[1]:
!pip install -r ../../../requirements.txt --quiet
!pip install ../../../ --quiet
VFBTerm DataSet Methods
This notebook demonstrates the usage of the vfb.term and vfb.terms methods for accessing VFB term information. We’ll explore how to create VFBTerm objects, access related terms, images, and use advanced features like lazy loading of parents and manipulating collections of terms with VFBTerms.
[ ]:
# Import the VFBConnect class
from vfb_connect import vfb
import os
# Configure VFB for CI/notebook execution performance
vfb._load_limit = int(os.getenv('VFB_LOAD_LIMIT', 20)) # limit to 20 results for brevity, can be overridden in CI
if os.getenv('VFB_CACHE_ENABLED', 'false').lower() == 'true':
vfb._use_cache = True
print(f"VFB load limit set to: {vfb._load_limit}")
Welcome to the Virtual Fly Brain API
See the documentation at: https://virtualflybrain.org/docs/tutorials/apis/
Establishing connections to https://VirtualFlyBrain.org services...
Session Established!
Type vfb. and press tab to see available queries. You can run help against any query e.g. help(vfb.terms)
Creating and Exploring VFBTerm DataSet Objects
We’ll start by creating a VFBTerm object using the vfb.term method.
[3]:
# Example of creating a VFBTerm object using a term name
vfb_dataset = vfb.term('EM FAFB Engert et al. 2022')
vfb_dataset
[3]:
VFBTerm(term=Term(term=MinimalEntityInfo(name=EM FAFB Engert et al. 2022, short_form=Engert2022), link=https://n2t.net/vfb:Engert2022))
[4]:
vfb_dataset.summary
[4]:
| ID | Name | Description | URL | Counts | Publications | License | Cross References | |
|---|---|---|---|---|---|---|---|---|
| 0 | Engert2022 | EM FAFB Engert et al. 2022 | FAFB EM reconstructed neurons from Engert et a... | https://n2t.net/vfb:Engert2022 | {'images': 144, 'types': 5} | [Engert et al., 2022, eLife 11: e78110] | CC-BY_4.0 | [https://fafb.catmaid.virtualflybrain.org/?pid... |
[5]:
vfb_dataset.publications
[5]:
[Publication(pub=MinimalEntityInfo(name=Engert et al., 2022, eLife 11: e78110, short_form=FBrf0253662), link=http://flybase.org/reports/FBrf0253662)]
[6]:
vfb_dataset.license
[6]:
Term(term=MinimalEntityInfo(name=CC-BY_4.0, short_form=VFBlicense_CC_BY_4_0), link=https://creativecommons.org/licenses/by/4.0/legalcode)
[7]:
vfb_dataset.counts
[7]:
{'images': 144, 'types': 5}
[8]:
vfb_dataset.xrefs
[8]:
[Xref(link_text=EM FAFB Engert et al. 2022 on VFB CATMAID Adult Brain (FAFB), link=https://fafb.catmaid.virtualflybrain.org/?pid=1&tool=tracingtool&sid0=1&s0=2&active_skeleton_id=17682008, accession=17682008)]
[9]:
vfb_dataset.debug=True
vfb_dataset._return_type = 'name'
vfb_dataset.instances
Updating cache due to change in attribute 'debug'...
Updating cache due to change in attribute '_return_type'...
Getting name...
Loading instances ids for the first time...
Loading instances for dataset: EM FAFB Engert et al. 2022
Loading 144 instances for dataset: EM FAFB Engert et al. 2022...
Updating cache due to change in attribute '_instances_ids'...
Updating cache due to change in attribute 'has_image'...
Updating cache due to change in attribute '_instances_names'...
[9]:
['Gustatory Receptor Neuron GRN 10154804 SE',
'Gustatory Receptor Neuron GRN G4644404161 SE',
'Gustatory Receptor Neuron GRN 7471729 SE',
'Gustatory Receptor Neuron GRN 11559901 FC',
'Gustatory Receptor Neuron GRN G5040452086 SE',
'Gustatory Receptor Neuron GRN G4515200063 SE',
'Gustatory Receptor Neuron GRN 9235134 KS',
'Gustatory Receptor Neuron GRN 10487736 LH',
'Gustatory Receptor Neuron GRN 7479778 SE',
'Gustatory Receptor Neuron GRN 10603490 JH',
'Gustatory Receptor Neuron GRN G5040453623 SE',
'Gustatory Receptor Neuron GRN G4646985724 SE',
'Gustatory Receptor Neuron GRN 11162510 JH',
'Gustatory Receptor Neuron GRN 7793753 SE',
'Gustatory Receptor Neuron GRN G4906095585 SE',
'Gustatory Receptor Neuron GRN 12817586 PV',
'Gustatory Receptor Neuron GRN G5172843286 SE',
'Gustatory Receptor Neuron GRN 7349239 SE',
'Gustatory Receptor Neuron GRN 11675070 JH',
'Gustatory Receptor Neuron GRN 7759554 SE',
'Gustatory Receptor Neuron GRN 10481114 JH',
'Gustatory Receptor Neuron GRN 11302521 NM',
'Gustatory Receptor Neuron GRN G4909940718 SE',
'Gustatory Receptor Neuron GRN G5176731138 SE',
'Gustatory Receptor Neuron GRN G4777505483 SE',
'Gustatory Receptor Neuron GRN G4776863549 PV',
'Gustatory Receptor Neuron GRN 10489652 SE',
'Gustatory Receptor Neuron GRN 10780426 JH',
'Gustatory Receptor Neuron GRN 9348644 KS',
'Gustatory Receptor Neuron GRN G4645707816 SE',
'Gustatory Receptor Neuron GRN 11559814 JH',
'Gustatory Receptor Neuron GRN 11559750 JH',
'Gustatory Receptor Neuron GRN 7471830 SE',
'Gustatory Receptor Neuron GRN 7716996 SE',
'Gustatory Receptor Neuron GRN G4906098406 SE',
'Gustatory Receptor Neuron GRN 7723245 SE',
'Gustatory Receptor Neuron GRN G5043015897 SE',
'Gustatory Receptor Neuron GRN 11559788 NM',
'Gustatory Receptor Neuron GRN G4513893288 SE',
'Gustatory Receptor Neuron GRN 11399581 MK',
'Gustatory Receptor Neuron GRN 11559822 JH',
'Gustatory Receptor Neuron GRN 10443083 LH',
'Gustatory Receptor Neuron GRN 7438475 SE',
'Gustatory Receptor Neuron GRN 11559723 NM',
'Gustatory Receptor Neuron GRN 11559755 NM',
'Gustatory Receptor Neuron GRN G4252896405 SE',
'Gustatory Receptor Neuron GRN 7796689 SE',
'Gustatory Receptor Neuron GRN G4385324783 SE',
'Gustatory Receptor Neuron GRN 7759743 SE',
'Gustatory Receptor Neuron GRN 12215914 PV',
'Gustatory Receptor Neuron GRN G4906713011 SE',
'Gustatory Receptor Neuron GRN 10223340 NM',
'Gustatory Receptor Neuron GRN G5039803870 SE',
'Gustatory Receptor Neuron GRN 9016929 KS',
'Gustatory Receptor Neuron GRN 10780408 JH',
'Gustatory Receptor Neuron GRN 11559859 MK',
'Gustatory Receptor Neuron GRN 11488258 JH',
'Gustatory Receptor Neuron GRN 7575589 SE',
'Gustatory Receptor Neuron GRN 11559784 JH',
'Gustatory Receptor Neuron GRN G5039812164 SE',
'Gustatory Receptor Neuron GRN 13216532 PV',
'Gustatory Receptor Neuron GRN 11559735 JH',
'Gustatory Receptor Neuron GRN 8210749 SE',
'Gustatory Receptor Neuron GRN 7759924 SE',
'Gustatory Receptor Neuron GRN 10368681 JH',
'Gustatory Receptor Neuron GRN 11206722 NM',
'Gustatory Receptor Neuron GRN G4906086997 SE',
'Gustatory Receptor Neuron GRN 7485476 SE',
'Gustatory Receptor Neuron GRN 7773851 SE',
'Gustatory Receptor Neuron GRN 11559793 JH',
'Gustatory Receptor Neuron GRN G4513279017 SE',
'Gustatory Receptor Neuron GRN 11559847 MK',
'Gustatory Receptor Neuron GRN 12226831 PV',
'Gustatory Receptor Neuron GRN G4908018043 SE',
'Gustatory Receptor Neuron GRN 7724240 SE',
'Gustatory Receptor Neuron GRN 11559731 NM',
'Gustatory Receptor Neuron GRN 11242645 LH',
'Gustatory Receptor Neuron GRN 7349220 SE',
'Gustatory Receptor Neuron GRN 11559805 JH',
'Gustatory Receptor Neuron GRN 11674091 KS',
'Gustatory Receptor Neuron GRN 11206728 NM',
'Gustatory Receptor Neuron GRN G4908019820 SE',
'Gustatory Receptor Neuron GRN 11373582 JH',
'Gustatory Receptor Neuron GRN 11488253 JH',
'Gustatory Receptor Neuron GRN 11559707 LH',
'Gustatory Receptor Neuron GRN 7759396 SE',
'Gustatory Receptor Neuron GRN 11559809 JH',
'Gustatory Receptor Neuron GRN 7487872 SE',
'Gustatory Receptor Neuron GRN 7802088 SE',
'Gustatory Receptor Neuron GRN G4903508810 SE',
'Gustatory Receptor Neuron GRN 7256299 SE',
'Gustatory Receptor Neuron GRN 7432035 SE',
'Gustatory Receptor Neuron GRN G4249071310 SE',
'Gustatory Receptor Neuron GRN 10223393 LH',
'Gustatory Receptor Neuron GRN 11559801 JH',
'Gustatory Receptor Neuron GRN 11162502 JH',
'Gustatory Receptor Neuron GRN G4908663174 SE',
'Gustatory Receptor Neuron GRN 7757555 SE',
'Gustatory Receptor Neuron GRN G4778779523 SE',
'Gustatory Receptor Neuron GRN 9391837 KS',
'Gustatory Receptor Neuron GRN 7881738 SE',
'Gustatory Receptor Neuron GRN 11522846 MK',
'Gustatory Receptor Neuron GRN 7753062 SE',
'Gustatory Receptor Neuron GRN 7774675 SE',
'Gustatory Receptor Neuron GRN 7179580 SE',
'Gustatory Receptor Neuron GRN 11559839 JH',
'Gustatory Receptor Neuron GRN 7708436 SE',
'Gustatory Receptor Neuron GRN 7774394 SE',
'Gustatory Receptor Neuron GRN 10780418 JH',
'Gustatory Receptor Neuron GRN 11522863 MK',
'Gustatory Receptor Neuron GRN 11559866 MK',
'Gustatory Receptor Neuron GRN 7474053 SE',
'Gustatory Receptor Neuron GRN 7451041 SE',
'Gustatory Receptor Neuron GRN 11302512 NM',
'Gustatory Receptor Neuron GRN 11559835 JH',
'Gustatory Receptor Neuron GRN 10223377 JH',
'Gustatory Receptor Neuron GRN 10626458 JH',
'Gustatory Receptor Neuron GRN 11242650 LH',
'Gustatory Receptor Neuron GRN 7456678 SE',
'Gustatory Receptor Neuron GRN 7468836 SE',
'Gustatory Receptor Neuron GRN 11488268 JH',
'Gustatory Receptor Neuron GRN G5041733229 SE',
'Gustatory Receptor Neuron GRN G4252894541 SE',
'Gustatory Receptor Neuron GRN G5035938111 SE',
'Gustatory Receptor Neuron GRN 11559828 JH',
'Gustatory Receptor Neuron GRN 7789718 SE',
'Gustatory Receptor Neuron GRN 7724245 SE',
'Gustatory Receptor Neuron GRN G4643155726 SE',
'Gustatory Receptor Neuron GRN 9451694 KS',
'Gustatory Receptor Neuron GRN G5040452150 SE',
'Gustatory Receptor Neuron GRN 10780444 JH',
'Gustatory Receptor Neuron GRN 10795559 LH',
'Gustatory Receptor Neuron GRN 7789763 SE',
'Gustatory Receptor Neuron GRN 7774115 SE',
'Gustatory Receptor Neuron GRN 7789607 SE',
'Gustatory Receptor Neuron GRN 11559890 FC',
'Gustatory Receptor Neuron GRN 10742201 SE',
'Gustatory Receptor Neuron GRN 10368702 NM',
'Gustatory Receptor Neuron GRN 7789758 SE',
'Gustatory Receptor Neuron GRN 11559797 JH',
'Gustatory Receptor Neuron GRN G4908661424 SE',
'Gustatory Receptor Neuron GRN 7723219 SE',
'Gustatory Receptor Neuron GRN G4906731848 SE',
'Gustatory Receptor Neuron GRN 7349286 SE']
[10]:
vfb_dataset.show()
Updating cache due to change in attribute '_return_type'...
Getting full...
Creating instances for the first time...
More thann the load limit of 20 requested. Loading first 20 terms out of 144
Pulling 20 terms from VFB...
['VFB_001029ja', 'VFB_001029l6', 'VFB_001029ic', 'VFB_001029kj', 'VFB_001029ly', 'VFB_001029lg', 'VFB_001029j7', 'VFB_001029jr', 'VFB_001029if', 'VFB_001029jj', 'VFB_001029lx', 'VFB_001029ll', 'VFB_001029jy', 'VFB_001029j1', 'VFB_001029lu', 'VFB_001029kz', 'VFB_001029l9', 'VFB_001029i5', 'VFB_001029ko', 'VFB_001029kr']
['VFB_001029ja', 'VFB_001029l6', 'VFB_001029ic', 'VFB_001029kj', 'VFB_001029ly', 'VFB_001029lg', 'VFB_001029j7', 'VFB_001029jr', 'VFB_001029if', 'VFB_001029jj', 'VFB_001029lx', 'VFB_001029ll', 'VFB_001029jy', 'VFB_001029j1', 'VFB_001029lu', 'VFB_001029kz', 'VFB_001029l9', 'VFB_001029i5', 'VFB_001029ko', 'VFB_001029kr']
Checking cache for results: short_forms=['VFB_001029ja', 'VFB_001029l6', 'VFB_001029ic', 'VFB_001029kj', 'VFB_001029ly', 'VFB_001029lg', 'VFB_001029j7', 'VFB_001029jr', 'VFB_001029if', 'VFB_001029jj', 'VFB_001029lx', 'VFB_001029ll', 'VFB_001029jy', 'VFB_001029j1', 'VFB_001029lu', 'VFB_001029kz', 'VFB_001029l9', 'VFB_001029i5', 'VFB_001029ko', 'VFB_001029kr']
Looking for 20 results.
Got 20 results.
Using cached results.
Loading Terms: 100%|██████████| 20/20 [00:00<00:00, 1898.26it/s]
Loading JSON data from dictionary
Loaded term: GRN L4#9 (FAFB:16149095)
Loaded 2 related terms from relationships
Loaded 0 related terms from related_individuals
Loaded 1 channel images
Parents: None
Parents: ['FBbt_00110887']
Parents: ['FBbt_00110887']
Loaded 0 definition publications
Loaded 0 synonym publications
Loaded 1 datasets
Loaded 1 cross references
Loaded 0 synonyms
Adding related_term as a property for part_of
Adding term to part_of
Adding term to cache...
Updating cache due to change in attribute '_load_complete'...
Loading JSON data from dictionary
Loaded term: GRN L4#1 (FAFB:10154803)
Loaded 2 related terms from relationships
Loaded 0 related terms from related_individuals
Loaded 1 channel images
Parents: None
Parents: ['FBbt_00110887']
Parents: ['FBbt_00110887']
Loaded 0 definition publications
Loaded 0 synonym publications
Loaded 1 datasets
Loaded 1 cross references
Loaded 0 synonyms
Adding related_term as a property for part_of
Adding term to part_of
Adding term to cache...
Updating cache due to change in attribute '_load_complete'...
Loading JSON data from dictionary
Loaded term: GRN R6#23 (FAFB:14947958)
Loaded 2 related terms from relationships
Loaded 0 related terms from related_individuals
Loaded 1 channel images
Parents: None
Parents: ['FBbt_00100042']
Parents: ['FBbt_00100042']
Loaded 0 definition publications
Loaded 0 synonym publications
Loaded 1 datasets
Loaded 1 cross references
Loaded 0 synonyms
Adding related_term as a property for part_of
Adding term to part_of
Adding term to cache...
Updating cache due to change in attribute '_load_complete'...
Loading JSON data from dictionary
Loaded term: GRN L2#4 (FAFB:11407091)
Loaded 2 related terms from relationships
Loaded 0 related terms from related_individuals
Loaded 1 channel images
Parents: None
Parents: ['FBbt_00048152']
Parents: ['FBbt_00048152']
Loaded 0 definition publications
Loaded 0 synonym publications
Loaded 1 datasets
Loaded 1 cross references
Loaded 0 synonyms
Adding related_term as a property for part_of
Adding term to part_of
Adding term to cache...
Updating cache due to change in attribute '_load_complete'...
Loading JSON data from dictionary
Loaded term: GRN R5#16 (FAFB:11967149)
Loaded 2 related terms from relationships
Loaded 0 related terms from related_individuals
Loaded 1 channel images
Parents: None
Parents: ['FBbt_00058156']
Parents: ['FBbt_00058156']
Loaded 0 definition publications
Loaded 0 synonym publications
Loaded 1 datasets
Loaded 1 cross references
Loaded 0 synonyms
Adding related_term as a property for part_of
Adding term to part_of
Adding term to cache...
Updating cache due to change in attribute '_load_complete'...
Loading JSON data from dictionary
Loaded term: GRN L4#15 (FAFB:16149178)
Loaded 2 related terms from relationships
Loaded 0 related terms from related_individuals
Loaded 1 channel images
Parents: None
Parents: ['FBbt_00110887']
Parents: ['FBbt_00110887']
Loaded 0 definition publications
Loaded 0 synonym publications
Loaded 1 datasets
Loaded 1 cross references
Loaded 0 synonyms
Adding related_term as a property for part_of
Adding term to part_of
Adding term to cache...
Updating cache due to change in attribute '_load_complete'...
Loading JSON data from dictionary
Loaded term: GRN L2#8 (FAFB:16149150)
Loaded 2 related terms from relationships
Loaded 0 related terms from related_individuals
Loaded 1 channel images
Parents: None
Parents: ['FBbt_00048152']
Parents: ['FBbt_00048152']
Loaded 0 definition publications
Loaded 0 synonym publications
Loaded 1 datasets
Loaded 1 cross references
Loaded 0 synonyms
Adding related_term as a property for part_of
Adding term to part_of
Adding term to cache...
Updating cache due to change in attribute '_load_complete'...
Loading JSON data from dictionary
Loaded term: GRN R4#17 (FAFB:14947934)
Loaded 2 related terms from relationships
Loaded 0 related terms from related_individuals
Loaded 1 channel images
Parents: None
Parents: ['FBbt_00058156']
Parents: ['FBbt_00058156']
Loaded 0 definition publications
Loaded 0 synonym publications
Loaded 1 datasets
Loaded 1 cross references
Loaded 0 synonyms
Adding related_term as a property for part_of
Adding term to part_of
Adding term to cache...
Updating cache due to change in attribute '_load_complete'...
Loading JSON data from dictionary
Loaded term: GRN L7#9 (FAFB:16149059)
Loaded 2 related terms from relationships
Loaded 0 related terms from related_individuals
Loaded 1 channel images
Parents: None
Parents: ['FBbt_00110887']
Parents: ['FBbt_00110887']
Loaded 0 definition publications
Loaded 0 synonym publications
Loaded 1 datasets
Loaded 1 cross references
Loaded 0 synonyms
Adding related_term as a property for part_of
Adding term to part_of
Adding term to cache...
Updating cache due to change in attribute '_load_complete'...
Loading JSON data from dictionary
Loaded term: GRN L4#4 (FAFB:12817585)
Loaded 2 related terms from relationships
Loaded 0 related terms from related_individuals
Loaded 1 channel images
Parents: None
Parents: ['FBbt_00110887']
Parents: ['FBbt_00110887']
Loaded 0 definition publications
Loaded 0 synonym publications
Loaded 1 datasets
Loaded 1 cross references
Loaded 0 synonyms
Adding related_term as a property for part_of
Adding term to part_of
Adding term to cache...
Updating cache due to change in attribute '_load_complete'...
Loading JSON data from dictionary
Loaded term: GRN L1#5 (FAFB:11675069)
Loaded 2 related terms from relationships
Loaded 0 related terms from related_individuals
Loaded 1 channel images
Parents: None
Parents: ['FBbt_00048152']
Parents: ['FBbt_00048152']
Loaded 0 definition publications
Loaded 0 synonym publications
Loaded 1 datasets
Loaded 1 cross references
Loaded 0 synonyms
Adding related_term as a property for part_of
Adding term to part_of
Adding term to cache...
Updating cache due to change in attribute '_load_complete'...
Loading JSON data from dictionary
Loaded term: GRN L4#14 (FAFB:16149171)
Loaded 2 related terms from relationships
Loaded 0 related terms from related_individuals
Loaded 1 channel images
Parents: None
Parents: ['FBbt_00110887']
Parents: ['FBbt_00110887']
Loaded 0 definition publications
Loaded 0 synonym publications
Loaded 1 datasets
Loaded 1 cross references
Loaded 0 synonyms
Adding related_term as a property for part_of
Adding term to part_of
Adding term to cache...
Updating cache due to change in attribute '_load_complete'...
Loading JSON data from dictionary
Loaded term: GRN L1#2 (FAFB:10603489)
Loaded 2 related terms from relationships
Loaded 0 related terms from related_individuals
Loaded 1 channel images
Parents: None
Parents: ['FBbt_00048152']
Parents: ['FBbt_00048152']
Loaded 0 definition publications
Loaded 0 synonym publications
Loaded 1 datasets
Loaded 1 cross references
Loaded 0 synonyms
Adding related_term as a property for part_of
Adding term to part_of
Adding term to cache...
Updating cache due to change in attribute '_load_complete'...
Loading JSON data from dictionary
Loaded term: GRN L1#4 (FAFB:10796200)
Loaded 2 related terms from relationships
Loaded 0 related terms from related_individuals
Loaded 1 channel images
Parents: None
Parents: ['FBbt_00048152']
Parents: ['FBbt_00048152']
Loaded 0 definition publications
Loaded 0 synonym publications
Loaded 1 datasets
Loaded 1 cross references
Loaded 0 synonyms
Adding related_term as a property for part_of
Adding term to part_of
Adding term to cache...
Updating cache due to change in attribute '_load_complete'...
Loading JSON data from dictionary
Loaded term: GRN R6#17 (FAFB:11559900)
Loaded 2 related terms from relationships
Loaded 0 related terms from related_individuals
Loaded 1 channel images
Parents: None
Parents: ['FBbt_00100042']
Parents: ['FBbt_00100042']
Loaded 0 definition publications
Loaded 0 synonym publications
Loaded 1 datasets
Loaded 1 cross references
Loaded 0 synonyms
Adding related_term as a property for part_of
Adding term to part_of
Adding term to cache...
Updating cache due to change in attribute '_load_complete'...
Loading JSON data from dictionary
Loaded term: GRN R2#1 (FAFB:7349238)
Loaded 2 related terms from relationships
Loaded 0 related terms from related_individuals
Loaded 1 channel images
Parents: None
Parents: ['FBbt_00048152']
Parents: ['FBbt_00048152']
Loaded 0 definition publications
Loaded 0 synonym publications
Loaded 1 datasets
Loaded 1 cross references
Loaded 0 synonyms
Adding related_term as a property for part_of
Adding term to part_of
Adding term to cache...
Updating cache due to change in attribute '_load_complete'...
Loading JSON data from dictionary
Loaded term: GRN R4#12 (FAFB:7793752)
Loaded 2 related terms from relationships
Loaded 0 related terms from related_individuals
Loaded 1 channel images
Parents: None
Parents: ['FBbt_00058156']
Parents: ['FBbt_00058156']
Loaded 0 definition publications
Loaded 0 synonym publications
Loaded 1 datasets
Loaded 1 cross references
Loaded 0 synonyms
Adding related_term as a property for part_of
Adding term to part_of
Adding term to cache...
Updating cache due to change in attribute '_load_complete'...
Loading JSON data from dictionary
Loaded term: GRN R6#9 (FAFB:9235133)
Loaded 2 related terms from relationships
Loaded 0 related terms from related_individuals
Loaded 1 channel images
Parents: None
Parents: ['FBbt_00100042']
Parents: ['FBbt_00100042']
Loaded 0 definition publications
Loaded 0 synonym publications
Loaded 1 datasets
Loaded 1 cross references
Loaded 0 synonyms
Adding related_term as a property for part_of
Adding term to part_of
Adding term to cache...
Updating cache due to change in attribute '_load_complete'...
Loading JSON data from dictionary
Loaded term: GRN R4#6 (FAFB:7471728)
Loaded 2 related terms from relationships
Loaded 0 related terms from related_individuals
Loaded 1 channel images
Parents: None
Parents: ['FBbt_00058156']
Parents: ['FBbt_00058156']
Loaded 0 definition publications
Loaded 0 synonym publications
Loaded 1 datasets
Loaded 1 cross references
Loaded 0 synonyms
Adding related_term as a property for part_of
Adding term to part_of
Adding term to cache...
Updating cache due to change in attribute '_load_complete'...
Loading JSON data from dictionary
Loaded term: GRN R5#4 (FAFB:7479777)
Loaded 2 related terms from relationships
Loaded 0 related terms from related_individuals
Loaded 1 channel images
Parents: None
Parents: ['FBbt_00058156']
Parents: ['FBbt_00058156']
Loaded 0 definition publications
Loaded 0 synonym publications
Loaded 1 datasets
Loaded 1 cross references
Loaded 0 synonyms
Adding related_term as a property for part_of
Adding term to part_of
Adding term to cache...
Updating cache due to change in attribute '_load_complete'...
Updating cache due to change in attribute '_instances'...
Getting full...
Getting full...
Defaulting to JRC2018Unisex template
Loading thumbnail for GRN L4#9 (FAFB:16149095)
Updating cache due to change in attribute '_return_type'...
[11]:
vfb_dataset.open(verbose=True)
Opening https://n2t.net/vfb:Engert2022
[12]:
vfb_dataset._return_type = 'id' # change return type to id
a=vfb_dataset.instances[5]
print(vfb.lookup_name(a))
vfb.term(a).channel_images[0].image.show()
Updating cache due to change in attribute '_return_type'...
Getting id...
Gustatory Receptor Neuron GRN G4515200063 SE
[13]:
vfb_dataset.plot3d()
Updating cache due to change in attribute '_mesh'...
Updating cache due to change in attribute '_volume'...
Updating cache due to change in attribute '_return_type'...
Getting full...
Getting full...
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
Cell In[13], line 1
----> 1 vfb_dataset.plot3d()
File /usr/local/anaconda3/lib/python3.10/site-packages/vfb_connect/schema/vfb_term.py:2796, in VFBTerm.plot3d(self, template, verbose, query_by_label, force_reload, include_template, **kwargs)
2794 self._return_type = temp
2795 return
-> 2796 self.instances.plot3d(template=template, verbose=verbose, query_by_label=query_by_label, force_reload=force_reload, **kwargs)
2797 self._return_type = temp
2798 return
File /usr/local/anaconda3/lib/python3.10/site-packages/vfb_connect/schema/vfb_term.py:3663, in VFBTerms.plot3d(self, template, verbose, query_by_label, force_reload, include_template, limit, **kwargs)
3650 def plot3d(self, template=None, verbose=False, query_by_label=True, force_reload=False, include_template=False, limit=False, **kwargs):
3651 """
3652 Plot the 3D representation of any neuron or expression.
3653
(...)
3661 :param kwargs: Additional arguments for plotting.
3662 """
-> 3663 skeletons, selected_template = self._get_plot_images(template=template, verbose=verbose, query_by_label=query_by_label, force_reload=force_reload)
3665 if skeletons:
3666 if limit and len(skeletons) > limit:
File /usr/local/anaconda3/lib/python3.10/site-packages/vfb_connect/schema/vfb_term.py:3722, in VFBTerms._get_plot_images(self, template, verbose, query_by_label, force_reload)
3712 """
3713 Load and return images for navis plot
3714
(...)
3719 :return: A list of skeletons and the selected template.
3720 """
3721 selected_template = None
-> 3722 template = VFBTerm.get_default_template(self, template)
3723 if template:
3724 if query_by_label:
File /usr/local/anaconda3/lib/python3.10/site-packages/vfb_connect/schema/vfb_term.py:2707, in VFBTerm.get_default_template(self, template)
2705 return self.vfb.lookup_id(template)
2706 else:
-> 2707 templates = [ci.image.template_anatomy.short_form for ci in self.channel_images] if self.channel_images else None
2708 if templates:
2709 if 'VFB_00101567' in templates:
AttributeError: 'VFBTerms' object has no attribute 'channel_images'
Please see VFBTerm Notebook for examples of how to load specific sets of terms and display neurons in context