Evidence map›Paper›PMID 25694962›Full record

ArticleQuantitative imaging in medicine and surgery2015

Algorithms for improved 3-D reconstruction of live mammalian embryo vasculature from optical coherence tomography data.

Prathamesh M Kulkarni, Nicolas Rey-Villamizar, Amine Merouane, Narendran Sudheendran, Shang Wang, Monica Garcia, Irina V Larina, Badrinath Roysam, Kirill V Larin

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Quantitative imaging in medicine and surgery, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.

0numbers the graph read from it
0cells of the map it votes in
11citing 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

11 citing papers in PubMed.

  1. Mouse embryo phenotyping with optical coherence tomography.Frontiers in cell and developmental biology · 2022
    Review
  2. Embryonic Mouse Cardiodynamic OCT Imaging.Journal of cardiovascular development and disease · 2020
    Review
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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

9 authors.

Prathamesh M Kulkarni1 Department of Electrical and Computer Engineering, 2 Department of Biomedical Engineering, University of Houston, Houston, TX, USA ; 3 Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA.
Nicolas Rey-Villamizar1 Department of Electrical and Computer Engineering, 2 Department of Biomedical Engineering, University of Houston, Houston, TX, USA ; 3 Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA.
Amine Merouane1 Department of Electrical and Computer Engineering, 2 Department of Biomedical Engineering, University of Houston, Houston, TX, USA ; 3 Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA.
Narendran Sudheendran1 Department of Electrical and Computer Engineering, 2 Department of Biomedical Engineering, University of Houston, Houston, TX, USA ; 3 Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA.
Shang Wang1 Department of Electrical and Computer Engineering, 2 Department of Biomedical Engineering, University of Houston, Houston, TX, USA ; 3 Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA.
Monica Garcia1 Department of Electrical and Computer Engineering, 2 Department of Biomedical Engineering, University of Houston, Houston, TX, USA ; 3 Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA.
Irina V Larina1 Department of Electrical and Computer Engineering, 2 Department of Biomedical Engineering, University of Houston, Houston, TX, USA ; 3 Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA.
Badrinath Roysam1 Department of Electrical and Computer Engineering, 2 Department of Biomedical Engineering, University of Houston, Houston, TX, USA ; 3 Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA.
Kirill V Larin1 Department of Electrical and Computer Engineering, 2 Department of Biomedical Engineering, University of Houston, Houston, TX, USA ; 3 Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA.

Funding

Consortium for Broad Based Disease Phenotyping of Knockout MiceU54HG006348 · NHGRI · BAYLOR COLLEGE OF MEDICINE · PI BEAUDET, ARTHUR L., PAYLOR, RICHARD E · 2011 to 2015
$17.0M
Optical Coherence Elastography of the CorneaR01EY022362 · NEI · UNIVERSITY OF HOUSTON · PI Salavat R Aglyamov, Kirill V Larin · 2012 to 2026
$6.7M
Biomechanics of early mammalian cardiogenesisR01HL120140 · NHLBI · BAYLOR COLLEGE OF MEDICINE · PI LARINA, IRINA · 2013 to 2017
$2.0M
NEI NIH HHS R01 EY022362NHGRI NIH HHS U54 HG006348NHLBI NIH HHS R01 HL120140
6 · The paper itself

Abstract

backgroundRobust reconstructions of the three-dimensional network of blood vessels in developing embryos imaged by optical coherence tomography (OCT) are needed for quantifying the longitudinal development of vascular networks in live mammalian embryos, in support of developmental cardiovascular research. Past computational methods [such as speckle variance (SV)] have demonstrated the feasibility of vascular reconstruction, but multiple challenges remain including: the presence of vessel structures at multiple spatial scales, thin blood vessels with weak flow, and artifacts resulting from bulk tissue motion (BTM).

methodsIn order to overcome these challenges, this paper introduces a robust and scalable reconstruction algorithm based on a combination of anomaly detection algorithms and a parametric dictionary based sparse representation of blood vessels from structural OCT data.

resultsValidation results using confocal data as the baseline demonstrate that the proposed method enables the detection of vessel segments that are either partially missed or weakly reconstructed using the SV method. Finally, quantitative measurements of vessel reconstruction quality indicate an overall higher quality of vessel reconstruction with the proposed method.

conclusionsResults suggest that sparsity-integrated speckle anomaly detection (SSAD) is potentially a valuable tool for performing accurate quantification of the progression of vascular development in the mammalian embryonic yolk sac as imaged using OCT.

Indexed as

3-D vessel reconstructionlive imagingOptical coherence tomography (OCT)

Identifiers

PMID25694962
PMCPMC4312302

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Registered trials

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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.