OSCR

Connectome-driven neural inventory of a complete visual system.

This page is built on request from the registry's record of the paper. The 6,000 most recent papers have a fuller page, built ahead of time, with the Code ↔ Paper reader, the tracing map and its validation, the record's versions, how to cite it and similar papers. This paper is older: its record, its code, its data and the requests about it are below.

Code

2,442 files of its code read; 20 matches between paragraphs and code. The Code ↔ Paper reader is built for the 6,000 most recent papers only: this paper's code is read at its source.

saalfeldlab/render

License: GPL-2.0
State: the link answers
Copies: kept by the registry: this license allows it

saalfeldlab/hot-knife

License: GPL-2.0
State: the link answers
Copies: kept by the registry: this license allows it

saalfeldlab/template-building

License: BSD-2-Clause
State: the link answers
Copies: kept by the registry: this license allows it

sp4cerat/Fast-Quadric-Mesh-Simplification

License: MIT
State: the link answers
Copies: kept by the registry: this license allows it

Zenodo 10891950

License: CC-BY-4.0
State: the link answers

navis-org/navis

License: GPL-3.0
State: the link answers
Copies: kept by the registry: this license allows it

flyconnectome/ol_annotations

License: none: the authors keep all their rights
State: the link answers
Copies: kept by the registry: this license allows it

reiserlab/male-drosophila-visual-system-connectome-code

License: GPL-3.0
State: the link answers
Copies: kept by the registry: this license allows it

Zenodo 7592899

License: BSD-3-Clause
State: the link answers

Zenodo 4699382

License: GPL-3.0
State: the link answers
Copies: kept by the registry: this license allows it

Zenodo 10366992

License: CC-BY-4.0
State: the link answers
Copies: kept by the registry: this license allows it

Zenodo 13633521

License: GPL-3.0
State: the link answers

Zenodo 15045306

License: GPL-3.0
State: the link answers

reiserlab/male-drosophila-visual-system-connectome

License: CC-BY-4.0
State: the link answers
Copies: kept by the registry: this license allows it

Zenodo 15015112

License: CC-BY-4.0
State: the link answers

connectome-neuprint/neuvid

License: BSD-3-Clause
State: the link answers
Copies: kept by the registry: this license allows it

connectome-neuprint/neuprint-python

License: BSD-3-Clause
State: the link answers
Copies: kept by the registry: this license allows it
Tools found in the code: AllenSDK, ANTs, ggplot2, h5py, igraph, ImageJ / Fiji, Matplotlib, NetworkX, NEURON, NiBabel, Numba, NumPy, pandas, Pillow, Plotly, reshape2, rpy2, scikit-image, scikit-learn, SciPy, seaborn, statsmodels, tidyverse, tifffile, UMAP

Overview

Authors: Aljoscha Nern, Frank Loesche, Shin-ya Takemura, Laura E. Burnett, Marisa Dreher, Eyal Gruntman, Judith Hoeller, Gary B. Huang, Michał Januszewski, Nathan C. Klapoetke, Sanna Koskela, Kit D. Longden, Zhiyuan Lu, Stephan Preibisch, Wei Qiu, Edward M. Rogers, Pavithraa Seenivasan, Arthur Zhao, John Bogovic, Brandon S. Canino
and 51 other authorsJody Clements, Michael Cook, Samantha Finley-May, Miriam A. Flynn, Imran Hameed, Alexandra M. C. Fragniere, Kenneth J. Hayworth, Gary Patrick Hopkins, Philip M. Hubbard, William T. Katz, Julie Kovalyak, Shirley A. Lauchie, Meghan Leonard, Alanna Lohff, Charli A. Maldonado, Caroline Mooney, Nneoma Okeoma, Donald J. Olbris, Christopher Ordish, Tyler Paterson, Emily M. Phillips, Tobias Pietzsch, Jennifer Rivas Salinas, Patricia K. Rivlin, Philipp Schlegel, Ashley L. Scott, Louis A. Scuderi, Satoko Takemura, Iris Talebi, Alexander Thomson, Eric T. Trautman, Lowell Umayam, Claire Walsh, John J. Walsh, C. Shan Xu, Emily A. Yakal, Tansy Yang, Ting Zhao, Jan Funke, Reed George, Harald F. Hess, Gregory S. X. E. Jefferis, Christopher Knecht, Wyatt Korff, Stephen M. Plaza, Sandro Romani, Stephan Saalfeld, Louis K. Scheffer, Stuart Berg, Gerald M. Rubin, Michael B. Reiser
Journal: Nature
Published: 26 March 2025
Type: Research article
Status: code verified (how the code is found and verified)
DOI: 10.1038/s41586-025-08746-0
License: CC BY
Institutions: Janelia Research Campus (United States), University of Toronto (Canada), Google (Switzerland) (Switzerland), MRC Laboratory of Molecular Biology (United Kingdom), University of Cambridge (United Kingdom)
Categories: drosophila (organism)

Data

Datasets cited

Contribute

The authors of this paper can claim it and correct its record, and the maintainers of its code (its owner, or a public member of its organization) correct what it says of their repository; anyone signed in can ask for its removal. Every request goes to the registry's own machine, which answers it; your account page follows them.

Sign in with ORCID to claim this paper as one of its authors or correct its record: when the paper's metadata lists your ORCID iD, you are recognized at once. Maintainers of its code: sign in with GitHub, then claim the repository on your account page.

Add the badge to the code's README

OSCR: the badge of this paper

Authors and maintainers of this paper's code: the badge says what OSCR knows of the paper and links the code to this page. Paste one of these under the README's title. Keep the two marks around it: they let the badge be replaced in place, never added twice. Nothing is changed for you.

Markdown
<!-- oscr-badge:start -->
[![OSCR](https://openscicode.org/badge/doi/10.1038/s41586-025-08746-0.svg)](https://openscicode.org/badge/doi/10.1038/s41586-025-08746-0)
<!-- oscr-badge:end -->
reStructuredText
.. oscr-badge:start

.. image:: https://openscicode.org/badge/doi/10.1038/s41586-025-08746-0.svg
   :target: https://openscicode.org/badge/doi/10.1038/s41586-025-08746-0
   :alt: OSCR

.. oscr-badge:end
HTML
<!-- oscr-badge:start -->
<a href="https://openscicode.org/badge/doi/10.1038/s41586-025-08746-0"><img src="https://openscicode.org/badge/doi/10.1038/s41586-025-08746-0.svg" alt="OSCR"></a>
<!-- oscr-badge:end -->

On GitHub, open the README, choose Edit (the pencil), paste the snippet under the title, then "Commit changes".

Or let it be kept for you, once you choose it: oscr badge --write from the command line, or the GitHub Action in your repository's workflows. Every other form is on the badge page.

Request its removal

To ask for this record, the copies of its authors' scripts or its tracing map to be removed, use the removal request page: signed in, you say who you are, what to remove and why, then review and confirm the request. Published rules decide every request (how).