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Publications about 'Software'
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Ghassan Hamarneh.
PC-Based Digital Oscilloscope.
Bachelor's thesis,
Department of Electrical Engineering, University of Jordan,
1994.
Keyword(s): Software and Tools.
[bibtex-key = bsee1994]
Articles in journal, book chapters
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Ben Cardoen,
Hanene Ben Yedder,
Sieun Lee,
Ivan Robert Nabi,
and Ghassan Hamarneh.
DataCurator.jl: Efficient, portable, and reproducible validation, curation, and transformation of large heterogeneous datasets using human-readable recipes compiled into machine verifiable templates.
BioInformatics Advances,
3(1-5):000-000,
2023.
Keyword(s): Microscopy,
Processing,
Single Molecule Localization,
Super Resolution Microscopy,
Software and Tools,
Reproducibility.
[bibtex-key = bioinfadv2023]
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Weina Jin,
Xiaoxiao Li,
Mostafa Fatehi,
and Ghassan Hamarneh.
Generating Post-Hoc Explanation from Deep Neural Networks for Multi-Modal Medical Image Analysis Tasks.
MethodX,
10(102009):1-7,
2023.
Keyword(s): Deep Learning,
Explainable AI (XAI),
Multimodal,
Software and Tools.
[bibtex-key = methodx2023]
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Ali Majd,
Mohammed AlJasser,
Hengameh Mirzaalian,
Jerry Shapiro,
Ghassan Hamarneh,
Harvey Lui,
Leopoldo Duailibe Nogueira Santos,
Thomas Chu,
and Tim K. Lee.
A novel automated approach to rapid and precise in vivo measurement of hair morphometrics using a smartphone.
Skin Research and Technology (SRT),
27:1128–1134,
2021.
Keyword(s): Anatomical Trees and Tubular Structures,
Dermatology,
Color/Multichannel/Vector-valued,
Software and Tools.
[bibtex-key = srt2021]
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Saurabh Garg,
Ghassan Hamarneh,
Allard Jongman,
Joan Sereno,
and Yue Wang.
ADFAC: Automatic Detection of Facial Articulatory Features.
MethodX,
7:101006,
2020.
Keyword(s): Segmentation,
Tracking,
Color/Multichannel/Vector-valued,
Speech and Language,
Facial Analysis,
Spatio-Temporal,
Software and Tools.
[bibtex-key = methodx2020]
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Chloe Lim,
Hayyan Liaqat,
William Siu,
Ghassan Hamarneh,
and George Medvedev.
Future implementation of automated analysis tools for Multiple Sclerosis on conventional magnetic resonance imaging (Lim and Liaqat: Joint first authors; Hamarneh and Medvedev: Joint senior authors).
Multiple Sclerosis. MSVirtual 2020 – Late Breaking News. Also appears in ACTRIMS-ECTRMS meeting,
1(3 SUPPL):99,
2020.
Keyword(s): Segmentation,
Software and Tools,
Multiple Sclerosis,
MRI.
[bibtex-key = msj2020]
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Preet Jassi and Ghassan Hamarneh.
VascuSynth: Vascular Tree Synthesis Software.
Insight Journal,
January-June:1-12,
2011.
Keyword(s): Segmentation,
Validation,
Shape Modelling and Analysis,
Software and Tools,
Anatomical Trees and Tubular Structures,
Synthesis/Simulation/Augmentation,
Datasets.
[bibtex-key = ij2011]
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Boris Shabash,
Zhi Feng Huang,
and Ghassan Hamarneh.
Medical Image Analysis with ITK on Apple iOS.
Kitware Source - Software Developer's Quarterly,
(16):3-5,
2011.
Keyword(s): Software and Tools.
[bibtex-key = source2011]
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Ghassan Hamarneh and Preet Jassi.
VascuSynth: Simulating Vascular Trees for Generating Volumetric Image data with Ground Truth Segmentation and Tree Analysis.
Computerized Medical Imaging and Graphics (CMIG),
34(8):605-616,
2010.
Keyword(s): Segmentation,
Validation,
Shape Modelling and Analysis,
Software and Tools,
Anatomical Trees and Tubular Structures,
Synthesis/Simulation/Augmentation.
[bibtex-key = cmig2010]
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Ahmed Saad,
Torsten Moeller,
and Ghassan Hamarneh.
ProbExplorer: An Uncertainty-based Visual Analysis Tool for Medical Imaging.
Computer Graphics Forum (CGF) (Special Issue of the proceedings of Eurographics/IEEE-VGTC Symposium on Visualization 2010),
29(3):1113-1122,
2010.
Keyword(s): Software and Tools,
Segmentation,
Uncertainty,
User Interaction,
Visualization,
Spatio-Temporal.
[bibtex-key = cgf2010]
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Boris Shabash,
Ghassan Hamarneh,
Zhi Feng Huang,
and Luis Ibanez.
ITK Image IO Interface with Apple iOS.
Insight Journal,
July-December:1-16,
2010.
Keyword(s): Software and Tools.
[bibtex-key = ij2010b]
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Boris Shabash,
Ghassan Hamarneh,
Zhi Feng Huang,
and Luis Ibanez.
ITK on the iOS.
Insight Journal,
July-December:1-9,
2010.
Keyword(s): Software and Tools.
[bibtex-key = ij2010a]
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Miranda Poon,
Ghassan Hamarneh,
and Rafeef Abugharbieh.
Efficient Interactive 3D Livewire Segmentation of Objects with Arbitrary Topologies.
Computerized Medical Imaging and Graphics (CMIG),
32(8):639-650,
2008.
Keyword(s): Segmentation,
Software and Tools,
User Interaction,
Graph based.
[bibtex-key = cmig2008]
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Andy Rova,
Anna Celler,
and Ghassan Hamarneh.
NMQC: A NEMA-Compliant Software Application for Gamma Camera Quality Control.
Journal of Digital Imaging,
21(2):243-255,
2008.
Keyword(s): Imaging,
Software and Tools.
[bibtex-key = jdi2008b]
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Warren Cheung and Ghassan Hamarneh.
Scale Invariant Feature Transform for n-Dimensional Images (n-SIFT).
Insight Journal,
July-December:1-7,
2007.
Keyword(s): Software and Tools,
Registration and Matching.
[bibtex-key = ij2007]
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Chris McIntosh and Ghassan Hamarneh.
I-DO: A Deformable Organisms framework for ITK.
Insight Journal,
Special Issue: MICCAI 2006 Open Science Workshop:1-14,
2006.
Keyword(s): Deformable Organisms,
Software and Tools,
Artificial Life.
[bibtex-key = ij2006]
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Vincent Chu and Ghassan Hamarneh.
MATITK: Extending MATLAB with ITK.
Insight Journal,
Aug-Dec:1-8,
2005.
Keyword(s): Processing,
Segmentation,
Registration and Matching,
Software and Tools.
[bibtex-key = ij2005]
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Ismail M. Khater,
Timothy H. Wong,
Christian Hallgrimson,
Satish Moparthi,
Stéphane Vassilopoulos,
Ghassan Hamarneh,
and Ivan Robert Nabi.
Molecular architecture of clathrin plaques and pits defined by super-resolution network analysis (SuperResNET) (Khater and Wong: Joint first authors; Hamarneh and Nabi: Joint senior authors).
In American Society of Cell Biology (ASCB) - Cell Bio,
2022.
Keyword(s): Super Resolution Microscopy,
Single Molecule Localization Microscopy,
Software and Tools,
Network Modelling and Analysis,
Machine Learning.
[bibtex-key = ascb2022b]
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Ismail M. Khater,
Timothy H. Wong,
Stéphane Vassilopoulos,
Ivan Robert Nabi,
and Ghassan Hamarneh.
SuperResNET: a GUI software package for single molecule localization microscopy cluster analysis (Nabi and Hamarneh: Joint senior authors).
In Single Molecule Localization Microscopy Symposium - Current Trends,
pages 1,
2021.
Keyword(s): Super Resolution Microscopy,
Single Molecule Localization Microscopy,
Software and Tools,
Network Modelling and Analysis,
Machine Learning.
[bibtex-key = smlms2021]
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Ismail M. Khater,
Ivan Robert Nabi,
and Ghassan Hamarneh.
SuperNet: Super-resolution Network Analysis and Quantification of Single Molecule Clusters.
In Single Molecule Localization Microscopy Symposium - Showtime,
pages 1,
2020.
Keyword(s): Super Resolution Microscopy,
Single Molecule Localization Microscopy,
Software and Tools,
Network Modelling and Analysis,
Machine Learning.
[bibtex-key = smlms2020]
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Chloe Lim,
Hayyan Liaqat,
William Siu,
Ghassan Hamarneh,
and George Medvedev.
Future implementation of automated analysis tools for Multiple Sclerosis on conventional magnetic resonance imaging (Lim and Liaqat: Joint first authors; Hamarneh and Medvedev: Joint senior authors).
In 8th joint Americas Committee for Treatment and Research in Multiple Sclerosis - European Committee for Treatment and Research in Multiple Sclerosis (joint ACTRIMS-ECTRMS),
pages 1,
2020.
Keyword(s): Segmentation,
Software and Tools,
Multiple Sclerosis,
MRI.
[bibtex-key = ectrms2020]
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Ali Majd,
Mohammed AlJasser,
Hengameh Mirzaalian,
Jerry Shapiro,
Ghassan Hamarneh,
and Tim K. Lee.
Automated Counting of Hair Using an iPhone.
In World Congress of Dermatology (WCD),
2015.
Keyword(s): Anatomical Trees and Tubular Structures,
Dermatology,
Color/Multichannel/Vector-valued,
Software and Tools.
[bibtex-key = wcd2015c]
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Brian G. Booth and Ghassan Hamarneh.
DTI-DeformIt: Generating Ground-Truth Validation Data for Diffusion Tensor Image Analysis Tasks.
In IEEE International Symposium on Biomedical Imaging (IEEE ISBI),
pages 730-733,
2014.
Keyword(s): Diffusion MRI/Tensor-valued,
Synthesis/Simulation/Augmentation,
Software and Tools,
Validation,
Physical Modelling.
[bibtex-key = isbi2014b]
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Shane Mottishaw,
Sergey Zhuravlev,
Lisa Y. W. Tang,
Alexandra Fedorova,
and Ghassan Hamarneh.
An Evaluation of Parallelization Techniques for MRF Image Segmentation.
In International Workshop on High-Performance Medical Image Computing for Image-Assisted Clinical Intervention and Decision-Making (MICCAI HP),
pages 10 pages,
2010.
Keyword(s): Segmentation,
Software,
Fast MIA.
[bibtex-key = miccai_hp2010b]
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Ahmed Saad,
Torsten Moeller,
and Ghassan Hamarneh.
ProbExplorer: An Uncertainty-based Visual Analysis Tool for Medical Imaging.
In Eurographics/IEEE-VGTC Symposium on Visualization (IEEE EuroVis) (also appears in the Special Issue of the Journal Computer Graphics Forum).,
volume 29,
pages 1113-1122,
2010.
Keyword(s): Software and Tools,
Segmentation,
Uncertainty,
User Interaction,
Visualization,
Spatio-Temporal.
[bibtex-key = eurovis2010]
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Ahmed Saad,
Torsten Moeller,
and Ghassan Hamarneh.
ProbExplorer: Uncertainty-guided Exploration and Editing of Probabilistic Medical Image Segmentation.
In SFU Exchange,
2010.
Keyword(s): Software and Tools,
Segmentation,
Uncertainty,
User Interaction,
Visualization,
Spatio-Temporal.
[bibtex-key = sfu_exchange2010a]
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Ben Smith,
Ghassan Hamarneh,
and Ahmed Saad.
Fast GPU Fitting of Kinetic Models for Dynamic PET.
In International Workshop on High-Performance Medical Image Computing for Image-Assisted Clinical Intervention and Decision-Making (MICCAI HP),
pages 10 pages,
2010.
Keyword(s): Functional/Molecular/Dynamic Imaging,
Software and Tools,
Fast MIA.
[bibtex-key = miccai_hp2010a]
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Ghassan Hamarneh,
Preet Jassi,
and Lisa Y. W. Tang.
Simulation of Ground-Truth Validation Data via Physically- and Statistically-based Warps.
In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI),
volume 5241,
pages 459-467,
2008.
Keyword(s): Registration and Matching,
Segmentation,
Shape Modelling and Analysis,
Software and Tools,
Validation,
Synthesis/Simulation/Augmentation,
Physical Modelling.
[bibtex-key = miccai2008b]
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Ghassan Hamarneh,
Aaron Ward,
Chris McIntosh,
Ben Smith,
Lisa Y. W. Tang,
Ahmed Saad,
Yonas Weldeselassie,
and Omer Ishaq.
Medical Image Analysis.
In TechMed, Vancouver, May 16,
2007.
Keyword(s): Segmentation,
Shape Modelling and Analysis,
Deformable Models,
Deformable Organisms,
Artificial Life,
Imaging,
Software and Tools.
[bibtex-key = techmed2007]
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Anna Celler,
Andy Rova,
and Ghassan Hamarneh.
NMQC: A NEMA-compliant software application for gamma camera quality control.
In Annual meeting of the Canadian Society of Nuclear Medicine (CSNM),
2006.
Keyword(s): Imaging,
Software and Tools.
[bibtex-key = csnm2006a]
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Vincent Chu and Ghassan Hamarneh.
MATLAB-ITK interface for medical image filtering, segmentation, and registration.
In SPIE Medical Imaging,
volume 61443T,
pages 1-8,
2006.
Keyword(s): Processing,
Segmentation,
Registration and Matching,
Software and Tools.
[bibtex-key = spiemi2006a]
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Chris McIntosh and Ghassan Hamarneh.
I-DO: A Deformable Organisms framework for ITK.
In Medical Image Computing and Computer-Assisted Intervention Open Science Workshop (also appears in the Insight Journal) (MICCAI OS),
pages 1-14,
2006.
Keyword(s): Deformable Organisms,
Software and Tools,
Artificial Life.
[bibtex-key = miccai_os2006]
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Andy Rova,
Anna Celler,
and Ghassan Hamarneh.
NMQC: A NEMA-compliant software application for gamma camera quality control.
In Annual meeting of the Society for Computer Applications in Radiology (SCAR),
pages 91-93,
2006.
Keyword(s): Imaging,
Software and Tools.
[bibtex-key = scar2006b]
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Andy Rova,
Anna Celler,
and Ghassan Hamarneh.
NMQC: A NEMA-compliant software for gamma camera quality control.
In Vancouver Coastal Health Research Institute (VCHRI),
2006.
Keyword(s): Imaging,
Software and Tools.
[bibtex-key = vchri2006a]
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Vincent Chu and Ghassan Hamarneh.
MATITK: MATLAB-ITK Interface for Medical Image Processing.
In 1st Annual Medical Technology Research Showcase, Vancouver, BC,
2005.
Keyword(s): Processing,
Segmentation,
Registration and Matching,
Software and Tools.
[bibtex-key = medical_showcase2005a]
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Kumar Abhishek,
Aditi Jain,
and Ghassan Hamarneh.
Investigating the Quality of DermaMNIST and Fitzpatrick17k Dermatological Image Datasets.
Technical report arXiv:2401.14497,
1 2024.
Keyword(s): Dermatology,
Machine Learning,
Deep Learning,
Software and Tools,
Datasets.
[bibtex-key = arxiv:2401.14497]
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Ashwin Samudre,
Guang Gao,
Ben Cardoen,
Ivan Robert Nabi,
and Ghassan Hamarneh.
nERdy: network analysis of endoplasmic reticulum (Nabi and Hamarneh: Joint senior authors).
Technical report biorxiv:2024.02.20.581259,
2 2024.
Keyword(s): Super Resolution Microscopy,
Software and Tools,
Network Modelling and Analysis,
Machine Learning,
Deep Learning,
Anatomical Trees and Tubular Structures,
Synthesis/Simulation/Augmentation.
[bibtex-key = biorxiv_2024_02_20_581259]
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Ben Cardoen,
Hanene Ben Yedder,
Sieun Lee,
Ivan Robert Nabi,
and Ghassan Hamarneh.
DataCurator.jl: Efficient, portable, and reproducible validation, curation, and transformation of large heterogeneous datasets using human-readable recipes compiled into machine verifiable templates.
Technical report techrxiv:22060118,
2 2023.
Keyword(s): Microscopy,
Processing,
Single Molecule Localization,
Super Resolution Microscopy,
Software and Tools,
Reproducibility.
[bibtex-key = techrxiv_22060118]
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Ben Cardoen,
Hanene Ben Yedder,
Sieun Lee,
Ivan Robert Nabi,
and Ghassan Hamarneh.
Log-Paradox: Necessary and sufficient conditions for confounding statistically significant pattern reversal under the log-transform.
Technical report arxiv.2302.04780,
000 2023.
Keyword(s): Microscopy,
Processing,
Single Molecule Localization,
Super Resolution Microscopy,
Software and Tools,
Statistics,
Geometric mean,
Log-transform.
[bibtex-key = arxiv:2302.04780]
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Weina Jin,
Jianyu Fan,
Diane Gromala,
Philippe Pasquier,
and Ghassan Hamarneh.
Invisible Users: Uncovering End-Users' Requirements for Explainable AI via Explanation Forms and Goals.
Technical report arxiv.2302.06609,
2 2023.
Keyword(s): Deep Learning,
Explainable AI (XAI),
Multimodal,
Software and Tools.
[bibtex-key = arxiv:2302.06609]
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Ryan Dickie,
Ghassan Hamarneh,
and Rafeef Abugharbieh.
Live-vessel: Interactive vascular image segmentation with simultaneous extraction of optimal medial and boundary paths.
Technical report TR 2009-23,
School of Computing Science, Simon Fraser University, Burnaby, BC, Canada,
11 2009.
Keyword(s): Segmentation,
Anatomical Trees and Tubular Structures,
Color/Multichannel/Vector-valued,
Optimization,
Software and Tools,
User Interaction,
Medial-based Shape Representation,
Graph based,
Bifurcation/Junction.
[bibtex-key = sfu_cs2009_23]
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Ghassan Hamarneh.
Digital Image Analysis of Fundus Photographs on the WWW.
Technical report R002/1999 (S2-IAG-99-1),
Department of Signals and Systems, School of Electrical and Computer Engineering, Chalmers University of Technology, Goteborg, Sweden,
2 1999.
Keyword(s): Software and Tools.
[bibtex-key = s2iag1999_1]
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Last modified: Thu Aug 1 12:06:05 2024
Author: hamarneh.
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