hemibrain_1point1 | 1640909284 | JRC_FlyEM_Hemibrain|JRC2018Unisex | Xu2020NeuronsV1point1 | https://creativecommons.org/licenses/by/4.0/le... |
| 52 | lLN11_R (FlyEM-HB:1670278227) | 1670278227 | VFB_jrchk89e | Entity|Adult|Anatomy|Cell|Individual|Nervous_s... | adult antennal lobe local neuron lLN11 | FBbt_20003745 | neuprint_JRC_Hemibrain_1point1 | 1670278227 | JRC2018Unisex|JRC_FlyEM_Hemibrain | 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 | |
|---|---|---|---|---|---|---|---|---|---|
| 67 | EM L1 Andrade et al. 2019 | Andrade2019 | Entity|DataSet|Individual|has_image | [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 | |
| 29 | 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 | |
| 64 | 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 | |
| 144 | EM FAFB Baltruschat et al 2021 | Baltruschat2021 | Entity|DataSet|Individual|has_image | [FAFB EM reconstructed neurons from Baltruscha... | Baltruschat et al., 2021, Cell Rep. 34(11): 10... | FBrf0248487 | 33730583 | 10.1016/j.celrep.2021.108871 | |
| 28 | 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 | |
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
| 88 | EM L1 Zarin, Mark et al. 2019 | Zarin2019 | Entity|DataSet|Individual|has_image | [L1 EM reconstructed neurons from Zarin, Mark ... | Zarin, Mark et al., 2019 | 10.1101/617977 | |||
| 86 | EM FAFB Zhao et al., 2023 | Zhao2023 | Entity|DataSet|Individual|FAFB | [FAFB EM reconstructed neurons from Zhao et al... | |||||
| 43 | EM FAFB Zheng et al 2018 | Zheng2018 | Entity|DataSet|Individual|has_image | [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 | |
| 44 | EM FAFB Zheng et al 2020 (published 2022) | Zheng2020 | Entity|DataSet|Individual|has_image | [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 | |
| 74 | Larval motor circuit neurons (Zwart2016) | Zwart2016 | Entity|DataSet|Individual|has_image | [Zwart et al. 2016] | Zwart et al., 2016, Neuron 91(3): 615--628 | FBrf0233076 | 27427461 | 10.1016/j.neuron.2016.06.031 |
145 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_jrchk089 | LPN_R (FlyEM-HB:480029788) | 43 | VFB_jrchk08a | LPN_R (FlyEM-HB:450034902) | LP neuron | LP neuron | None | None | None | None |
| 1 | VFB_jrchk08a | LPN_R (FlyEM-HB:450034902) | 30 | VFB_jrchk089 | LPN_R (FlyEM-HB:480029788) | LP neuron | LP neuron | None | None | None | None |
| 2 | VFB_jrchjtf3 | DN1pA_R (FlyEM-HB:387166379) | 30 | VFB_jrchjzxy | LNd_R (FlyEM-HB:5813069648) | DN1p neuron | LNd neuron | None | None | None | None |
| 3 | VFB_jrchjtf1 | DN1pA_R (FlyEM-HB:325529237) | 30 | VFB_jrchjzxy | LNd_R (FlyEM-HB:5813069648) | DN1p neuron | LNd neuron | None | None | None | None |
| 4 | VFB_jrchjtey | DN1a_R (FlyEM-HB:5813022274) | 75 | VFB_jrchjzxy | LNd_R (FlyEM-HB:5813069648) | DN1a neuron | LNd neuron | None | None | None | None |
| 5 | VFB_jrchjtex | DN1a_R (FlyEM-HB:264083994) | 79 | VFB_jrchjzxy | LNd_R (FlyEM-HB:5813069648) | DN1a neuron | LNd neuron | None | None | None | None |
| 6 | VFB_jrchjtf2 | DN1pA_R (FlyEM-HB:387944118) | 34 | VFB_jrchjzxy | LNd_R (FlyEM-HB:5813069648) | DN1p neuron | LNd neuron | None | None | None | None |
| 7 | VFB_jrchk8e0 | 5th s-LNv (FlyEM-HB:511051477) | 40 | VFB_jrchjzxy | LNd_R (FlyEM-HB:5813069648) | s-LNv neuron | LNd neuron | None | None | None | None |
| 8 | VFB_jrchjtf0 | DN1pA_R (FlyEM-HB:324846570) | 37 | VFB_jrchjzxy | LNd_R (FlyEM-HB:5813069648) | DN1p neuron | LNd neuron | None | None | None | None |
| 9 | VFB_jrchjzxy | LNd_R (FlyEM-HB:5813069648) | 29 | VFB_jrchjzxw | LNd_R (FlyEM-HB:5813056917) | LNd neuron | LNd neuron | None | None | None | None |
| 10 | VFB_jrchjzxy | LNd_R (FlyEM-HB:5813069648) | 21 | VFB_jrchjzxx | LNd_R (FlyEM-HB:5813021192) | LNd neuron | LNd neuron | None | None | None | None |
| 11 | VFB_jrchk8e0 | 5th s-LNv (FlyEM-HB:511051477) | 25 | VFB_jrchjzxx | LNd_R (FlyEM-HB:5813021192) | s-LNv neuron | LNd neuron | None | None | None | None |
| 12 | VFB_jrchjtf2 | DN1pA_R (FlyEM-HB:387944118) | 22 | VFB_jrchk8e0 | 5th s-LNv (FlyEM-HB:511051477) | DN1p neuron | s-LNv neuron | None | None | None | None |
| 13 | VFB_jrchjtez | DN1pA_R (FlyEM-HB:5813010153) | 25 | VFB_jrchk8e0 | 5th s-LNv (FlyEM-HB:511051477) | DN1p neuron | s-LNv neuron | None | None | None | None |
| 14 | VFB_jrchjtex | DN1a_R (FlyEM-HB:264083994) | 55 | VFB_jrchk8e0 | 5th s-LNv (FlyEM-HB:511051477) | DN1a neuron | s-LNv neuron | None | None | None | None |
| 15 | VFB_jrchjtf3 | DN1pA_R (FlyEM-HB:387166379) | 25 | VFB_jrchk8e0 | 5th s-LNv (FlyEM-HB:511051477) | DN1p neuron | s-LNv neuron | None | None | None | None |
| 16 | VFB_jrchjtf0 | DN1pA_R (FlyEM-HB:324846570) | 25 | VFB_jrchk8e0 | 5th s-LNv (FlyEM-HB:511051477) | DN1p neuron | s-LNv neuron | None | None | None | None |
| 17 | VFB_jrchjzxy | LNd_R (FlyEM-HB:5813069648) | 37 | VFB_jrchk8e0 | 5th s-LNv (FlyEM-HB:511051477) | LNd neuron | s-LNv neuron | None | None | None | None |
| 18 | VFB_jrchjtey | DN1a_R (FlyEM-HB:5813022274) | 63 | VFB_jrchk8e0 | 5th s-LNv (FlyEM-HB:511051477) | DN1a neuron | s-LNv neuron | None | None | None | None |
| 19 | VFB_jrchjtf1 | DN1pA_R (FlyEM-HB:325529237) | 33 | VFB_jrchk8e0 | 5th s-LNv (FlyEM-HB:511051477) | DN1p neuron | s-LNv 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_jrchk5qg | SLP244_R (FlyEM-HB:297533212) | 33 | VFB_jrchjti6 | DSKMP3_R (FlyEM-HB:327937328) | adult superior lateral protocerebrum neuron 244 | adult Drosulfakinin neuron | None | None | None | None |
| 1 | VFB_jrchk5qf | SLP244_R (FlyEM-HB:298214577) | 27 | VFB_jrchjti6 | DSKMP3_R (FlyEM-HB:327937328) | adult superior lateral protocerebrum neuron 244 | adult Drosulfakinin neuron | None | None | None | None |
| 2 | VFB_jrchjyu7 | LHAV3j1_R (FlyEM-HB:297851977) | 24 | VFB_jrchjti6 | DSKMP3_R (FlyEM-HB:327937328) | adult lateral horn AV3j1 neuron | adult Drosulfakinin neuron | None | None | None | None |
| 3 | VFB_jrchk64p | SMP001_R (FlyEM-HB:5813056887) | 22 | VFB_jrchjti6 | DSKMP3_R (FlyEM-HB:327937328) | adult superior medial protocerebrum neuron 001 | adult Drosulfakinin neuron | None | None | None | None |
| 4 | VFB_jrchk0fd | MBON23(a2sp)_R (FlyEM-HB:423382015) | 21 | VFB_jrchjti6 | DSKMP3_R (FlyEM-HB:327937328) | mushroom body output neuron 23 | adult Drosulfakinin neuron | None | None | None | None |
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
| 56 | VFB_jrchjti6 | DSKMP3_R (FlyEM-HB:327937328) | 39 | VFB_jrchjti4 | DSKMP1B_R (FlyEM-HB:1352077058) | adult Drosulfakinin neuron | adult Drosulfakinin neuron | None | None | None | None |
| 57 | VFB_jrchk8dv | pC1c_R (FlyEM-HB:267551639) | 84 | VFB_jrchjti4 | DSKMP1B_R (FlyEM-HB:1352077058) | adult doublesex pC1 (female) neuron | adult Drosulfakinin neuron | None | None | None | None |
| 58 | VFB_jrchk5jv | SLP152_R (FlyEM-HB:487812620) | 28 | VFB_jrchjti4 | DSKMP1B_R (FlyEM-HB:1352077058) | adult superior lateral protocerebrum neuron 152 | adult Drosulfakinin neuron | None | None | None | None |
| 59 | VFB_jrchk5eo | SLP066_R (FlyEM-HB:327843160) | 42 | VFB_jrchjti4 | DSKMP1B_R (FlyEM-HB:1352077058) | adult superior lateral protocerebrum neuron 066 | adult Drosulfakinin neuron | None | None | None | None |
| 60 | VFB_jrchjti7 | DSKMP3_R (FlyEM-HB:328559607) | 53 | VFB_jrchjti4 | DSKMP1B_R (FlyEM-HB:1352077058) | adult Drosulfakinin neuron | adult Drosulfakinin neuron | 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 None
4 adult antennal olfactory receptor neuron FBbt_00007352 male organism
sample_tissue \
0 [antenna, adult tracheal system, wing, haltere...
1 [adult head, adult, wing, proboscis, testis, m...
2 [leg, adult, adult fat body, adult abdomen, ad...
3 [leg, adult, adult fat body, adult abdomen, ad...
4 [adult head, adult, wing, proboscis, testis, m...
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 [] 0.709302 1613.5887
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', 'Dopamine_receptor', 'Enzyme', 'GABA_receptor', 'GPCR', 'Glutamate_receptor', 'Gustatory_receptor', 'Histamine_receptor', 'Hormone', 'Ion_channel', 'Mechanosensory_ion_channel', 'Neuropeptide', 'Octopamine_receptor', 'Odorant_binding', 'Olfactory_receptor', 'Peptide_or_protein_hormone_receptor', 'Photoreceptor', 'Serotonin_receptor', 'Thermosensory_ion_channel', 'Transcription_factor', '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 olfactory receptor neuron FBbt_00007386 female organism
1 adult olfactory receptor neuron FBbt_00007386 male organism
2 adult olfactory receptor neuron FBbt_00007386 None
3 adult olfactory receptor neuron FBbt_00007386 female organism
4 adult olfactory receptor neuron FBbt_00007386 None
sample_tissue \
0 [antenna]
1 [adult head, adult, wing, proboscis, testis, m...
2 [antenna]
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 Orco FBgn0037324
4 Li et al., 2022, Science 375(6584): eabk2432 Orco FBgn0037324
function extent level
0 [Olfactory_receptor, Ion_channel, Odorant_bind... 0.726703 1699.4030
1 [Olfactory_receptor, Ion_channel, Odorant_bind... 0.734430 2036.3027
2 [Olfactory_receptor, Ion_channel, Odorant_bind... 0.759753 1789.3881
3 [Olfactory_receptor, Ion_channel, Odorant_bind... 0.719388 2769.3171
4 [Olfactory_receptor, Ion_channel, Odorant_bind... 0.702703 2649.6653