---
title: "3D-MAESTRO: Scalable Pipeline for Large-Scale Volumetric Brain Microscopy Processing"
id: "biorxiv-17-3d-maestro-a-scalable-modular-portable-pipeline-for-automated-processing-of"
canonical_url: "https://medichelpline.com/clinical-feed/biorxiv-17-3d-maestro-a-scalable-modular-portable-pipeline-for-automated-processing-of"
content_type: "clinical_feed_article"
specialty: "Neurology"
source_name: "bioRxiv (Biomedical Preprints)"
source_url: "https://www.biorxiv.org/content/10.64898/2026.09.09.750494v1?rss=1"
published_at: "2026-09-15T12:00:00.000Z"
evidence_level: "Verified Feed"
license: "CC-BY-NC-4.0 / Informational Use"
---
# 3D-MAESTRO: Scalable Pipeline for Large-Scale Volumetric Brain Microscopy Processing
## Provenance & Clinical Metadata
- **Canonical URL:** https://medichelpline.com/clinical-feed/biorxiv-17-3d-maestro-a-scalable-modular-portable-pipeline-for-automated-processing-of
- **Specialty:** [Neurology](https://medichelpline.com/clinical-feed/neurology.md)
- **Primary Source:** bioRxiv (Biomedical Preprints)
- **Source URL:** [Original Journal Publication](https://www.biorxiv.org/content/10.64898/2026.09.09.750494v1?rss=1)
- **Published At:** 2026-09-15T12:00:00.000Z
- **Evidence Rating:** Verified Feed
## Executive GIST (TL;DR)
- The authors introduce **3D-MAESTRO**, an automated image-processing **pipeline** designed for large-scale volumetric brain microscopy data that runs on cloud and local computing environments. - 3D-MAESTRO orchestrates key image-processing stages including **denoising**, tile **stitching**, **atlas registration**, and **segmentation** to convert raw microscopy tiles into analysis-ready volumetric datasets. - The workflow is modular and portable, permitting substitution, integration, and benchmarking of new algorithms and packages so performance can evolve as methods improve. - The team developed a new **3D image template** specifically for automated registration of mouse brains cleared with aqueous reagents to support reliable alignment across samples. - An efficient method for detection of fluorescent cells in volumetric data is described and integrated into the pipeline to support cell-level mapping across whole brains. - 3D-MAESTRO is demonstrated on lightsheet imaging of whole mouse brains across diverse anatomical and functional experiments, illustrating its use for high-throughput and reproducible mapping of microscopic structures. - The work was produced by a multi-author team at the Allen Institute; correspondence contact is provided. The authors declared no competing interests. - Funding sources reported include the National Institute of Mental Health, National Institute of Neurological Disorders and Stroke, and National Institute on Drug Abuse. The preprint is available under a CC-BY-NC 4.0 license. - The source does not report quantitative performance metrics, benchmarking results, or specific runtime/resource requirements in the abstract; those details were not reported in the provided source text.
## Clinical Analysis & Structured Key Points
3D-MAESTRO: A scalable, modular, portable pipeline for automated processing of large-scale volumetric brain microscopy data | bioRxiv Skip to main content New Results 3D-MAESTRO: A scalable, modular, portable pipeline for automated processing of large-scale volumetric brain microscopy data View ORCID Profile Camilo Laiton , View ORCID Profile Nicholas Lusk , View ORCID Profile Yoni Browning , View ORCID Profile Mathew Summers , View ORCID Profile Michael Taormina , Di Wang , View ORCID Profile Joshua Siegle , View ORCID Profile Holly Myers , Bowen Tan , View ORCID Profile Polina Kosillo , Erica Peterson , View ORCID Profile Daphne Toglia , View ORCID Profile Anna Lakunina , Sasha Burckhardt , Jon Young , Mekhla Kapoor , Tim Wang , John Rohde , View ORCID Profile Galen Lynch , Shenqin Yao , View ORCID Profile Sujatha Narayan , View ORCID Profile Marcus Hooper , View ORCID Profile Sharon Way , View ORCID Profile Jack Waters , View ORCID Profile Bosiljka Tasic , View ORCID Profile Jayaram Chandrashekar , View ORCID Profile Adam Glaser , View ORCID Profile David Feng , View ORCID Profile Sharmishtaa Seshamani , View ORCID Profile Karel Svoboda doi: https://doi.org/10.64898/2026.09.09.750494 Camilo Laiton Allen Institute Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Camilo Laiton Nicholas Lusk Allen Institute Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Nicholas Lusk Yoni Browning Allen Institute Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Yoni Browning Mathew Summers Allen Institute Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Mathew Summers Michael Taormina Allen Institute Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Michael Taormina Di Wang Allen Institute Find this author on Google Scholar Find this author on PubMed Search for this author on this site Joshua Siegle Allen Institute Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Joshua Siegle Holly Myers Allen Institute Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Holly Myers Bowen Tan Allen Institute Find this author on Google Scholar Find this author on PubMed Search for this author on this site Polina Kosillo Allen Institute Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Polina Kosillo Erica Peterson Allen Institute Find this author on Google Scholar Find this author on PubMed Search for this author on this site Daphne Toglia Allen Institute Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Daphne Toglia Anna Lakunina Allen Institute Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Anna Lakunina Sasha Burckhardt Allen Institute Find this author on Google Scholar Find this author on PubMed Search for this author on this site Jon Young Allen Institute Find this author on Google Scholar Find this author on PubMed Search for this author on this site Mekhla Kapoor Allen Institute Find this author on Google Scholar Find this author on PubMed Search for this author on this site Tim Wang Allen Institute Find this author on Google Scholar Find this author on PubMed Search for this author on this site John Rohde Allen Institute Find this author on Google Scholar Find this author on PubMed Search for this author on this site Galen Lynch Allen Institute Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Galen Lynch Shenqin Yao Allen Institute Find this author on Google Scholar Find this author on PubMed Search for this author on this site Sujatha Narayan Allen Institute Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Sujatha Narayan Marcus Hooper Allen Institute Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Marcus Hooper Sharon Way Allen Institute Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Sharon Way Jack Waters Allen Institute Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Jack Waters Bosiljka Tasic Allen Institute Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Bosiljka Tasic Jayaram Chandrashekar Allen Institute Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Jayaram Chandrashekar Adam Glaser Allen Institute Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Adam Glaser David Feng Allen Institute Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for David Feng Sharmishtaa Seshamani Allen Institute Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Sharmishtaa Seshamani For correspondence: sharmishtaas{at}alleninstitute.org Karel Svoboda Allen Institute Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Karel Svoboda Abstract Info/History Metrics Preview PDF Abstract Light microscopy is routinely used to explore the cellular and molecular structure of tissues, but the scale and complexity of data remains a bottleneck for discovery. We introduce 3D-MAESTRO (3D-Microscopy Automation and Execution with Scalable Tools, Rendering, and Orchestration): an automated image processing workflow for large-scale microscopy data, built for scalable execution across cloud and local computing environments. 3D-MAESTRO orchestrates denoising, stitching of image tiles, atlas registration, and segmentation. Its modular architecture permits the integration and benchmarking of new packages, ensuring that performance evolves as more efficient or accurate algorithms emerge. We introduce a new 3D image template for automated registration of mouse brains cleared with aqueous reagents and an efficient method for detection of fluorescent cells. We apply 3D-MAESTRO to lightsheet images of whole mouse brains in the context of diverse anatomical and functional experiments, illustrating high-throughput and reproducible mapping of microscopic structures across the brain. Competing Interest Statement The authors have declared no competing interest. Funder Information Declared National Institute of Mental Health, https://ror.org/04xeg9z08 , UF1MH128339 , U01MH139778 , RF1MH128841 National Institute of Neurological Disorders and Stroke, https://ror.org/01s5ya894 , U19NS123714 National Institute on Drug Abuse, https://ror.org/00fq5cm18 , U19NS123714 Copyright The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license . Back to top Previous Next Posted September 15, 2026. Download PDF Email Thank you for your interest in spreading the word about bioRxiv. NOTE: Your email address is requested solely to identify you as the sender of this article. Your Email * Your Name * Send To * Enter multiple addresses on separate lines or separate them with commas. 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Share 3D-MAESTRO: A scalable, modular, portable pipeline for automated processing of large-scale volumetric brain microscopy data Camilo Laiton , Nicholas Lusk , Yoni Browning , Mathew Summers , Michael Taormina , Di Wang , Joshua Siegle , Holly Myers , Bowen Tan , Polina Kosillo , Erica Peterson , Daphne Toglia , Anna Lakunina , Sasha Burckhardt , Jon Young , Mekhla Kapoor , Tim Wang , John Rohde , Galen Lynch , Shenqin Yao , Sujatha Narayan , Marcus Hooper , Sharon Way , Jack Waters , Bosiljka Tasic , Jayaram Chandrashekar , Adam Glaser , David Feng , Sharmishtaa Seshamani , Karel Svoboda bioRxiv 2026.09.09.750494; doi: https://doi.org/10.64898/2026.09.09.750494 Share This Article: Copy Citation Tools 3D-MAESTRO: A scalable, modular, portable pipeline for automated processing of large-scale volumetric brain microscopy data Camilo Laiton , Nicholas Lusk , Yoni Browning , Mathew Summers , Michael Taormina , Di Wang , Joshua Siegle , Holly Myers , Bowen Tan , Polina Kosillo , Erica Peterson , Daphne Toglia , Anna Lakunina , Sasha Burckhardt , Jon Young , Mekhla Kapoor , Tim Wang , John Rohde , Galen Lynch , Shenqin Yao , Sujatha Narayan , Marcus Hooper , Sharon Way , Jack Waters , Bosiljka Tasic , Jayaram Chandrashekar , Adam Glaser , David Feng , Sharmishtaa Seshamani , Karel Svoboda bioRxiv 2026.09.09.750494; doi: https://doi.org/10.64898/2026.09.09.750494 Citation Manager Formats BibTeX Bookends EasyBib EndNote (tagged) EndNote 8 (xml) Medlars Mendeley Papers RefWorks Tagged Ref Manager RIS Zotero Tweet Widget Facebook Like Google Plus One Subject Areas All Articles Animal Behavior and Cognition (7998) Biochemistry (18705) Bioengineering (14824) Bioinformatics (44323) Biophysics (22545) Cancer Biology (19664) Cell Biology (26832) Clinical Trials (138) Developmental Biology (13929) Ecology (20965) Epidemiology (2067) Evolutionary Biology (25405) Genetics (16143) Genomics (23459) Immunology (18664) Microbiology (42377) Molecular Biology (18015) Neuroscience (93278) Paleontology (699) Pathology (2976) Pharmacology and Toxicology (5082) Physiology (8097) Plant Biology (15963) Scientific Communication and Education (2094) Synthetic Biology (4546) Systems Biology (10214) Zoology (2382)
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