Evidence map›Paper›PMID 33347572›Full record

ArticleGigaScience2020

Toward a scalable framework for reproducible processing of volumetric, nanoscale neuroimaging datasets.

Erik C Johnson, Miller Wilt, Luis M Rodriguez, Raphael Norman-Tenazas, Corban Rivera, Nathan Drenkow, Dean Kleissas, Theodore J LaGrow, Hannah P Cowley, Joseph Downs and 7 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in GigaScience, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

5 citing papers in PubMed.

  1. Article
  2. An Integrated Toolkit for Extensible and Reproducible Neuroscience.Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference · 2021
    Article
  3. CONFIRMS: A Toolkit for Scalable, Black Box Connectome Assessment and Investigation.Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference · 2021
    Article
  4. Article
  5. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

17 authors.

Erik C JohnsonResearch And Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Rd., Laurel, MD, 20723 USA.
Miller WiltResearch And Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Rd., Laurel, MD, 20723 USA.
Luis M RodriguezResearch And Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Rd., Laurel, MD, 20723 USA.
Raphael Norman-TenazasResearch And Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Rd., Laurel, MD, 20723 USA.
Corban RiveraResearch And Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Rd., Laurel, MD, 20723 USA.
Nathan DrenkowResearch And Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Rd., Laurel, MD, 20723 USA.
Dean KleissasResearch And Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Rd., Laurel, MD, 20723 USA.
Theodore J LaGrowSchool of Electrical & Computer Engineering, Georgia Institute of Technology, 777 Atlantic Dr. NW, Atlanta, GA, 30332 USA.
Hannah P CowleyResearch And Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Rd., Laurel, MD, 20723 USA.
Joseph DownsResearch And Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Rd., Laurel, MD, 20723 USA.
Jordan K MatelskyResearch And Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Rd., Laurel, MD, 20723 USA.
Marisa J HughesResearch And Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Rd., Laurel, MD, 20723 USA.
Elizabeth P ReillyResearch And Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Rd., Laurel, MD, 20723 USA.
Brock A WesterResearch And Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Rd., Laurel, MD, 20723 USA.
Eva L DyerSchool of Electrical & Computer Engineering, Georgia Institute of Technology, 777 Atlantic Dr. NW, Atlanta, GA, 30332 USA.
Konrad P KordingDepartment of Biomedical Engineering, University of Pennsylvania, 210 South 33rd St., Philadelphia, PA, 19104 USA.
William R Gray-RoncalResearch And Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Rd., Laurel, MD, 20723 USA.

Funding

Boss: A cloud-based data archive for electron microscopy and x-ray microtomographyR24MH114785 · NIMH · JOHNS HOPKINS UNIVERSITY · PI BROCK A. WESTER · 2018 to 2026
$6.9M
SABER: Scalable Analytics for Brain Exploration Research using X-Ray Microtomography and Electron MicroscopyR24MH114799 · NIMH · JOHNS HOPKINS UNIVERSITY · PI GRAY RONCAL, WILLIAM R · 2017 to 2019
$1.2M
NIMH NIH HHS R24 MH114785NIMH NIH HHS R24 MH114799
6 · The paper itself

Abstract

backgroundEmerging neuroimaging datasets (collected with imaging techniques such as electron microscopy, optical microscopy, or X-ray microtomography) describe the location and properties of neurons and their connections at unprecedented scale, promising new ways of understanding the brain. These modern imaging techniques used to interrogate the brain can quickly accumulate gigabytes to petabytes of structural brain imaging data. Unfortunately, many neuroscience laboratories lack the computational resources to work with datasets of this size: computer vision tools are often not portable or scalable, and there is considerable difficulty in reproducing results or extending methods.

resultsWe developed an ecosystem of neuroimaging data analysis pipelines that use open-source algorithms to create standardized modules and end-to-end optimized approaches. As exemplars we apply our tools to estimate synapse-level connectomes from electron microscopy data and cell distributions from X-ray microtomography data. To facilitate scientific discovery, we propose a generalized processing framework, which connects and extends existing open-source projects to provide large-scale data storage, reproducible algorithms, and workflow execution engines.

conclusionsOur accessible methods and pipelines demonstrate that approaches across multiple neuroimaging experiments can be standardized and applied to diverse datasets. The techniques developed are demonstrated on neuroimaging datasets but may be applied to similar problems in other domains.

Indexed as

EcosystemSoftwareAlgorithmsNeuroimagingWorkflowcomputational neurosciencecontainerselectron microscopymicrotomographyoptimizationreproducible scienceworkflows

Identifiers

PMID33347572
PMCPMC7751400

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.