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Fast and Accurate Monomodal 3D High Resolution Deep Registration of Drosophila Larval Brain Volumes

quality89

Updated 4 h ago · first seen 11 Sept 2026

paper_01M294H1XY2DTYYTZRHR2ANV4S

Published: 11 Sept 2026; T1 · 4 h ago
arXiv: 2609.11240; T1 · 4 h ago
Category: cs.CV; T1 · 4 h ago

Abstract

The larval stage of Drosophila melanogaster is a compact model system for neuroscience whose genetic toolkit allows fluorescent markers to be expressed in defined neural populations, and comparing the resulting expression patterns across animals requires every brain to be registered into a shared anatomical reference space. Existing pipelines for this task are predominantly based on classical registration methods, which perform a new optimization for each volume, often require per-case parameter tuning, and can take minutes per brain, limiting their use as a routine preprocessing step. We present a trained deep registration pipeline that deformably aligns a larval brain to a reference template in a single forward pass at high spatial resolution, on volumes that hold several times more voxels than those learned 3D registration is normally reported on, together with the preprocessing and anatomy-anchored evaluation pipeline required to apply it. Against eleven classical and seven further learned baselines on a held-out collection acquired with different acquisition and quality strata, the proposed pipeline is the most accurate, improving on the strongest classical baseline by 23 percentage points of anatomical landmark-local mutual information. It registers a volume one to two orders of magnitude faster than the classical deformable pipelines, and it retains more of its accuracy than any other method as acquisition quality degrades. The network, its trained weights and the full pipeline are released as the open-source deep larval brain registration framework: https://github.com/agentdr1/deep-larval-brain-reg

Authors 6

Daniel Reisenb\"uchler, Yousef Sadegheih, Michael Dittrich, Pratibha Kumari, Muhammad Usman, Dorit Merhof

Specification

Official page: arxiv.org/abs/2609.11240
Source:arXiv (Atom API + RSS)T1observed 4 h agohigh
Arxiv announce type: new
Source:arXiv (Atom API + RSS)T1observed 4 h agohigh
arXiv id: 2609.11240
Source:arXiv (Atom API + RSS)T1observed 4 h agohigh
Categories: cs.CV
Source:arXiv (Atom API + RSS)T1observed 4 h agohigh
PDF: arxiv.org/pdf/2609.11240
Source:arXiv (Atom API + RSS)T1observed 4 h agohigh
Primary category: cs.CV
Source:arXiv (Atom API + RSS)T1observed 4 h agohigh
Published: 11 Sept 2026
Source:arXiv (Atom API + RSS)T1observed 4 h agohigh

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T19

Freshest observation

4 h ago

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None

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Claim history

9 claims · 9 properties

Official pageofficial_url1

Claim history for Official page
Value	Valid from → to	Status	Source	Confidence	Extractor
https://arxiv.org/abs/2609.11240	11 Sept 2026 21:03 UTC → current	current	arXiv (Atom API + RSS)T1	high	deterministic

Abstractabstract1

Claim history for Abstract
Value	Valid from → to	Status	Source	Confidence	Extractor
The larval stage of Drosophila melanogaster is a compact model system for neuroscience whose genetic toolkit allows fluorescent markers to be expressed in defined neural populations, and comparing the resulting expression patterns across animals requires every brain to be registered into a shared anatomical reference space. Existing pipelines for this task are predominantly based on classical registration methods, which perform a new optimization for each volume, often require per-case parameter tuning, and can take minutes per brain, limiting their use as a routine preprocessing step. We present a trained deep registration pipeline that deformably aligns a larval brain to a reference template in a single forward pass at high spatial resolution, on volumes that hold several times more voxels than those learned 3D registration is normally reported on, together with the preprocessing and anatomy-anchored evaluation pipeline required to apply it. Against eleven classical and seven further learned baselines on a held-out collection acquired with different acquisition and quality strata, the proposed pipeline is the most accurate, improving on the strongest classical baseline by 23 percentage points of anatomical landmark-local mutual information. It registers a volume one to two orders of magnitude faster than the classical deformable pipelines, and it retains more of its accuracy than any other method as acquisition quality degrades. The network, its trained weights and the full pipeline are released as the open-source deep larval brain registration framework: https://github.com/agentdr1/deep-larval-brain-reg	11 Sept 2026 21:03 UTC → current	current	arXiv (Atom API + RSS)T1	high	deterministic

Arxiv announce typearxiv_announce_type1

Claim history for Arxiv announce type
Value	Valid from → to	Status	Source	Confidence	Extractor
new	11 Sept 2026 21:03 UTC → current	current	arXiv (Atom API + RSS)T1	high	deterministic

arXiv idarxiv_id1

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Value	Valid from → to	Status	Source	Confidence	Extractor
2609.11240	11 Sept 2026 21:03 UTC → current	current	arXiv (Atom API + RSS)T1	high	deterministic

Authorsauthors1

Claim history for Authors
Value	Valid from → to	Status	Source	Confidence	Extractor
Daniel Reisenb\"uchler, Yousef Sadegheih, Michael Dittrich, Pratibha Kumari, Muhammad Usman, Dorit Merhof	11 Sept 2026 21:03 UTC → current	current	arXiv (Atom API + RSS)T1	high	deterministic

Categoriescategories1

Claim history for Categories
Value	Valid from → to	Status	Source	Confidence	Extractor
cs.CV	11 Sept 2026 21:03 UTC → current	current	arXiv (Atom API + RSS)T1	high	deterministic

PDFpdf_url1

Claim history for PDF
Value	Valid from → to	Status	Source	Confidence	Extractor
https://arxiv.org/pdf/2609.11240	11 Sept 2026 21:03 UTC → current	current	arXiv (Atom API + RSS)T1	high	deterministic

Primary categoryprimary_category1

Claim history for Primary category
Value	Valid from → to	Status	Source	Confidence	Extractor
cs.CV	11 Sept 2026 21:03 UTC → current	current	arXiv (Atom API + RSS)T1	high	deterministic

Publishedpublished_at1

Claim history for Published
Value	Valid from → to	Status	Source	Confidence	Extractor
11 Sept 2026	11 Sept 2026 21:03 UTC → current	current	arXiv (Atom API + RSS)T1	high	deterministic

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Source documents
Source	Document	Type	Tier	Last observed	Snapshots
arXiv (Atom API + RSS)	rss.arxiv.org/rss/cs.CV	feed	T1· Official	3 h ago	1

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