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male-drosophila-visual-system-connectome-code

Supplemental source code for Nern et al. 2025: "Connectome-driven neural inventory of a complete visual system" (https://doi.org/10.1038/s41586-025-08746-0). The Cell type explorer repository is at https://github.com/reiserlab/male-drosophila-visual-system-connectome

https://github.com/reiserlab/male-drosophila-visual-system-connectome-code

Science Score: 44.0%

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    Low similarity (13.5%) to scientific vocabulary

Keywords

connectome drosophila visual-system
Last synced: 7 months ago · JSON representation ·

Repository

Supplemental source code for Nern et al. 2025: "Connectome-driven neural inventory of a complete visual system" (https://doi.org/10.1038/s41586-025-08746-0). The Cell type explorer repository is at https://github.com/reiserlab/male-drosophila-visual-system-connectome

Basic Info
Statistics
  • Stars: 6
  • Watchers: 4
  • Forks: 3
  • Open Issues: 0
  • Releases: 2
Topics
connectome drosophila visual-system
Created about 2 years ago · Last pushed 9 months ago
Metadata Files
Readme Contributing License Citation

README.md

Optic Lobe Connectome

This repository is a collection of code for analyzing the optic lobe in the new male brain dataset (Janelia FlyEM).

Infrastructure

To allow others in the team to replicate the analysis, the code should be human-readable and run on several systems.

Set up a Python environment

In the guide on "Getting started in Python", we provide a step-by-step documentation on how to set up a working environment and run you through a first analysis. In essence, we suggest to install pixi and create a copy of the .env-sample file with the name .env. After completion, you can open a Jupyter notebook via pixi run jupyter lab src/python-bootcamp/local_demo.ipynb. The first time this command is run, all necessary dependencies are installed automatically, which might take up to two minutes. Running the example notebook itself on local data inside the Jupyter Lab environment will not require a connection to neuPrint and takes less than a second to produce two interactive plots for a neuron.

Changing the number of the bodyId is enough to run the same analysis on the most recent neuPrint database, but requires additional setup steps from our "Getting started in Python" guide. In our guide Editing Python files we show two different ways to edit and run Jupyter notebooks.

Our software depends on Blender>3.6, Python>3.10, and a number of python libraries. The comprehensive list of python libraries and their versions are listed in the pyproject.toml file navis, neuprint-python, kaleido, snakemake, pymupdf, snakemake-executor-plugin-lsf, cloud-volume, google-cloud-storage, fastcluster, ipykernel, numpy, nptyping, pynrrd, python-dotenv, alphashape, openpyxl, ipywidgets, nbformat, cmap, k3d, datrie, nbconvert, kneed, jupyterlab, jupytext, and pylint.

Our software has been tested with Python 3.10 to 3.12 and Blender 3.6 to 4.2 on Linux, MacOS, and Windows.

Owner

  • Name: Reiser Lab
  • Login: reiserlab
  • Kind: organization

Citation (CITATION.cff) 

cff-version: 1.2.0
message: Please cite the following works when using this software.
authors:
  - family-names: Loesche
    given-names: Frank
    orcid: https://orcid.org/0000-0002-7780-6438
  - family-names: Koskela
    given-names: Sanna
    orcid: https://orcid.org/0000-0002-0496-5016
  - family-names: Burnett
    given-names: Laura E
    orcid: https://orcid.org/0000-0002-8937-410X  
  - family-names: Rogers
    given-names: Edward M
    orcid: https://orcid.org/0000-0002-8275-1830
  - family-names: Hoeller
    given-names: Judith
    orcid: https://orcid.org/0009-0004-7261-4156
  - family-names: Gruntman
    given-names: Eyal
    orcid: https://orcid.org/0000-0003-1383-7347
  - family-names: Longden
    given-names: Kit D
    orcid: https://orcid.org/0000-0002-7686-6447
  - family-names: Zhao
    given-names: Arthur
    orcid: https://orcid.org/0000-0003-2869-4393
  - family-names: Seenivasan
    given-names: Pavithraa
    orcid: https://orcid.org/0000-0002-1527-208X
  - family-names: Dreher
    given-names: Marisa
    orcid: https://orcid.org/0000-0002-0041-9229
  - family-names: Berg
    given-names: Stuart
    orcid: https://orcid.org/0000-0002-0766-0488
  - family-names: Nern
    given-names: Aljoscha
    orcid: https://orcid.org/0000-0002-3822-489X
  - family-names: Reiser
    given-names: Michael B
    orcid: https://orcid.org/0000-0002-4108-4517
title: "Supplemental source code for 'Connectome-driven neural inventory of a complete visual system'"
version: 1.0
doi: 10.5281/zenodo.13633521
date-released: 2025-03-12
url: "https://github.com/reiserlab/male-drosophila-visual-system-connectome-code"
preferred-citation:
  abstract: >-
    <jats:p>Vision provides animals with detailed information about their
    surroundings, conveying diverse features such as color, form, and movement
    across the visual scene. Computing these parallel spatial features requires
    a large and diverse network of neurons, such that in animals as distant as
    flies and humans, visual regions comprise half the brain's volume. These
    visual brain regions often reveal remarkable structure-function
    relationships, with neurons organized along spatial maps with shapes that
    directly relate to their roles in visual processing. To unravel the stunning
    diversity of a complex visual system, a careful mapping of the neural
    architecture matched to tools for targeted exploration of that circuitry is
    essential. Here, we report a new connectome of the right optic lobe from a
    male Drosophila central nervous system FIB-SEM volume and a comprehensive
    inventory of the fly's visual neurons. We developed a computational
    framework to quantify the anatomy of visual neurons, establishing a basis
    for interpreting how their shapes relate to spatial vision. By integrating
    this analysis with connectivity information, neurotransmitter identity, and
    expert curation, we classified the ~53,000 neurons into 727 types, about
    half of which are systematically described and named for the first time.
    Finally, we share an extensive collection of split-GAL4 lines matched to our
    neuron type catalog. Together, this comprehensive set of tools and data
    unlock new possibilities for systematic investigations of vision in
    Drosophila, a foundation for a deeper understanding of sensory
    processing.</jats:p>
  authors:
    - family-names: Nern
      given-names: Aljoscha
      orcid: https://orcid.org/0000-0002-3822-489X
    - family-names: Loesche
      given-names: Frank
      orcid: https://orcid.org/0000-0002-7780-6438
    - family-names: Takemura
      given-names: Shin-ya
      orcid: https://orcid.org/0000-0003-2400-6426
    - family-names: Burnett
      given-names: Laura E
      orcid: https://orcid.org/0000-0002-8937-410X
    - family-names: Dreher
      given-names: Marisa
      orcid: https://orcid.org/0000-0002-0041-9229
    - family-names: Gruntman
      given-names: Eyal
      orcid: https://orcid.org/0000-0003-1383-7347
    - family-names: Hoeller
      given-names: Judith
      orcid: https://orcid.org/0009-0004-7261-4156
    - family-names: Huang
      given-names: Gary B
      orcid: https://orcid.org/0000-0002-9606-3510
    - family-names: Januszewski
      given-names: Michal
      orcid: https://orcid.org/0000-0002-3480-2744
    - family-names: Klapoetke
      given-names: Nathan C
      orcid: https://orcid.org/0000-0002-3270-1966
    - family-names: Koskela
      given-names: Sanna
      orcid: https://orcid.org/0000-0002-0496-5016
    - family-names: Longden
      given-names: Kit D
      orcid: https://orcid.org/0000-0002-7686-6447
    - family-names: Lu
      given-names: Zhiyuan
      orcid: https://orcid.org/0000-0002-4128-9774
    - family-names: Preibisch
      given-names: Stephan
      orcid: https://orcid.org/0000-0002-0276-494X
    - family-names: Qiu
      given-names: Wei
      orcid: https://orcid.org/0009-0008-1764-5928
    - family-names: Rogers
      given-names: Edward M
      orcid: https://orcid.org/0000-0002-8275-1830
    - family-names: Seenivasan
      given-names: Pavithraa
      orcid: https://orcid.org/0000-0002-1527-208X
    - family-names: Zhao
      given-names: Arthur
      orcid: https://orcid.org/0000-0003-2869-4393
    - family-names: Bogovic
      given-names: John
      orcid: https://orcid.org/0000-0002-4829-9457
    - family-names: Canino
      given-names: Brandon S
      orcid: https://orcid.org/0000-0002-8454-865X
    - family-names: Clements
      given-names: Jody
      orcid: https://orcid.org/0000-0003-3932-8188
    - family-names: Cook
      given-names: Michael
      orcid: https://orcid.org/0000-0002-7892-6845
    - family-names: Finley-May
      given-names: Samantha
      orcid: https://orcid.org/0000-0002-8086-206X
    - family-names: Flynn
      given-names: Miriam A
      orcid: https://orcid.org/0000-0002-3314-4823
    - family-names: Fragniere
      given-names: Alexandra MC
    - family-names: Hameed
      given-names: Imran
      orcid: https://orcid.org/0000-0001-5431-9162
    - family-names: Hayworth
      given-names: Kenneth J
      orcid: https://orcid.org/0000-0002-6467-7024
    - family-names: Hopkins
      given-names: Gary Patrick
      orcid: https://orcid.org/0000-0002-6918-1589
    - family-names: Hubbard
      given-names: Philip M
      orcid: https://orcid.org/0000-0002-6746-5035
    - family-names: Katz
      given-names: William T
      orcid: https://orcid.org/0000-0002-9417-6212
    - family-names: Kovalyak
      given-names: Julie
      orcid: https://orcid.org/0000-0001-7864-7734
    - family-names: Lauchie
      given-names: Shirley A
      orcid: https://orcid.org/0000-0001-8223-9522
    - family-names: Leonard
      given-names: Meghan
      orcid: https://orcid.org/0009-0005-4678-8213
    - family-names: Lohff
      given-names: Alanna
      orcid: https://orcid.org/0000-0002-1242-1836
    - family-names: Maldonado
      given-names: Charli A
      orcid: https://orcid.org/0000-0002-0151-3719
    - family-names: Mooney
      given-names: Caroline
      orcid: https://orcid.org/0000-0003-4938-532X
    - family-names: Okeoma
      given-names: Nneoma
      orcid: https://orcid.org/0000-0001-8829-5007
    - family-names: Olbris
      given-names: Donald J
      orcid: https://orcid.org/0009-0008-8581-0550
    - family-names: Ordish
      given-names: Christopher
      orcid: https://orcid.org/0000-0001-8439-9714
    - family-names: Paterson
      given-names: Tyler
      orcid: https://orcid.org/0000-0002-9297-5504
    - family-names: Phillips
      given-names: Emily M
      orcid: https://orcid.org/0000-0001-7615-301X
    - family-names: Pietzsch
      given-names: Tobias
      orcid: https://orcid.org/0000-0002-9477-3957
    - family-names: Rivas Salinas
      given-names: Jennifer
      orcid: https://orcid.org/0009-0005-4244-793X
    - family-names: Rivlin
      given-names: Patricia K
      orcid: https://orcid.org/0000-0002-3435-1955
    - family-names: Schlegel
      given-names: Philipp
      orcid: https://orcid.org/0000-0002-5633-1314
    - family-names: Scott
      given-names: Ashley L
      orcid: https://orcid.org/0000-0002-1835-5016
    - family-names: Scuderi
      given-names: Louis A
      orcid: https://orcid.org/0009-0002-6238-5789
    - family-names: Takemura
      given-names: Satoko
      orcid: https://orcid.org/0000-0002-2863-0050
    - family-names: Talebi
      given-names: Iris
      orcid: https://orcid.org/0000-0002-0173-8053
    - family-names: Thomson
      given-names: Alexander
      orcid: https://orcid.org/0000-0001-8462-2090
    - family-names: Trautman
      given-names: Eric T
      orcid: https://orcid.org/0000-0001-8588-0569
    - family-names: Umayam
      given-names: Lowell
      orcid: https://orcid.org/0000-0002-0255-1522
    - family-names: Walsh
      given-names: Claire
      orcid: https://orcid.org/0000-0002-6774-7307
    - family-names: Walsh
      given-names: John J
      orcid: https://orcid.org/0000-0002-7176-4708
    - family-names: Xu
      given-names: C Shan
      orcid: https://orcid.org/0000-0002-8564-7836
    - family-names: Yakal
      given-names: Emily A
      orcid: https://orcid.org/0000-0002-4467-124X
    - family-names: Yang
      given-names: Tansy
      orcid: https://orcid.org/0000-0003-1131-0410
    - family-names: Zhao
      given-names: Ting
      orcid: https://orcid.org/0000-0002-8053-412X
    - family-names: Funke
      given-names: Jan
      orcid: https://orcid.org/0000-0003-4388-7783
    - family-names: George
      given-names: Reed
    - family-names: Hess
      given-names: Harald F
      orcid: https://orcid.org/0000-0003-3000-1533
    - family-names: Jefferis
      given-names: Gregory S X E
      orcid: https://orcid.org/0000-0002-0587-9355
    - family-names: Knecht
      given-names: Christopher
      orcid: https://orcid.org/0000-0002-9230-2772
    - family-names: Korff
      given-names: Wyatt
      orcid: https://orcid.org/0000-0001-8396-1533
    - family-names: Plaza
      given-names: Stephen M
      orcid: https://orcid.org/0000-0001-7425-8555
    - family-names: Romani
      given-names: Sandro
      orcid: https://orcid.org/0000-0002-4727-4207
    - family-names: Saalfeld
      given-names: Stephan
      orcid: https://orcid.org/0000-0002-4106-1761
    - family-names: Scheffer
      given-names: Louis K
      orcid: https://orcid.org/0000-0002-3289-6564
    - family-names: Berg
      given-names: Stuart
      orcid: https://orcid.org/0000-0002-0766-0488
    - family-names: Rubin
      given-names: Gerald M
      orcid: https://orcid.org/0000-0001-8762-8703
    - family-names: Reiser
      given-names: Michael B
      orcid: https://orcid.org/0000-0002-4108-4517
  doi: 10.1101/2024.04.16.589741
  identifiers:
    - type: doi
      value: 10.1101/2024.04.16.589741
    - type: url
      value: http://dx.doi.org/10.1101/2024.04.16.589741
  title: Connectome-driven neural inventory of a complete visual system
  url: http://dx.doi.org/10.1101/2024.04.16.589741
  database: Crossref
  date-published: 2024-04-18
  year: 2024
  month: 4
  publisher:
    name: Cold Spring Harbor Laboratory
  type: article

GitHub Events

Total
  • Release event: 1
  • Watch event: 6
  • Push event: 12
  • Fork event: 3
  • Create event: 2
Last Year
  • Release event: 1
  • Watch event: 6
  • Push event: 12
  • Fork event: 3
  • Create event: 2

Dependencies

pyproject.toml pypi
  • cloud-volume >=10.4.0,<11
  • fastcluster >=1.2.6,<2
  • google-cloud-storage >=2.18.2,<3
  • kaleido >=0.2.1,<0.3
  • navis >=1.7.0,<2
  • neuprint-python >=0.4.26,<0.5
  • pymupdf >=1.24.10,<2
  • snakemake >=8.20.3,<9
  • snakemake-executor-plugin-lsf >=0.2.6,<0.3