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Documentation

Here you will find explanations and tutorial for the concepts and tools that are utilised by Virtual Fly Brain (VFB).

1 - Overview

An overiew video showing some examples of what you can do with Virtual Fly Brain

2 - Getting Started

How to use the Virtual Fly Brain 3D browser

Below are a few overview pages to help you get started using VFB:

2.1 - Starting to explore VFB

Text search and query tools and how to explore the 3D images.

VFB integrates data curated from the literature with image data from many bulk sources. The search system allows you to search for neurons and neuroanatomical structures using almost any name found in the literature. The query system can identify neurons innervating any specified neuropil or fasciculating with any specified tract. It also allows queries for genes, transgenes and phenotypes expressed in any brain region or neuron. Search and query results combine referenced textual descriptions with 3D images and links to originating data sources. VFB features tens of thousands of 3D images of neurons, clones and expression patterns, registered to standard template brains. Any combination of these images can be viewed together. A BLAST-type query system (NBLAST) allows you to find similar neurons and drivers starting from a registered neuron.

Search for the item you’re interested in

Hover to explore brain regions in the Stack Viewer

Query for related terms and images

Virtual Fly Brain (VFB) Overview

2.2 - This is the Slice Viewer tab

The Slice Viewer displays single slices of the template, showing all selected painted anatomy, neurons and expression patterns

Hover to explore, click to list or shift + click to add painted anatomy

Use the arrow icons or scroll with the mouse to move through the stack

Home resets your view

Use the zoom icons or pinch gesture to zoom

Toggles through orthogonal views

Toggles the slice position on the 3D Viewer on/off

Virtual Fly Brain (VFB) Slice Viewer

2.3 - This is the 3D Viewer tab

The 3D Viewer displays 3D models of the template, showing all selected painted anatomy, neurons and expression patterns

Point and click to select neurons/expression

Click and drag with the mouse or use the directional icons to rotate/move

Use the zoom icons or scroll with the mouse to zoom in/out

Home resets your view

The camera icon starts/stops a rotation animation of the scene

The sphere icon toggles wireframes on/off

Virtual Fly Brain (VFB) 3D Viewer

2.4 - This is the Term Info tab

Term Info displays information on the currently selected painted anatomy region, neuron, expression pattern or non-image term definitions

Click on thumbnails to add that image to the viewer

Click on terms to select them

Click on download items to begin downloading

Run term related queries

Virtual Fly Brain (VFB) 3D Viewer

2.5 - This is the Term Context tab

Term Context displays grapical information on the currently selected term’s location or classification

Home resets your view

Use the zoom icons or scroll with the mouse to zoom in/out

Click to refresh to the current focus term

Select either the location or the classification for the current term

Virtual Fly Brain (VFB) 3D Viewer

2.6 - This is the Circuit Browser tab

The Circuit Browser allows you to find the strongest paths from one neuron (the source neuron) to another (the target neuron).

The ‘strongest’ paths are the shortest/highest weighted paths. Paths are arranged from the ‘strongest’ at the bottom to the ‘weakest’ at the top. A detailed explanation for the algorithm used to determine path strengths can be found here.

Search for the source neuron to start from (Note: query is directional)

Search for the target neuron

Maximum number of paths to return (only the ‘strongest’ paths will be returned)

A minimum weight for the synapse count of each connection can be applied, paths containing individual connections below this minimum will not be returned

Virtual Fly Brain (VFB) 3D Viewer

3 - Examples

Examples of usecases for VFB or different data types that are available.

3.1 - Circuit diagram of the mushroom body

Schematic representation of the 21 cell types of MBONs in the lobes and one cell type of MBON in the calyx based on the data presented in the accompanying manuscript (Aso et al., 2014): circles, cell bodies; semicircles, dendrites; arrowheads, axon terminals; color-coding is by neurotransmitter as in panel (A) Three MBON cell-types (GABAergic MBON-γ1pedc>α/β, glutamatergic MBON-γ4>γ1γ2 and MBON-β1>α; marked as 11, 5 and 6 respectively) send axons into the MB lobes. Axons of MBON-γ4>γ1γ2 project from γ4 to γ1 and γ2, and thus have the potential to affect activity of MBON-γ1pedc>α/β. From γ1, the axon of MBON-γ1pedc>α/β projects to compartments in the α/β lobes including β1, where dendrites of MBON-β1>α arborize. Axons of both MBON-γ1pedc>α/β and MBON-β1>α project to the compartments in the α lobe. Therefore activity of MBONs in the α lobe can be regulated by these layered inter-compartmental connections. These three types of MBONs (11, 5 and 6) do not project back to their own dendrites. Therefore, the organization of the MBONs can be viewed as forming a multilayered feed-forward network (Aso et al., 2014). MBONs project to a small number of brain areas: the crepine (CRE; a region surrounding the horizontal/medial lobes), the superior medial protocerebrum (SMP), superior intermediate protocerebrum (SIP) and superior lateral protocerebrum (SLP) and the lateral horn (LH). The size of the arrowhead reflects the relative number of termini in each area. The MBONs are numbered and listed in Table 1. See the accompanying manuscript (Aso et al., 2014) and Table 1 for details.

https://doi.org/10.7554/eLife.04580.003

4 - Concepts

Details of concepts or terms used in Virtual Fly Brain

4.1 - Transgene Expression

These techniques work by driving the expression of a target transgenes.

Here we present details of how single transgenes are curated

Transgene expression into FlyBase and Virtual Fly Brain (VFB)

Expression of single transgenes are curated from the published literature into FlyBase as expression statements. Virtual Fly Brain (VFB) combines hosted images with neuroanatomical, expression and genetic data from FlyBase in Neo4j and maps them onto Central Nervious System (CNS) templates where they can be queried using Web Ontology Language (OWL) and Solr.

4.2 - Split Expression

This techniques works by driving the expression of target transgenes at the intersection between the expression patterns of two hemi-driver transgenes.

Thousands of hemi-driver transgenes are now available, meaning that millions of combinations/splits are possible, each targeting some precise subset of the 10s-100s of thousands of neurons in a fly Central Nervous System (CNS). Finding the right combination for an experiment is a serious bottleneck for researchers.

FlyBase & Virtual Fly Brain (VFB) solve this problem by curating information and images recording where expression is driven by combinations of hemi-drivers. Each combination gets a standard name on VFB reflecting the names of the component hemidrivers (see figure below) and is also associated with any short names for the combination used in the literature (e.g. “P{VT017411-GAL4.DBD} ∩ P{VT019018-p65.AD} expression pattern” has_exact_synonym: SS02256")

This techniques work by driving the expression of target transgenes at the intersection between the expression patterns of two hemi-driver transgenes.This techniques work by driving the expression of target transgenes at the intersection between the expression patterns of two hemi-driver transgenes.

We use programmatic methods to generate expression statements for hemi-driver combinations with FlyLight image data hosted by VFB. Combinations are validated against a local copy of the FlyLight dataset and a structured user readable comment is generated as part of the expression statement. These hyperlink to the partner hemi-driver in FlyBase, contain the strain designation (where available) and can be automatically parsed by Virtual Fly Brain to attach expression and genetic data to a node representing the intersection.

split expression shown in Virtual Fly Brain (VFB)

4.3 - Templates

Canonical templates not only allow for spatial alignment of image data but also are often painted to make a reference atlas of anatomical regions.

Many central nervious system (CNS) templates exist for Drosophila, below we provide a summary of those used in VFB.

Central Nervious System from Janelia Research Campus JRC2018

VFB displays data aligned to either the JRC 2018 unisex brain template for cephalic or JRC 2018 unisex Ventral Nerve Cord (VNC) for non-cephalic data.

Bogovic et al., “An unbiased template of the Drosophila brain and ventral nerve cord”

The files are available from Janelia: JRC 2018 Brain templates

Adult Brain from Janelia Research Campus/VFB (JFRC2010/JFRC2)

Superceeded by [JRC2018]({{ < ref “#central-nervious-system-from-janelia-research-campus-jrc2018” > }})

Template brain created by Arnim Jenett (Janelia Research Campus), Kazunori Shinomiya and Kei Ito (Tokyo University) from a staining with the neuropil marker nc82.

The voxel size is 0.62x0.62x0.62 micron.

The files are available here.

4.4 - Bridging Registrations

Transformations to map between different cononical Drosophila templates.

Many transforms to map between different Drosophila template brains are available.

You can see how to use the above in python using navis-flybrains or in R using nat.flybrains

5 - Tutorials

This is where we show you how to use VFB and other tools to explore the available data.

5.1 - Application Programming Interfaces (APIs)

This is where we show you how to use VFBs Application Programming Interfaces (APIs) and other tools to explore the available data.

5.1.1 - Hacking the connectome

Tutorials from the Virtual Fly Brain “Hacking the connectome” workshop that was run in collaboration with the Drosophila Connectomics Group based at the Dept of Zoology, University of Cambridge.

Below you can watch the recorded introduction session of our workshop and follow along with the workshop notebooks we work through to show examples of how you can use the available {{ ref “tools.md” tools }} to explore and analyse the published connectomes available on VFB.

5.1.1.1 - Tool landscape

There are multiple tools to query the various data sources. Fortunately they play together nicely. Here is a quick overview

Below are brief descriptions of the libraries/packages. For details, I defer to their respective (excellent) documentations.

Querying VFB

Queries against VFB’s REST API are easiest with vfb_connect for Python. For R there is a vfb_connect wrapper, vfbconnectr. See also David’s presentation for details.

R

In R, the natverse is your one-stop-shop for all things neuron: it’s a collection of various R packages that are built on top of the neuroanatomy toolbox, nat. Of particular relevance for this workshop:

  1. nat is a general purpose library for working with morphological neuron data. In this workshop, we make heavy use of nat’s plotting capabilities but its capabilities extend far beyond that. If you want to run any morphological analysis, I highly recommend you have a look at the “Articles” in nat’s doc.
  2. neuprintr and hemibrainr provide an interface with neuprint and the Janelia hemibrain dataset (link). The former lets you run queries against neuprint’s neo4j database while the latter contains meta data and various convenience functions to work with the hemibrain dataset.
  3. rcatmaid provides an interface with CATMAID servers such as those the VFB uses to host published from the FAFB or larval fruit fly dataset. rcatmaid is built on top of nat and you can use nat functions with neurons pulled via rcatmaid.

Python

In Python, we find packages analogous to those in R:

  1. navis is nat’s serpentine sibling: a general purpose neuron library for visualization and analysis of neuronal morphologies. It also features interfaces e.g. with Blender 3D and the natverse via rpy2.
  2. python-neuprint is a Python library to interface with neuprint maintained by Janelia. Note that navis wraps this library and adds some convenience functions. See this tutorial.
  3. pymaid lets you interface with CATMAID servers. Critically, it’s built on top of navis and you can natively use navis functions with pymaid neurons. Note that due to a name clash the library is called python-catmaid on PyPI.

Noteworthy mentions

There are a few more packages/functions that you might hear of over the course of the workshop.

NBLAST

NBLAST is an algorithm that computes morphological similarity between neurons (Costa et al., 2016). This has proven incredibly useful to find similar neurons across datasets but also to cluster neurons into cell types.

On the R side the algorithm is implemented in nat.nblast and in Python it is part of navis (see this tutorial).

Transforms

You will note that neurons pulled from VFB are typically in the same template space which makes co-visualization of neurons from different datasets a breeze. If you want to transform spatial data between template brains, e.g. from FAFB (“FAFB14”) to hemibrain (“JRCFIB2018F”), you should look for nat.flybrains & nat.jrcbrains in R and navis-flybrains in Python.

5.1.1.2 - Introduction to connectomic data and tools

Introduction session from the Virtual Fly Brain “Hacking the connectome” workshop that was run in collaboration with the Drosophila Connectomics Group based at the Dept of Zoology, University of Cambridge.

5.1.1.3 - Discovery

VFB integrates images and connectomics profiles of neurons from many sources. It classifies and records their properties using a standard, queryable classification. 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.

Required packages: vfb-connect and python-catmaid (pymaid & navis)

!pip install vfb-connect --upgrade
!pip install python-catmaid --upgrade

A note on using these notebooks

This is designed as an interactive tutorial. Feel free to add code cells below each example to try out variations of your own.

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.

# 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}')

WARNING: Could not load OpenGL library.
INFO  : Global CATMAID instance set. Caching is ON. (pymaid)
Server is running CATMAID version 2020.02.15-905-g93a969b37

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:

Use either the full name or the Symbol to query for neurons:

DA3adPN = vc.get_instances("adult Drosulfakinin neuron", summary=True)
pd.DataFrame.from_records(DA3adPN)

label symbol id tags parents_label parents_id data_source accession templates dataset license
0 DSKMP3_R - 327937328 VFB_jrchjti6 Entity|has_image|Adult|Anatomy|has_neuron_conn... adult Drosulfakinin neuron FBbt_00048999 neuprint_JRC_Hemibrain_1point1 327937328 JRC2018Unisex|JRC_FlyEM_Hemibrain Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
1 DSKMP1A(PVM02)_L - 1260833150 VFB_jrchjti3 Entity|has_image|Adult|Anatomy|has_neuron_conn... adult Drosulfakinin neuron FBbt_00048999 neuprint_JRC_Hemibrain_1point1 1260833150 JRC2018Unisex|JRC_FlyEM_Hemibrain Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
2 DSKMP3_R - 328559607 VFB_jrchjti7 Entity|has_image|Adult|Anatomy|has_neuron_conn... adult Drosulfakinin neuron FBbt_00048999 neuprint_JRC_Hemibrain_1point1 328559607 JRC_FlyEM_Hemibrain|JRC2018Unisex Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
3 DSKMP1B_R - 1352077058 VFB_jrchjti4 Entity|has_image|Adult|Anatomy|has_neuron_conn... adult Drosulfakinin neuron FBbt_00048999 neuprint_JRC_Hemibrain_1point1 1352077058 JRC2018Unisex|JRC_FlyEM_Hemibrain Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
4 DSKMP1B(PVM02)_L - 1011184205 VFB_jrchjti5 Entity|has_image|Adult|Anatomy|has_neuron_conn... adult Drosulfakinin neuron FBbt_00048999 neuprint_JRC_Hemibrain_1point1 1011184205 JRC2018Unisex|JRC_FlyEM_Hemibrain Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
5 DSKMP1A_R - 1135837629 VFB_jrchjti2 Entity|has_image|Adult|Anatomy|has_neuron_conn... adult Drosulfakinin neuron FBbt_00048999 neuprint_JRC_Hemibrain_1point1 1135837629 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.

# 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

label symbol id tags parents_label parents_id data_source accession templates dataset license
0 lLN2T_a(Tortuous)_R - 5813056598 VFB_jrchk8bi Entity|has_image|Adult|Anatomy|has_neuron_conn... adult antennal lobe lateral local neuron 2T FBbt_00049816 neuprint_JRC_Hemibrain_1point1 5813056598 JRC2018Unisex|JRC_FlyEM_Hemibrain Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
1 ORN_DL3_R - 1671625186 VFB_jrchk1hj Entity|has_image|Adult|Anatomy|has_neuron_conn... adult olfactory receptor neuron Or65 FBbt_00067011 neuprint_JRC_Hemibrain_1point1 1671625186 JRC_FlyEM_Hemibrain|JRC2018Unisex Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
2 DA4m_adPN_R - 574037266 VFB_jrchjtdq Entity|has_image|Adult|Anatomy|has_neuron_conn... adult antennal lobe projection neuron DA4m adPN FBbt_00047714 neuprint_JRC_Hemibrain_1point1 574037266 JRC2018Unisex|JRC_FlyEM_Hemibrain Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
3 Uniglomerular mALT DA3 adPN#L1 (FAFB:2449792) VFB_0010123h Entity|has_image|Adult|Anatomy|has_neuron_conn... adult antennal lobe projection neuron DA3 adPN FBbt_00100384 catmaid_fafb 2449792 JRC2018Unisex BatesSchlegel2020 https://creativecommons.org/licenses/by-sa/4.0...
4 lLN2T_e(Tortuous)_R - 1699974843 VFB_jrchk8br Entity|has_image|Adult|Anatomy|has_neuron_conn... adult antennal lobe lateral local neuron 2T FBbt_00049816 neuprint_JRC_Hemibrain_1point1 1699974843 JRC2018Unisex|JRC_FlyEM_Hemibrain Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
# 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

label symbol id tags parents_label parents_id data_source accession templates dataset license
0 lLN16b_R - 1887168462 VFB_jrchk89w Entity|has_image|Adult|Anatomy|has_neuron_conn... adult local interneuron of the lateral ALl1 ne... FBbt_00007394 neuprint_JRC_Hemibrain_1point1 1887168462 JRC_FlyEM_Hemibrain|JRC2018Unisex Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
1 lLN1_c_R - 5813047691 VFB_jrchk8ae Entity|has_image|Adult|Anatomy|has_neuron_conn... adult local interneuron of the lateral ALl1 ne... FBbt_00007394 neuprint_JRC_Hemibrain_1point1 5813047691 JRC_FlyEM_Hemibrain|JRC2018Unisex Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
2 lLN2S(Star)_R - 1670627928 VFB_jrchk8bb Entity|has_image|Adult|Anatomy|has_neuron_conn... adult antennal lobe lateral local neuron 2S FBbt_00049815 neuprint_JRC_Hemibrain_1point1 1670627928 JRC2018Unisex|JRC_FlyEM_Hemibrain Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
3 lLN2F_b(Full)_R - 5813024698 VFB_jrchk8an Entity|has_image|Adult|Anatomy|has_neuron_conn... adult antennal lobe lateral local neuron 2F FBbt_00049812 neuprint_JRC_Hemibrain_1point1 5813024698 JRC_FlyEM_Hemibrain|JRC2018Unisex Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
4 lLN2T_c(Tortuous)_R - 1671292719 VFB_jrchk8bo Entity|has_image|Adult|Anatomy|has_neuron_conn... adult antennal lobe lateral local neuron 2T FBbt_00049816 neuprint_JRC_Hemibrain_1point1 1671292719 JRC_FlyEM_Hemibrain|JRC2018Unisex Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
5 lLN1_c_R - 5813062199 VFB_jrchk8af Entity|has_image|Adult|Anatomy|has_neuron_conn... adult local interneuron of the lateral ALl1 ne... FBbt_00007394 neuprint_JRC_Hemibrain_1point1 5813062199 JRC2018Unisex|JRC_FlyEM_Hemibrain Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
6 lLN1_a_R - 5813130064 VFB_jrchk8a4 Entity|has_image|Adult|Anatomy|has_neuron_conn... adult local interneuron of the lateral ALl1 ne... FBbt_00007394 neuprint_JRC_Hemibrain_1point1 5813130064 JRC2018Unisex|JRC_FlyEM_Hemibrain Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
7 lLN1_c_R - 1702651358 VFB_jrchk8aj Entity|has_image|Adult|Anatomy|has_neuron_conn... adult local interneuron of the lateral ALl1 ne... FBbt_00007394 neuprint_JRC_Hemibrain_1point1 1702651358 JRC_FlyEM_Hemibrain|JRC2018Unisex Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
8 lLN2T_e(Tortuous)_R - 1640922516 VFB_jrchk8bs Entity|has_image|Adult|Anatomy|has_neuron_conn... adult antennal lobe lateral local neuron 2T FBbt_00049816 neuprint_JRC_Hemibrain_1point1 1640922516 JRC2018Unisex|JRC_FlyEM_Hemibrain Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
9 lLN11_R - 1670278227 VFB_jrchk89e Entity|has_image|Adult|Anatomy|has_neuron_conn... adult local interneuron of the lateral ALl1 ne... FBbt_00007394 neuprint_JRC_Hemibrain_1point1 1670278227 JRC_FlyEM_Hemibrain|JRC2018Unisex Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
10 lLN2P_c(Patchy)_R - 2105086391 VFB_jrchk8b0 Entity|has_image|Adult|Anatomy|has_neuron_conn... adult antennal lobe lateral local neuron 2P FBbt_00049813 neuprint_JRC_Hemibrain_1point1 2105086391 JRC_FlyEM_Hemibrain|JRC2018Unisex Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
11 lLN2T_b(Tortuous)_R - 1640572741 VFB_jrchk8bl Entity|has_image|Adult|Anatomy|has_neuron_conn... adult antennal lobe lateral local neuron 2T FBbt_00049816 neuprint_JRC_Hemibrain_1point1 1640572741 JRC2018Unisex|JRC_FlyEM_Hemibrain Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
12 lLN1_c_R - 1578826464 VFB_jrchk8ah Entity|has_image|Adult|Anatomy|has_neuron_conn... adult local interneuron of the lateral ALl1 ne... FBbt_00007394 neuprint_JRC_Hemibrain_1point1 1578826464 JRC_FlyEM_Hemibrain|JRC2018Unisex Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
13 lLN2P_a(Patchy)_R - 2041621893 VFB_jrchk8ao Entity|has_image|Adult|Anatomy|has_neuron_conn... adult antennal lobe lateral local neuron 2P FBbt_00049813 neuprint_JRC_Hemibrain_1point1 2041621893 JRC_FlyEM_Hemibrain|JRC2018Unisex Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
14 lLN2S(Star)_R - 1762359683 VFB_jrchk8bc Entity|has_image|Adult|Anatomy|has_neuron_conn... adult antennal lobe lateral local neuron 2S FBbt_00049815 neuprint_JRC_Hemibrain_1point1 1762359683 JRC2018Unisex|JRC_FlyEM_Hemibrain Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
15 lLN1_b_R - 5813054622 VFB_jrchk8a8 Entity|has_image|Adult|Anatomy|has_neuron_conn... adult local interneuron of the lateral ALl1 ne... FBbt_00007394 neuprint_JRC_Hemibrain_1point1 5813054622 JRC2018Unisex|JRC_FlyEM_Hemibrain Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
16 lLN2F_a(Full)_R - 1670287030 VFB_jrchk8al Entity|has_image|Adult|Anatomy|has_neuron_conn... adult antennal lobe lateral local neuron 2F FBbt_00049812 neuprint_JRC_Hemibrain_1point1 1670287030 JRC2018Unisex|JRC_FlyEM_Hemibrain Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
17 lLN12a_R - 1826445251 VFB_jrchk89g Entity|has_image|Adult|Anatomy|has_neuron_conn... adult local interneuron of the lateral ALl1 ne... FBbt_00007394 neuprint_JRC_Hemibrain_1point1 1826445251 JRC2018Unisex|JRC_FlyEM_Hemibrain Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
18 lLN11_R - 2040301572 VFB_jrchk89d Entity|has_image|Adult|Anatomy|has_neuron_conn... adult local interneuron of the lateral ALl1 ne... FBbt_00007394 neuprint_JRC_Hemibrain_1point1 2040301572 JRC2018Unisex|JRC_FlyEM_Hemibrain Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
19 il3LN6_R - 5813018460 VFB_jrchk88v Entity|has_image|Adult|Anatomy|has_neuron_conn... local interneuron of adult antennal lobe FBbt_00007390 neuprint_JRC_Hemibrain_1point1 5813018460 JRC_FlyEM_Hemibrain|JRC2018Unisex Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
20 lLN2R_b(Regional)_R - 5813076969 VFB_jrchk8b6 Entity|has_image|Adult|Anatomy|has_neuron_conn... adult antennal lobe lateral local neuron 2R FBbt_00049814 neuprint_JRC_Hemibrain_1point1 5813076969 JRC_FlyEM_Hemibrain|JRC2018Unisex Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
21 lLN16a_R - 1702318692 VFB_jrchk89t Entity|has_image|Adult|Anatomy|has_neuron_conn... adult local interneuron of the lateral ALl1 ne... FBbt_00007394 neuprint_JRC_Hemibrain_1point1 1702318692 JRC_FlyEM_Hemibrain|JRC2018Unisex Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
22 lLN2T_d(Tortuous)_R - 1667251683 VFB_jrchk8bp Entity|has_image|Adult|Anatomy|has_neuron_conn... adult antennal lobe lateral local neuron 2T FBbt_00049816 neuprint_JRC_Hemibrain_1point1 1667251683 JRC_FlyEM_Hemibrain|JRC2018Unisex Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
23 lLN2R_b(Regional)_R - 1702305987 VFB_jrchk8b5 Entity|has_image|Adult|Anatomy|has_neuron_conn... adult antennal lobe lateral local neuron 2R FBbt_00049814 neuprint_JRC_Hemibrain_1point1 1702305987 JRC2018Unisex|JRC_FlyEM_Hemibrain Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
24 v2LN35_R - 1733056086 VFB_jrchk8ew Entity|has_image|Adult|Anatomy|has_neuron_conn... local interneuron of adult antennal lobe FBbt_00007390 neuprint_JRC_Hemibrain_1point1 1733056086 JRC2018Unisex|JRC_FlyEM_Hemibrain Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
25 lLN1_b_R - 1610530558 VFB_jrchk8ac Entity|has_image|Adult|Anatomy|has_neuron_conn... adult local interneuron of the lateral ALl1 ne... FBbt_00007394 neuprint_JRC_Hemibrain_1point1 1610530558 JRC_FlyEM_Hemibrain|JRC2018Unisex Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
26 lLN2S(Star)_R - 1640922754 VFB_jrchk8b8 Entity|has_image|Adult|Anatomy|has_neuron_conn... adult antennal lobe lateral local neuron 2S FBbt_00049815 neuprint_JRC_Hemibrain_1point1 1640922754 JRC_FlyEM_Hemibrain|JRC2018Unisex Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
27 lLN1_c_R - 1824101645 VFB_jrchk8ag Entity|has_image|Adult|Anatomy|has_neuron_conn... adult local interneuron of the lateral ALl1 ne... FBbt_00007394 neuprint_JRC_Hemibrain_1point1 1824101645 JRC_FlyEM_Hemibrain|JRC2018Unisex Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
28 lLN1_c_R - 1547454812 VFB_jrchk8ai Entity|has_image|Adult|Anatomy|has_neuron_conn... adult local interneuron of the lateral ALl1 ne... FBbt_00007394 neuprint_JRC_Hemibrain_1point1 1547454812 JRC_FlyEM_Hemibrain|JRC2018Unisex Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
29 lLN1_b_R - 5813069055 VFB_jrchk8aa Entity|has_image|Adult|Anatomy|has_neuron_conn... adult local interneuron of the lateral ALl1 ne... FBbt_00007394 neuprint_JRC_Hemibrain_1point1 5813069055 JRC_FlyEM_Hemibrain|JRC2018Unisex Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
30 lLN1_b_R - 1642623277 VFB_jrchk8ad Entity|has_image|Adult|Anatomy|has_neuron_conn... adult local interneuron of the lateral ALl1 ne... FBbt_00007394 neuprint_JRC_Hemibrain_1point1 1642623277 JRC2018Unisex|JRC_FlyEM_Hemibrain Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
31 lLN2T_a(Tortuous)_R - 5813054726 VFB_jrchk8bh Entity|has_image|Adult|Anatomy|has_neuron_conn... adult antennal lobe lateral local neuron 2T FBbt_00049816 neuprint_JRC_Hemibrain_1point1 5813054726 JRC_FlyEM_Hemibrain|JRC2018Unisex Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
32 lLN2F_b(Full)_R - 1640909284 VFB_jrchk8am Entity|has_image|Adult|Anatomy|has_neuron_conn... adult antennal lobe lateral local neuron 2F FBbt_00049812 neuprint_JRC_Hemibrain_1point1 1640909284 JRC_FlyEM_Hemibrain|JRC2018Unisex Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
33 lLN2F_a(Full)_R - 5901218894 VFB_jrchk8ak Entity|has_image|Adult|Anatomy|has_neuron_conn... adult antennal lobe lateral local neuron 2F FBbt_00049812 neuprint_JRC_Hemibrain_1point1 5901218894 JRC_FlyEM_Hemibrain|JRC2018Unisex Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
34 lLN2T_e(Tortuous)_R - 1699974843 VFB_jrchk8br Entity|has_image|Adult|Anatomy|has_neuron_conn... adult antennal lobe lateral local neuron 2T FBbt_00049816 neuprint_JRC_Hemibrain_1point1 1699974843 JRC2018Unisex|JRC_FlyEM_Hemibrain Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
35 lLN10_R - 1825789179 VFB_jrchk89b Entity|has_image|Adult|Anatomy|has_neuron_conn... adult local interneuron of the lateral ALl1 ne... FBbt_00007394 neuprint_JRC_Hemibrain_1point1 1825789179 JRC_FlyEM_Hemibrain|JRC2018Unisex Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
36 lLN2S(Star)_R - 1702306037 VFB_jrchk8b7 Entity|has_image|Adult|Anatomy|has_neuron_conn... adult antennal lobe lateral local neuron 2S FBbt_00049815 neuprint_JRC_Hemibrain_1point1 1702306037 JRC2018Unisex|JRC_FlyEM_Hemibrain Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
37 lLN2S(Star)_R - 1732995501 VFB_jrchk8ba Entity|has_image|Adult|Anatomy|has_neuron_conn... adult antennal lobe lateral local neuron 2S FBbt_00049815 neuprint_JRC_Hemibrain_1point1 1732995501 JRC_FlyEM_Hemibrain|JRC2018Unisex Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
38 lLN2S(Star)_R - 5813069085 VFB_jrchk8b9 Entity|has_image|Adult|Anatomy|has_neuron_conn... adult antennal lobe lateral local neuron 2S FBbt_00049815 neuprint_JRC_Hemibrain_1point1 5813069085 JRC_FlyEM_Hemibrain|JRC2018Unisex Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
39 v2LN3b_R - 1888199872 VFB_jrchk8fg Entity|has_image|Adult|Anatomy|has_neuron_conn... local interneuron of adult antennal lobe FBbt_00007390 neuprint_JRC_Hemibrain_1point1 1888199872 JRC2018Unisex|JRC_FlyEM_Hemibrain Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
40 lLN1_b_R - 1640887603 VFB_jrchk8a6 Entity|has_image|Adult|Anatomy|has_neuron_conn... adult local interneuron of the lateral ALl1 ne... FBbt_00007394 neuprint_JRC_Hemibrain_1point1 1640887603 JRC_FlyEM_Hemibrain|JRC2018Unisex Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
41 lLN1_b_R - 5813078440 VFB_jrchk8a7 Entity|has_image|Adult|Anatomy|has_neuron_conn... adult local interneuron of the lateral ALl1 ne... FBbt_00007394 neuprint_JRC_Hemibrain_1point1 5813078440 JRC_FlyEM_Hemibrain|JRC2018Unisex Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
42 lLN2T_b(Tortuous)_R - 5813034493 VFB_jrchk8bm Entity|has_image|Adult|Anatomy|has_neuron_conn... adult antennal lobe lateral local neuron 2T FBbt_00049816 neuprint_JRC_Hemibrain_1point1 5813034493 JRC2018Unisex|JRC_FlyEM_Hemibrain Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
43 lLN1_b_R - 5813054777 VFB_jrchk8a9 Entity|has_image|Adult|Anatomy|has_neuron_conn... adult local interneuron of the lateral ALl1 ne... FBbt_00007394 neuprint_JRC_Hemibrain_1point1 5813054777 JRC2018Unisex|JRC_FlyEM_Hemibrain Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
44 v2LN30_R - 1671620613 VFB_jrchk8e8 Entity|has_image|Adult|Anatomy|has_neuron_conn... local interneuron of adult antennal lobe FBbt_00007390 neuprint_JRC_Hemibrain_1point1 1671620613 JRC_FlyEM_Hemibrain|JRC2018Unisex Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
45 v2LN3b_R - 5813034455 VFB_jrchk8ff Entity|has_image|Adult|Anatomy|has_neuron_conn... local interneuron of adult antennal lobe FBbt_00007390 neuprint_JRC_Hemibrain_1point1 5813034455 JRC2018Unisex|JRC_FlyEM_Hemibrain Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
46 lLN2T_a(Tortuous)_R - 5813032595 VFB_jrchk8bd Entity|has_image|Adult|Anatomy|has_neuron_conn... adult antennal lobe lateral local neuron 2T FBbt_00049816 neuprint_JRC_Hemibrain_1point1 5813032595 JRC2018Unisex|JRC_FlyEM_Hemibrain Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
47 lLN2T_a(Tortuous)_R - 5813056598 VFB_jrchk8bi Entity|has_image|Adult|Anatomy|has_neuron_conn... adult antennal lobe lateral local neuron 2T FBbt_00049816 neuprint_JRC_Hemibrain_1point1 5813056598 JRC2018Unisex|JRC_FlyEM_Hemibrain Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
48 lLN1_b_R - 5813054725 VFB_jrchk8ab Entity|has_image|Adult|Anatomy|has_neuron_conn... adult local interneuron of the lateral ALl1 ne... FBbt_00007394 neuprint_JRC_Hemibrain_1point1 5813054725 JRC2018Unisex|JRC_FlyEM_Hemibrain Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
49 lLN2P_b(Patchy)_R - 1946178096 VFB_jrchk8au Entity|has_image|Adult|Anatomy|has_neuron_conn... adult antennal lobe lateral local neuron 2P FBbt_00049813 neuprint_JRC_Hemibrain_1point1 1946178096 JRC2018Unisex|JRC_FlyEM_Hemibrain Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
50 lLN2T_a(Tortuous)_R - 5813055277 VFB_jrchk8bf Entity|has_image|Adult|Anatomy|has_neuron_conn... adult antennal lobe lateral local neuron 2T FBbt_00049816 neuprint_JRC_Hemibrain_1point1 5813055277 JRC_FlyEM_Hemibrain|JRC2018Unisex Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
51 l2LN18_R - 5813054773 VFB_jrchk891 Entity|has_image|Adult|Anatomy|has_neuron_conn... local interneuron of adult antennal lobe FBbt_00007390 neuprint_JRC_Hemibrain_1point1 5813054773 JRC_FlyEM_Hemibrain|JRC2018Unisex Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
52 lLN2T_a(Tortuous)_R - 1762354941 VFB_jrchk8bg Entity|has_image|Adult|Anatomy|has_neuron_conn... adult antennal lobe lateral local neuron 2T FBbt_00049816 neuprint_JRC_Hemibrain_1point1 1762354941 JRC_FlyEM_Hemibrain|JRC2018Unisex Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
# Find neurons by dataset/paper - on CATMAID

bates = pymaid.find_neurons(annotations='Paper: Bates and Schlegel et al 2020')
bates
INFO  : Found 583 neurons matching the search parameters (pymaid)

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
... ... ... ... ... ... ... ... ... ... ...
581 CatmaidNeuron Multiglomerular mlALT vPN VM7d+VM5d+DC4+6 LTS ... 4624378 NA NA NA NA NA NA 1 nanometer
582 CatmaidNeuron Uniglomerular mALT DL2d adPN 57342 ML 57341 NA NA NA NA NA NA 1 nanometer
# 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'])

label symbol id tags description miniref FlyBase PMID DOI
81 EM L1 Andrade et al. 2019 Andrade2019 Entity|Individual|DataSet [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
16 MBONs and split-GAL4 lines that target them (A... Aso2014 Entity|Individual|DataSet [] Aso et al., 2014, eLife 3: e04577 FBrf0227179 25535793 10.7554/eLife.04577
19 split-GAL4 lines for dopaminergic neurons (Aso... AsoRubin2016 Entity|Individual|DataSet [For comparison of the properties of memories ... Aso and Rubin, 2016, eLife 5: e16135 FBrf0233230 27441388 10.7554/eLife.16135
52 EM FAFB Bates and Schlegel et al 2020 BatesSchlegel2020 Entity|Individual|DataSet [FAFB EM reconstructed neurons from Bates and ... Bates and Schlegel et al., 2020 10.1016/j.cub.2020.06.042
0 Larval olfactory system neurons - EM (Berk2016) Berck2016 Entity|Individual|DataSet [Berck, Khandelwal et al. 2016] Berck et al., 2016, eLife 5: e14859 FBrf0232785 27177418 10.7554/eLife.14859
... ... ... ... ... ... ... ... ... ...
30 Lee lab adult brain lineage clone image set Yu2013 Entity|Individual|DataSet [An exhaustive set of lineage clones covering ... Yu et al., 2013, Curr. Biol. 23(8): 633--643 FBrf0221412 23541733 10.1016/j.cub.2013.02.057
15 EM L1 Zarin, Mark et al. 2019 Zarin2019 Entity|Individual|DataSet [L1 EM reconstructed neurons from Zarin, Mark ... Zarin, Mark et al., 2019 10.1101/617977
48 EM FAFB Zheng et al 2018 Zheng2018 Entity|Individual|DataSet [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
34 EM FAFB Zheng et al 2020 Zheng2020 Entity|Individual|DataSet [FAFB EM reconstructed neurons from Zheng et a... Zheng et al. 2020 10.1101/2020.04.17.047167
28 Larval motor circuit neurons (Zwart2016) Zwart2016 Entity|Individual|DataSet [Zwart et al. 2016] Zwart et al., 2016, Neuron 91(3): 615--628 FBrf0233076 27427461 10.1016/j.neuron.2016.06.031

83 rows × 9 columns

sayin_tab = pd.DataFrame.from_records(vc.get_instances_by_dataset('Sayin2019', summary=True))
sayin_tab

label symbol id tags parents_label parents_id data_source accession templates dataset license
0 OA-VPM3 (FAFB:1329078) VFB_001001dr Entity|Octopaminergic|Adult|Anatomy|has_image|... 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|Octopaminergic|Adult|Anatomy|has_image|... octopaminergic VPM4 neuron FBbt_00110152 catmaid_fafb 1191261 JRC2018Unisex Sayin2019 https://creativecommons.org/licenses/by-sa/4.0...
vc.get_connected_neurons_by_type(upstream_type='LNd', downstream_type='adult descending neuron', weight=20)

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 - 5813021192 25 VFB_jrchjthm DNp27_R - 1072063538 LNd neuron descending neuron of the posterior brain DNp27 neuprint_JRC_Hemibrain_1point1 5813021192 neuprint_JRC_Hemibrain_1point1 1072063538
# Intra pacemaker neuron neuron connections

vc.get_connected_neurons_by_type(upstream_type='pacemaker neuron', downstream_type='pacemaker neuron', weight=20)

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_jrchjzxy LNd_R - 5813069648 37 VFB_jrchk8e0 5th s-LNv - 511051477 LNd neuron s-LNv neuron neuprint_JRC_Hemibrain_1point1 5813069648 neuprint_JRC_Hemibrain_1point1 511051477
1 VFB_jrchk089 LPN_R - 480029788 43 VFB_jrchk08a LPN_R - 450034902 LP neuron LP neuron neuprint_JRC_Hemibrain_1point1 480029788 neuprint_JRC_Hemibrain_1point1 450034902
2 VFB_jrchjtf0 DN1pA_R - 324846570 25 VFB_jrchk8e0 5th s-LNv - 511051477 DN1p neuron s-LNv neuron neuprint_JRC_Hemibrain_1point1 324846570 neuprint_JRC_Hemibrain_1point1 511051477
3 VFB_jrchjtf0 DN1pA_R - 324846570 37 VFB_jrchjzxy LNd_R - 5813069648 DN1p neuron LNd neuron neuprint_JRC_Hemibrain_1point1 324846570 neuprint_JRC_Hemibrain_1point1 5813069648
4 VFB_jrchk8e0 5th s-LNv - 511051477 40 VFB_jrchjzxy LNd_R - 5813069648 s-LNv neuron LNd neuron neuprint_JRC_Hemibrain_1point1 511051477 neuprint_JRC_Hemibrain_1point1 5813069648
5 VFB_jrchjtf3 DN1pA_R - 387166379 25 VFB_jrchk8e0 5th s-LNv - 511051477 DN1p neuron s-LNv neuron neuprint_JRC_Hemibrain_1point1 387166379 neuprint_JRC_Hemibrain_1point1 511051477
6 VFB_jrchjtf1 DN1pA_R - 325529237 30 VFB_jrchjzxy LNd_R - 5813069648 DN1p neuron LNd neuron neuprint_JRC_Hemibrain_1point1 325529237 neuprint_JRC_Hemibrain_1point1 5813069648
7 VFB_jrchk8e0 5th s-LNv - 511051477 25 VFB_jrchjzxx LNd_R - 5813021192 s-LNv neuron LNd neuron neuprint_JRC_Hemibrain_1point1 511051477 neuprint_JRC_Hemibrain_1point1 5813021192
8 VFB_jrchjtez DN1pA_R - 5813010153 25 VFB_jrchk8e0 5th s-LNv - 511051477 DN1p neuron s-LNv neuron neuprint_JRC_Hemibrain_1point1 5813010153 neuprint_JRC_Hemibrain_1point1 511051477
9 VFB_jrchjzxy LNd_R - 5813069648 29 VFB_jrchjzxw LNd_R - 5813056917 LNd neuron LNd neuron neuprint_JRC_Hemibrain_1point1 5813069648 neuprint_JRC_Hemibrain_1point1 5813056917
10 VFB_jrchjtf2 DN1pA_R - 387944118 22 VFB_jrchk8e0 5th s-LNv - 511051477 DN1p neuron s-LNv neuron neuprint_JRC_Hemibrain_1point1 387944118 neuprint_JRC_Hemibrain_1point1 511051477
11 VFB_jrchjtf2 DN1pA_R - 387944118 34 VFB_jrchjzxy LNd_R - 5813069648 DN1p neuron LNd neuron neuprint_JRC_Hemibrain_1point1 387944118 neuprint_JRC_Hemibrain_1point1 5813069648
12 VFB_jrchjtf1 DN1pA_R - 325529237 33 VFB_jrchk8e0 5th s-LNv - 511051477 DN1p neuron s-LNv neuron neuprint_JRC_Hemibrain_1point1 325529237 neuprint_JRC_Hemibrain_1point1 511051477
13 VFB_jrchk08a LPN_R - 450034902 30 VFB_jrchk089 LPN_R - 480029788 LP neuron LP neuron neuprint_JRC_Hemibrain_1point1 450034902 neuprint_JRC_Hemibrain_1point1 480029788
14 VFB_jrchjtey DN1a_R - 5813022274 63 VFB_jrchk8e0 5th s-LNv - 511051477 DN1a neuron s-LNv neuron neuprint_JRC_Hemibrain_1point1 5813022274 neuprint_JRC_Hemibrain_1point1 511051477
15 VFB_jrchjtex DN1a_R - 264083994 55 VFB_jrchk8e0 5th s-LNv - 511051477 DN1a neuron s-LNv neuron neuprint_JRC_Hemibrain_1point1 264083994 neuprint_JRC_Hemibrain_1point1 511051477
16 VFB_jrchjtey DN1a_R - 5813022274 75 VFB_jrchjzxy LNd_R - 5813069648 DN1a neuron LNd neuron neuprint_JRC_Hemibrain_1point1 5813022274 neuprint_JRC_Hemibrain_1point1 5813069648
17 VFB_jrchjtex DN1a_R - 264083994 79 VFB_jrchjzxy LNd_R - 5813069648 DN1a neuron LNd neuron neuprint_JRC_Hemibrain_1point1 264083994 neuprint_JRC_Hemibrain_1point1 5813069648
18 VFB_jrchjtf3 DN1pA_R - 387166379 30 VFB_jrchjzxy LNd_R - 5813069648 DN1p neuron LNd neuron neuprint_JRC_Hemibrain_1point1 387166379 neuprint_JRC_Hemibrain_1point1 5813069648
19 VFB_jrchjzxy LNd_R - 5813069648 21 VFB_jrchjzxx LNd_R - 5813021192 LNd neuron LNd neuron neuprint_JRC_Hemibrain_1point1 5813069648 neuprint_JRC_Hemibrain_1point1 5813021192

vc.get_connected_neurons_by_type(upstream_type='adult neuron', downstream_type='adult Drosulfakinin neuron', weight=20)

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_jrchjsj3 AstA1_L - 362473525 28 VFB_jrchjti4 DSKMP1B_R - 1352077058 adult neuron adult Drosulfakinin neuron neuprint_JRC_Hemibrain_1point1 362473525 neuprint_JRC_Hemibrain_1point1 1352077058
1 VFB_jrchk5zh SLP384_R - 482702027 20 VFB_jrchjti6 DSKMP3_R - 327937328 adult superior lateral protocerebrum neuron 384 adult Drosulfakinin neuron neuprint_JRC_Hemibrain_1point1 482702027 neuprint_JRC_Hemibrain_1point1 327937328
2 VFB_jrchjrjn AVLP001_R - 1321564092 26 VFB_jrchjti2 DSKMP1A_R - 1135837629 adult anterior ventrolateral protocerebrum neu... adult Drosulfakinin neuron neuprint_JRC_Hemibrain_1point1 1321564092 neuprint_JRC_Hemibrain_1point1 1135837629
3 VFB_jrchk5eo SLP066_R - 327843160 42 VFB_jrchjti4 DSKMP1B_R - 1352077058 adult superior lateral protocerebrum neuron 066 adult Drosulfakinin neuron neuprint_JRC_Hemibrain_1point1 327843160 neuprint_JRC_Hemibrain_1point1 1352077058
4 VFB_jrchk5qf SLP244_R - 298214577 27 VFB_jrchjti6 DSKMP3_R - 327937328 adult superior lateral protocerebrum neuron 244 adult Drosulfakinin neuron neuprint_JRC_Hemibrain_1point1 298214577 neuprint_JRC_Hemibrain_1point1 327937328
... ... ... ... ... ... ... ... ... ... ... ...
56 VFB_jrchk6zu SMP449_R - 5813026592 25 VFB_jrchjti4 DSKMP1B_R - 1352077058 adult superior medial protocerebrum neuron 449 adult Drosulfakinin neuron neuprint_JRC_Hemibrain_1point1 5813026592 neuprint_JRC_Hemibrain_1point1 1352077058
57 VFB_jrchk5jv SLP152_R - 487812620 28 VFB_jrchjti4 DSKMP1B_R - 1352077058 adult superior lateral protocerebrum neuron 152 adult Drosulfakinin neuron neuprint_JRC_Hemibrain_1point1 487812620 neuprint_JRC_Hemibrain_1point1 1352077058
58 VFB_jrchjrxe AVLP223_R - 1356743512 27 VFB_jrchjti2 DSKMP1A_R - 1135837629 adult anterior ventrolateral protocerebrum neu... adult Drosulfakinin neuron neuprint_JRC_Hemibrain_1point1 1356743512 neuprint_JRC_Hemibrain_1point1 1135837629
59 VFB_jrchk5qg SLP244_R - 297533212 33 VFB_jrchjti6 DSKMP3_R - 327937328 adult superior lateral protocerebrum neuron 244 adult Drosulfakinin neuron neuprint_JRC_Hemibrain_1point1 297533212 neuprint_JRC_Hemibrain_1point1 327937328
60 VFB_jrchk6g5 SMP157_R - 421041565 32 VFB_jrchjti4 DSKMP1B_R - 1352077058 adult superior medial protocerebrum neuron 157 adult Drosulfakinin neuron neuprint_JRC_Hemibrain_1point1 421041565 neuprint_JRC_Hemibrain_1point1 1352077058

61 rows × 11 columns

5.1.1.4 - Mapping

If you have a single neuron, how can you find other neurons of the same or similar type within or between data sources?
!pip install vfb-connect --upgrade
# 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}')

# Many functions return JSON-compatible nested data structures. This function coverts them to DataFrame.
def summary_2_df(summary, sort=None):
    """Convert summary to DataFrame.  Optionally specify a set of columns to sort as a list of strings"""
    if sort:
        return pd.DataFrame.from_records(summary).sort_values(sort)
    else:
        return pd.DataFrame.from_records(summary)
WARNING: Could not load OpenGL library.
INFO  : Global CATMAID instance set. Caching is ON. (pymaid)
Server is running CATMAID version 2020.02.15-925-gf56795c9c

Mapping

Use case: If I have a single neuron, how can I find other neurons of the same or similar type within or between data sources?

Mapping via common parent type

# lets take some examples from a discovery query on the previous spreadhseet
sayin_tab = pd.DataFrame.from_records(vc.get_instances_by_dataset('Sayin2019', summary=True))
sayin_tab

label symbol id tags parents_label parents_id data_source accession templates dataset license
0 OA-VPM3 (FAFB:1329078) VFB_001001dr Entity|Octopaminergic|Adult|Anatomy|has_image|... 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|Octopaminergic|Adult|Anatomy|has_image|... octopaminergic VPM4 neuron FBbt_00110152 catmaid_fafb 1191261 JRC2018Unisex Sayin2019 https://creativecommons.org/licenses/by-sa/4.0...
oct_VPM3 = summary_2_df(vc.get_instances('octopaminergic VPM3 neuron', summary=True))
oct_VPM3

label symbol id tags parents_label parents_id data_source accession templates dataset license
0 OA-VPM3(NO2/NO3)_R - 329566174 VFB_jrchk10d Entity|Octopaminergic|Adult|Anatomy|has_image|... octopaminergic VPM3 neuron FBbt_00110151 neuprint_JRC_Hemibrain_1point1 329566174 JRC2018Unisex|JRC_FlyEM_Hemibrain Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
1 OA-VPM3(NO2/NO3)_L - 5813061260 VFB_jrchk10e Entity|Octopaminergic|Adult|Anatomy|has_image|... octopaminergic VPM3 neuron FBbt_00110151 neuprint_JRC_Hemibrain_1point1 5813061260 JRC_FlyEM_Hemibrain|JRC2018Unisex Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le...
2 OA-VPM3 (FAFB:1329078) VFB_001001dr Entity|Octopaminergic|Adult|Anatomy|has_image|... octopaminergic VPM3 neuron FBbt_00110151 catmaid_fafb 1329078 JRC2018Unisex Sayin2019 https://creativecommons.org/licenses/by-sa/4.0...
oct_VPM3_images = vc.neo_query_wrapper.get_images(oct_VPM3['id'], stomp=True, template='JRC2018Unisex', image_folder = 'oct_VPM3b')
oct_VPM3_images

label symbol id tags parents_label parents_id data_source accession templates dataset license filename
0 OA-VPM3 (FAFB:1329078) VFB_001001dr Entity|Octopaminergic|Adult|Anatomy|has_image|... octopaminergic VPM3 neuron FBbt_00110151 catmaid_fafb 1329078 JRC2018Unisex Sayin2019 https://creativecommons.org/licenses/by-sa/4.0... OA_VPM3__FAFB_1329078_.swc
1 OA-VPM3(NO2/NO3)_L - 5813061260 VFB_jrchk10e Entity|Octopaminergic|Adult|Anatomy|has_image|... octopaminergic VPM3 neuron FBbt_00110151 neuprint_JRC_Hemibrain_1point1 5813061260 JRC_FlyEM_Hemibrain|JRC2018Unisex Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le... OA_VPM3_NO2_NO3__L___5813061260.swc
2 OA-VPM3(NO2/NO3)_R - 329566174 VFB_jrchk10d Entity|Octopaminergic|Adult|Anatomy|has_image|... octopaminergic VPM3 neuron FBbt_00110151 neuprint_JRC_Hemibrain_1point1 329566174 JRC2018Unisex|JRC_FlyEM_Hemibrain Xu2020NeuronsV1point1 https://creativecommons.org/licenses/by/4.0/le... OA_VPM3_NO2_NO3__R___329566174.swc
oct_VPM3_images = vc.get_images_by_type('octopaminergic VPM3 neuron', stomp=True, template='JRC2018Unisex', image_folder = 'oct_VPM3')
nl = navis.read_swc('./oct_VPM3')
navis.plot3d(nl)
Running query: FBbt:00110151
Query URL: http://owl.virtualflybrain.org/kbs/vfb/instances?object=FBbt%3A00110151&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: 3