Literature DB >> 27845654

DeepCut: Object Segmentation From Bounding Box Annotations Using Convolutional Neural Networks.

Martin Rajchl, Matthew C H Lee, Ozan Oktay, Konstantinos Kamnitsas, Jonathan Passerat-Palmbach, Wenjia Bai, Mellisa Damodaram, Mary A Rutherford, Joseph V Hajnal, Bernhard Kainz, Daniel Rueckert.   

Abstract

In this paper, we propose DeepCut, a method to obtain pixelwise object segmentations given an image dataset labelled weak annotations, in our case bounding boxes. It extends the approach of the well-known GrabCut [1] method to include machine learning by training a neural network classifier from bounding box annotations. We formulate the problem as an energy minimisation problem over a densely-connected conditional random field and iteratively update the training targets to obtain pixelwise object segmentations. Additionally, we propose variants of the DeepCut method and compare those to a naïve approach to CNN training under weak supervision. We test its applicability to solve brain and lung segmentation problems on a challenging fetal magnetic resonance dataset and obtain encouraging results in terms of accuracy.

Entities:  

Mesh:

Year:  2016        PMID: 27845654      PMCID: PMC7115996          DOI: 10.1109/TMI.2016.2621185

Source DB:  PubMed          Journal:  IEEE Trans Med Imaging        ISSN: 0278-0062            Impact factor:   10.048


  11 in total

1.  Foetal volumetry using magnetic resonance imaging in intrauterine growth restriction.

Authors:  Mellisa S Damodaram; Lisa Story; Elisanda Eixarch; Prachi Patkee; Abhilasha Patel; Sailesh Kumar; Mary Rutherford
Journal:  Early Hum Dev       Date:  2012-01-29       Impact factor: 2.079

2.  Predicting Semantic Descriptions from Medical Images with Convolutional Neural Networks.

Authors:  Thomas Schlegl; Sebastian M Waldstein; Wolf-Dieter Vogl; Ursula Schmidt-Erfurth; Georg Langs
Journal:  Inf Process Med Imaging       Date:  2015

3.  Left ventricle segmentation in MRI via convex relaxed distribution matching.

Authors:  Cyrus M S Nambakhsh; Jing Yuan; Kumaradevan Punithakumar; Aashish Goela; Martin Rajchl; Terry M Peters; Ismail Ben Ayed
Journal:  Med Image Anal       Date:  2013-06-10       Impact factor: 8.545

4.  Interactive Hierarchical-Flow Segmentation of Scar Tissue From Late-Enhancement Cardiac MR Images.

Authors:  Martin Rajchl; Jing Yuan; James A White; Eranga Ukwatta; John Stirrat; Cyrus M S Nambakhsh; Feng P Li; Terry M Peters
Journal:  IEEE Trans Med Imaging       Date:  2013-09-20       Impact factor: 10.048

5.  A nonparametric method for automatic correction of intensity nonuniformity in MRI data.

Authors:  J G Sled; A P Zijdenbos; A C Evans
Journal:  IEEE Trans Med Imaging       Date:  1998-02       Impact factor: 10.048

6.  Segmentation of brain tissue from magnetic resonance images.

Authors:  T Kapur; W E Grimson; W M Wells; R Kikinis
Journal:  Med Image Anal       Date:  1996-06       Impact factor: 8.545

7.  Hierarchical max-flow segmentation framework for multi-atlas segmentation with Kohonen self-organizing map based Gaussian mixture modeling.

Authors:  Martin Rajchl; John S H Baxter; A Jonathan McLeod; Jing Yuan; Wu Qiu; Terry M Peters; Ali R Khan
Journal:  Med Image Anal       Date:  2015-05-29       Impact factor: 8.545

8.  3-D carotid multi-region MRI segmentation by globally optimal evolution of coupled surfaces.

Authors:  Eranga Ukwatta; Jing Yuan; Martin Rajchl; Wu Qiu; David Tessier; Aaron Fenster
Journal:  IEEE Trans Med Imaging       Date:  2013-01-04       Impact factor: 10.048

9.  Multi-atlas Segmentation as a Graph Labelling Problem: Application to Partially Annotated Atlas Data.

Authors:  Lisa M Koch; Martin Rajchl; Tong Tong; Jonathan Passerat-Palmbach; Paul Aljabar; Daniel Rueckert
Journal:  Inf Process Med Imaging       Date:  2015

10.  Automated fetal brain segmentation from 2D MRI slices for motion correction.

Authors:  K Keraudren; M Kuklisova-Murgasova; V Kyriakopoulou; C Malamateniou; M A Rutherford; B Kainz; J V Hajnal; D Rueckert
Journal:  Neuroimage       Date:  2014-07-22       Impact factor: 6.556

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  28 in total

Review 1.  Role of deep learning in infant brain MRI analysis.

Authors:  Mahmoud Mostapha; Martin Styner
Journal:  Magn Reson Imaging       Date:  2019-06-20       Impact factor: 2.546

2.  Deep learning with mixed supervision for brain tumor segmentation.

Authors:  Pawel Mlynarski; Hervé Delingette; Antonio Criminisi; Nicholas Ayache
Journal:  J Med Imaging (Bellingham)       Date:  2019-08-10

Review 3.  High Efficiency Video Coding (HEVC)-Based Surgical Telementoring System Using Shallow Convolutional Neural Network.

Authors:  Ali Hassan; Mubeen Ghafoor; Syed Ali Tariq; Tehseen Zia; Waqas Ahmad
Journal:  J Digit Imaging       Date:  2019-12       Impact factor: 4.056

4.  Co-localization of fluorescent signals using deep learning with Manders overlapping coefficient.

Authors:  Yimeng Dou; Yi-Hua Tsai; Chih-Chieh Liu; Brad A Hobson; Pamela J Lein
Journal:  Proc SPIE Int Soc Opt Eng       Date:  2021-02-15

5.  Iterative Label Denoising Network: Segmenting Male Pelvic Organs in CT From 3D Bounding Box Annotations.

Authors:  Shuai Wang; Qian Wang; Yeqin Shao; Liangqiong Qu; Chunfeng Lian; Jun Lian; Dinggang Shen
Journal:  IEEE Trans Biomed Eng       Date:  2020-01-27       Impact factor: 4.538

6.  anTraX, a software package for high-throughput video tracking of color-tagged insects.

Authors:  Asaf Gal; Jonathan Saragosti; Daniel Jc Kronauer
Journal:  Elife       Date:  2020-11-19       Impact factor: 8.140

7.  Cardiac substructure segmentation with deep learning for improved cardiac sparing.

Authors:  Eric D Morris; Ahmed I Ghanem; Ming Dong; Milan V Pantelic; Eleanor M Walker; Carri K Glide-Hurst
Journal:  Med Phys       Date:  2019-12-29       Impact factor: 4.071

8.  DeepIGeoS: A Deep Interactive Geodesic Framework for Medical Image Segmentation.

Authors:  Guotai Wang; Maria A Zuluaga; Wenqi Li; Rosalind Pratt; Premal A Patel; Michael Aertsen; Tom Doel; Anna L David; Jan Deprest; Sebastien Ourselin; Tom Vercauteren
Journal:  IEEE Trans Pattern Anal Mach Intell       Date:  2018-06-01       Impact factor: 6.226

9.  Interactive Medical Image Segmentation Using Deep Learning With Image-Specific Fine Tuning.

Authors:  Guotai Wang; Wenqi Li; Maria A Zuluaga; Rosalind Pratt; Premal A Patel; Michael Aertsen; Tom Doel; Anna L David; Jan Deprest; Sebastien Ourselin; Tom Vercauteren
Journal:  IEEE Trans Med Imaging       Date:  2018-07       Impact factor: 10.048

10.  Weakly Supervised Estimation of Shadow Confidence Maps in Fetal Ultrasound Imaging.

Authors:  Qingjie Meng; Matthew Sinclair; Veronika Zimmer; Benjamin Hou; Martin Rajchl; Nicolas Toussaint; Ozan Oktay; Jo Schlemper; Alberto Gomez; James Housden; Jacqueline Matthew; Daniel Rueckert; Julia A Schnabel; Bernhard Kainz
Journal:  IEEE Trans Med Imaging       Date:  2019-04-25       Impact factor: 10.048

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