Evidence map›Paper›PMID 39625436›Full record

ArticleTranslational vision science & technology2024

Development of an Open-Source Dataset of Flat-Mounted Images for the Murine Oxygen-Induced Retinopathy Model of Ischemic Retinopathy.

Kyle V Marra, Jimmy S Chen, Hailey K Robles-Holmes, Kristine B Ly, Joseph Miller, Guoqin Wei, Edith Aguilar, Felicitas Bucher, Yoichi Ideguchi, Fritz Gerald P Kalaw and 5 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Translational vision science & technology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing 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

3 citing papers in PubMed.

  1. Article
  2. Article
  3. Review
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

15 authors.

Kyle V MarraShiley Eye Institute, Viterbi Family Department of Ophthalmology, University of California San Diego, San Diego, CA, USA.
Jimmy S ChenShiley Eye Institute, Viterbi Family Department of Ophthalmology, University of California San Diego, San Diego, CA, USA.
Hailey K Robles-HolmesShiley Eye Institute, Viterbi Family Department of Ophthalmology, University of California San Diego, San Diego, CA, USA.
Kristine B LyCollege of Optometry, Pacific University, Forest Grove, OR, USA.
Joseph MillerShiley Eye Institute, Viterbi Family Department of Ophthalmology, University of California San Diego, San Diego, CA, USA.
Guoqin WeiMolecular Medicine, The Scripps Research Institute, San Diego, CA, USA.
Edith AguilarMolecular Medicine, The Scripps Research Institute, San Diego, CA, USA.
Felicitas BucherEye Center, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
Yoichi IdeguchiMolecular Medicine, The Scripps Research Institute, San Diego, CA, USA.
Fritz Gerald P KalawShiley Eye Institute, Viterbi Family Department of Ophthalmology, University of California San Diego, San Diego, CA, USA.
Andrew C LinShiley Eye Institute, Viterbi Family Department of Ophthalmology, University of California San Diego, San Diego, CA, USA.
Napoleone FerraraShiley Eye Institute, Viterbi Family Department of Ophthalmology, University of California San Diego, San Diego, CA, USA.
J Peter CampbellCasey Eye Institute, Department of Ophthalmology, Oregon Health & Science University, Portland, OR, USA.
Martin FriedlanderMolecular Medicine, The Scripps Research Institute, San Diego, CA, USA.
Eric NudlemanShiley Eye Institute, Viterbi Family Department of Ophthalmology, University of California San Diego, San Diego, CA, USA.

Funding

MEDICAL SCIENTIST TRAINING PROGRAMT32GM007198 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI CHI, NEIL C, INSEL, PAUL A · 1985 to 2024
$29.3M
Proteomics CoreP30EY010572 · NEI · OREGON HEALTH & SCIENCE UNIVERSITY · PI Kate E Keller · 1995 to 2026
$19.4M
INTEGRINS AND OCULAR ANGIOGENESISR01EY011254 · NEI · SCRIPPS RESEARCH INSTITUTE, THE · PI FRIEDLANDER, MARTIN · 1996 to 2016
$11.5M
Clinical and Genetic Analysis of Retinopathy of PrematurityR01EY019474 · NEI · OREGON HEALTH & SCIENCE UNIVERSITY · PI CAMPBELL, JOHN PETER · 2010 to 2020
$7.0M
Novel Long-Acting Inhibitors of Vascular Endothelial Growth Factor (VEGF) for Treatment of Intraocular Vascular DisordersR01EY031345 · NEI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI FERRARA, NAPOLEONE · 2020 to 2024
$2.3M
Role of PDLIM1 in Retinal Vascular Leakage and ProliferationK08EY028999 · NEI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI NUDLEMAN, ERIC D · 2018 to 2020
$713k
Cellular and Molecular Mechanisms of Retinal FibrosisR56EY032513 · NEI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI NUDLEMAN, ERIC D · 2023 to 2023
$427k
Artificial intelligence assisted panoramic Optical Coherence Tomography Angiography for Retinopathy of PrematurityR01EY031331 · NEI · OREGON HEALTH & SCIENCE UNIVERSITY · PI CAMPBELL, JOHN PETER, JIAN, YIFAN · 2020 to 2020
$342k
Extracellular vesicles from endothelial colony forming cells as paracrine mediators of neurovasculotrophic repair of the retinaF30EY029141 · NEI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI MARRA, KYLE VINCENT · 2018 to 2023
$216k
NEI NIH HHS F30 EY029141NEI NIH HHS K08 EY028999NEI NIH HHS P30 EY010572NEI NIH HHS R01 EY011254NEI NIH HHS R01 EY019474NEI NIH HHS R01 EY031331NEI NIH HHS R01 EY031345NEI NIH HHS R56 EY032513NIGMS NIH HHS T32 GM007198
6 · The paper itself

Abstract

Purpose: To describe an open-source dataset of flat-mounted retinal images and vessel segmentations from mice subject to the oxygen-induced retinopathy (OIR) model. Methods: Flat-mounted retinal images from mice killed at postnatal days 12 (P12), P17, and P25 used in prior OIR studies were compiled. Mice subjected to normoxic conditions were killed at P12, P17, and P25, and their retinas were flat-mounted for imaging. Major blood vessels from the OIR images were manually segmented by four graders (JSC, HKR, KBL, JM), with cross-validation performed to ensure similar grading. Results: Overall, 1170 images were included in this dataset. Of these images, 111 were of normoxic mice retina, and 1048 were mice subject to OIR. The majority of images from OIR mice were obtained at P17. The 50 images obtained from an external dataset, OIRSeg, did not have age labels. All images were manually segmented and used in the training or testing of a previously published deep learning algorithm. Conclusions: This is the first open-source dataset of original and segmented flat-mounted retinal images. The dataset has potential applications for expanding the development of generalizable and larger-scale artificial intelligence and analyses for OIR. This dataset is published online and publicly available at dx.doi.org/10.6084/m9.figshare.23690973. Translational Relevance: This open access dataset serves as a source of raw data for future research involving big data and artificial intelligence research concerning oxygen-induced retinopathy.

Indexed as

Disease Models, AnimalMice, Inbred C57BLOxygenRetinal VesselsAnimalsAnimals, NewbornImage Processing, Computer-AssistedIschemiaMiceRetinopathy of PrematurityOxygen

Identifiers

PMID39625436
PMCPMC11620014

What Socratic holds

Textmetadata
LicenceCC BY-NC-ND
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 Socratic graph.