Evidence map›Paper›PMID 32153349›Full record

ArticleFrontiers in neuroscience2020

Segmentation and Classification in Digital Pathology for Glioma Research: Challenges and Deep Learning Approaches.

Tahsin Kurc, Spyridon Bakas, Xuhua Ren, Aditya Bagari, Alexandre Momeni, Yue Huang, Lichi Zhang, Ashish Kumar, Marc Thibault, Qi Qi and 14 more

Abstract read
In one paragraph

Article in Frontiers in neuroscience, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
38citing papers in PubMed, 1 pooled it
–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

38 citing papers in PubMed, 1 synthesis or guideline pooled it.

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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

24 authors.

Tahsin KurcDepartment of Biomedical Informatics, Stony Brook University, Stony Brook, NY, United States.
Spyridon BakasCenter for Biomedical Image Computing and Analytics, University of Pennsylvania, Philadelphia, PA, United States.
Xuhua RenInstitute for Medical Imaging Technology, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.
Aditya BagariDepartment of Engineering Design, Indian Institute of Technology Madras, Chennai, India.
Alexandre MomeniDepartment of Medicine and Biomedical Data Science, Stanford University, Stanford, CA, United States.
Yue HuangSchool of Informatics, Xiamen University, Xiamen, China.
Lichi ZhangInstitute for Medical Imaging Technology, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.
Ashish KumarDepartment of Engineering Design, Indian Institute of Technology Madras, Chennai, India.
Marc ThibaultDepartment of Medicine and Biomedical Data Science, Stanford University, Stanford, CA, United States.
Qi QiSchool of Informatics, Xiamen University, Xiamen, China.
Qian WangInstitute for Medical Imaging Technology, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.
Avinash KoriDepartment of Engineering Design, Indian Institute of Technology Madras, Chennai, India.
Olivier GevaertDepartment of Medicine and Biomedical Data Science, Stanford University, Stanford, CA, United States.
Yunlong ZhangSchool of Informatics, Xiamen University, Xiamen, China.
Dinggang ShenDepartment of Radiology and BRIC, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.
Mahendra KhenedDepartment of Engineering Design, Indian Institute of Technology Madras, Chennai, India.
Xinghao DingSchool of Informatics, Xiamen University, Xiamen, China.
Ganapathy KrishnamurthiDepartment of Engineering Design, Indian Institute of Technology Madras, Chennai, India.
Jayashree Kalpathy-CramerDepartment of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States.
James DavisDepartment of Pathology, Stony Brook University, Stony Brook, NY, United States.
Tianhao ZhaoDepartment of Pathology, Stony Brook University, Stony Brook, NY, United States.
Rajarsi GuptaDepartment of Biomedical Informatics, Stony Brook University, Stony Brook, NY, United States.
Joel SaltzDepartment of Biomedical Informatics, Stony Brook University, Stony Brook, NY, United States.
Keyvan FarahaniCancer Imaging Program, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States.

Funding

Statistical atlases of brain tumor MRI:do imaging phenotypes predict progression?R01NS042645 · NINDS · UNIVERSITY OF PENNSYLVANIA · PI DAVATZIKOS, CHRISTOS · 2002 to 2024
$8.7M
TCIA Sustainment and Scalability - Platforms for Quantitative Imaging Informatics in Precision MedicineU24CA215109 · NCI · UNIV OF ARKANSAS FOR MED SCIS · PI BANERJEE, IMON, PRIOR, FRED WILLIAM · 2017 to 2021
$8.5M
Image Mining for Comparative Analysis of Expression Patterns in Tissue MicroarrayR01LM009239 · NLM · UNIV OF MED/DENT NJ-R W JOHNSON MED SCH · PI FORAN, DAVID J, SALTZ, JOEL H. · 2007 to 2016
$4.5M
Tools to Analyze Morphology and Spatially Mapped Molecular DataU24CA180924 · NCI · STATE UNIVERSITY NEW YORK STONY BROOK · PI SALTZ, JOEL H. · 2014 to 2019
$3.6M
Cancer imaging phenomics software suite: application to brain and breast cancerU24CA189523 · NCI · UNIVERSITY OF PENNSYLVANIA · PI DAVATZIKOS, CHRISTOS, KONTOS, DESPINA · 2015 to 2019
$3.2M
Biomedical Image Computing and Informatics ClusterS10OD023495 · OD · UNIVERSITY OF PENNSYLVANIA · PI DAVATZIKOS, CHRISTOS · 2017 to 2017
$1.9M
Informatics for Integrative Brain Tumor Whole Slide AnalysisR01LM011119 · NLM · STATE UNIVERSITY NEW YORK STONY BROOK · PI FORAN, DAVID J, SALTZ, JOEL H. · 2011 to 2014
$1.8M
Methods and Tools for Integrating Pathomics Data into Cancer RegistriesUG3CA225021 · NCI · STATE UNIVERSITY NEW YORK STONY BROOK · PI DURBIN, ERIC B., FORAN, DAVID J · 2018 to 2019
$815k
NCI NIH HHS U24 CA180924NCI NIH HHS U24 CA189523NCI NIH HHS U24 CA215109NCI NIH HHS UG3 CA225021NIH HHS S10 OD023495NINDS NIH HHS R01 NS042645NLM NIH HHS R01 LM009239NLM NIH HHS R01 LM011119
6 · The paper itself

Abstract

Biomedical imaging Is an important source of information in cancer research. Characterizations of cancer morphology at onset, progression, and in response to treatment provide complementary information to that gleaned from genomics and clinical data. Accurate extraction and classification of both visual and latent image features Is an increasingly complex challenge due to the increased complexity and resolution of biomedical image data. In this paper, we present four deep learning-based image analysis methods from the Computational Precision Medicine (CPM) satellite event of the 21st International Medical Image Computing and Computer Assisted Intervention (MICCAI 2018) conference. One method Is a segmentation method designed to segment nuclei in whole slide tissue images (WSIs) of adult diffuse glioma cases. It achieved a Dice similarity coefficient of 0.868 with the CPM challenge datasets. Three methods are classification methods developed to categorize adult diffuse glioma cases into oligodendroglioma and astrocytoma classes using radiographic and histologic image data. These methods achieved accuracy values of 0.75, 0.80, and 0.90, measured as the ratio of the number of correct classifications to the number of total cases, with the challenge datasets. The evaluations of the four methods indicate that (1) carefully constructed deep learning algorithms are able to produce high accuracy in the analysis of biomedical image data and (2) the combination of radiographic with histologic image information improves classification performance.

Indexed as

classificationdeep learningdigital pathologyimage analysisradiologysegmentation

Identifiers

PMID32153349
PMCPMC7046596

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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.