News

2024

August

Carlos Rivas presenting his REU project titled Automatic unique identification of multiple sclerosis lesions from MR images.

• Carlos Rivas presented his REU project titled Automatic unique identification of multiple sclerosis lesions from MR images.

July

Meeting at the Henry Jackson Foundation for the team behind the Brain Biomechanics Imaging Resources on NITRC, made possible by the NIH through U01 NS112120 (PI: P.V. Bayly).

• Brain Biomechanics Imaging Resources (BBIR) now has over 150 datasets available for download.
  • 50 subjects from the Henry Jackson Foundation, imaged with tagged magnetic resonance.
  • 61 subjects from the University of Delaware, imaged with high resolution magnetic resonance elastography at multiple frequencies (30Hz, 50Hz, 70Hz).
  • 52 subjects from Washington University in St. Louis, imaged with magnetic resonance elastography at multiple frequencies (20Hz, 30Hz, 50Hz, 70Hz, 90Hz).
  • All data includes structural magnetic resonance images (T1-w, T2-w) and diffusion weighted images.
  • The structural images have been processed with SLANT-MACRUISE and the diffusion images with TORTOISE.
  • Site information and subject details can be found in the available BBIR documents.
  • Additional information is available in our related publications:
    • R.J. Okamoto et al., "Effect Of Direction And Frequency Of Skull Motion On Mechanical Vulnerability Of The Human Brain" in Journal of Biomechanical Engineering  (doi)
    • A. Alshareef et al., "Integrating Linear Viscoelastic Material Properties Derived from Magnetic Resonance Elastography into Subject-Specific Brain Models" in Brain Multiphysics  (doi)
    • P.V. Bayly et al., "MR imaging of human brain mechanics in vivo: New measurements to facilitate the development of computational models of brain injury" in Annals of Biomedical Engineering  (doi)

May

Drs. Yihao Liu and Lianrui Zuo celebrating their hooding by Prof. J.L. Prince.

• Congratulations to Yihao Liu and Lianrui Zuo on receiving their PhDs.
• Congratulations to Junyi Liu, Shimeng Wang, and Zejun Wu on receiving their masters. Junyi Liu will be pursuing her PhD at Ohio State, Shimeng Wang will be staying at Hopkins to join the PhD program, and Zejun Wu will be joining the PhD program at University of Virginia.

April

Savannah Hays as part of the latest Percy Pierre Doctoral Fellowship cohort who are inspired to follow in the footsteps of distinguished academic and engineer, Percy Pierre, Engr 1967 (PhD). Enjoy the YouTube Video.

• Savannah Hays as part of the latest Percy Pierre Doctoral Fellowship cohort who are inspired to follow in the footsteps of distinguished academic and engineer, Pierre Percy, Engr 1967 (PhD).

• Yihao Liu's paper titled "On Finite Difference Jacobian Computation in Deformable Image Registration" appears in International Journal of Computer Vision.  (doi)

March

NeuroImage Special Issue on Advances in Harmonization Techniques for Magnetic Resonance Imaging is open for submissions through December 31, 2024.

NeuroImage Special Issue on Advances in Harmonization Techniques for Magnetic Resonance Imaging is open for submissions through December 31, 2024. The guest editors are:

• Aaron Carass, Johns Hopkins University
• Lianrui Zuo, Vanderbilt University
• Yihao Liu, Vanderbilt University
• Jerry Prince, Johns Hopkins University
• Neda Jahanshad, University of Southern California

We welcome submissions of original research articles and comprehensive review papers focusing on, but not limited to, the following topics:

1. Advanced approaches for MRI harmonization, which may include:
   • Hybrid methods that combine different approaches
   • Image synthesis methods
   • Statistical methods
2. Detailed evaluations of existing harmonization approaches in various neuroimage analysis tasks. Exploring strengths, limitations, and potential pitfalls of the existing methods.
3. In-depth investigations of the applicability and effectiveness of harmonization methods across different MRI modalities, including:
   • Structural MRI
   • Diffusion MRI, such as diffusion tensor imagimg (DTI), high angular resolution diffusion imaging (HARDI), and diffusion kurtosis imaging (DKI)
   • Functional MR

February

Zhangxing Bian's award for best paper titled "Is Registering Raw Tagged-MR Enough for Strain Estimation in the Era of Deep Learning?" at the Proceedings of SPIE Medical Imaging (SPIE-MI 2024), San Diego, CA, February 18–22, 2024.

• Congratulations to Zhangxing Bian on winning a Best Paper Award at the Proceedings of SPIE Medical Imaging (SPIE-MI 2024), San Diego, CA, February 18–22, 2024.
• IACL papers at the Proceedings of SPIE Medical Imaging (SPIE-MI 2024), San Diego, CA, February 18–22, 2024.
  • Zhangxing Bian presented "Is Registering Raw Tagged-MR Enough for Strain Estimation in the Era of Deep Learning?".
  • Savannah P. Hays presented "Revisiting registration-based synthesis: A focus on unsupervised MR image synthesis".
  • Samuel Remedios presented "Pushing the limits of zero-shot self-supervised super-resolution of anisotropic MR Images" and "Harmonization-enriched domain adaptation with light fine-tuning for multiple sclerosis lesion segmentation".
  • Dr. Yihao Liu presented "Deep learning-based segmentation of hydrocephalus brain ventricle from ultrasound".
  • Zejun Wu presented "AniRes2D: Anisotropic residual-enhanced diffusion for 2D MR super-resolution".
  • Junyi Liu "Exploratory magnetic resonance elastography synthesis from magnetic resonance and diffusion tensor imaging".

• Other accepted papers at SPIE-MI 2024 coming from collaborations with IACL.
  • Xiaofeng Liu from Massachusetts General Hospital, presented "Speech motion anomaly detection via cross-modal translation of 4D motion fields from tagged MRI".

IACL at SPIE-MI 2024
Dr. Yihao Liu presenting Yuli Wang's work titled "Deep learning-based segmentation of hydrocephalus brain ventricle from ultrasound".			Zhangxing Bian presenting "Is Registering Raw Tagged-MR Enough for Strain Estimation in the Era of Deep Learning?".
Savannah P. Hays and Dr. Yihao Liu saying "Ayyy".			Samuel W. Remedios and Savannah P. Hays showing some SPIE pride.
IACL Lab members (new and old) at SPIE-MI 2024.			Samuel W. Remedios presenting "Harmonization-enriched domain adaptation with light fine-tuning for multiple sclerosis lesion segmentation".
Junyi Liu presenting her poster titled "Exploratory magnetic resonance elastography synthesis from magnetic resonance and diffusion tensor imaging".

IACL at the Johns Hopkins School of Medicine and Whiting School of Engineering Research Retreat 2024

January

• Yihao Liu successfully defends his thesis titled "Methods for Automated Analysis of OCT and OCTA Images".
• Lianrui Zuo successfully defends his thesis titled "Unsupervised structural MRI harmonization by learning disentangled representations".

2023

November

"Deep Learning for Medical Image Analysis" 2^nd edition is available for pre-order before its release in December 2023.

• "Deep Learning for Medical Image Analysis" 2^nd edition is available for pre-order before its release in December 2023. It features two chapters from IACL Lab Members.
  • Lianrui Zuo is the lead author of Chapter 5 titled "An overview of disentangled representation learning for MR images".  (doi)
  • Yihao Liu is the lead author of Chapter 16 titled "OCTA Segmentation with limited training data using disentangled representation learning".  (doi)
• The book is available direct from Elsevier, as well as from Amazon.

• Chenyu Gao at Vanderbilt has co-authored a paper with us titled "Reproducibility evaluation of the effects of MRI defacing on brain segmentation" that has appeared in the Journal of Medical Imaging.  (doi)

IACL Lab members attending the ACTRIMS Young Scientist Summit in Clinical Neuroimmunology in Scottsdale, AZ.

• IACL group members attending the Americas Committee for Treatment and Research in Multiple Sclerosis (ACTRIMS) Young Scientist Summit in Clinical Neuroimmunology from October 30 thru November 2 in Scottsdale, Arizona, include:
  • Savannah Hays     
  • Yihao Liu    
  • Samuel W. Remedios
  • Lianrui Zuo     

October

Samuel Remedios wins best paper at the Simulation and Synthesis in Medical Imaging workshop (SASHIMI 2023).

• IACL papers at the 26^th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2023), Vancouver, Canada, October 8–12, 2023.
  • Dr. Shuwen Wei presented "Recurrent Self Fusion: Iterative Denoising for Consistent Retinal OCT Segmentation", 10^th Ophthalmic Medical Image Analysis Workshop (OMIA 2023) in conjunction with the 26^th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2023), Vancouver, Canada, October 8–12, 2023. (doi) 
  • Samuel W. Remedios presented "Self-Supervised Super-Resolution for Slice Gap MRI", Simulation and Synthesis in Medical Imaging (SASHIMI 2023) in conjunction with the 26^th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2023), Vancouver, Canada, October 8–12, 2023. (doi) 
  • Zhangxing Bian presented "MomentaMorph: Unsupervised Spatial-Temporal Registration with Momenta, Shooting, and Correction", MICCAI Workshop on Time-Series Data Analytics and Learning (MTSAIL 2023) in conjunction with the 26^th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2023), Vancouver, Canada, October 8–12, 2023. 

• HACA3 Code for MR Harmonization is available. The method is described in:

L. Zuo, Y. Liu, Y. Xue, B.E. Dewey, S.W. Remedios, S.P. Hays, M. Bilgel, E.M. Mowry, S.D. Newsome, P.A. Calabresi, S.M. Resnick, J.L. Prince, and A. Carass, "HACA3: A unified approach for multi-site MR image harmonization", Computerized Medical Imaging and Graphics, 109:102285, 2023. (doi) 

September

IACL at Johns Hopkins AIX 2023
Savannah Hays recapping her 2023 MIDL work titled "Exploring the Optimal Operating MR Contrast for Brain Ventricle Parcellation".			Dr. Wei previewing his 2023 MICCAI work titled "Recurrent Self Fusion: Iterative Denoising for Consistent Retinal OCT Segmentation".  (doi)			Samuel Remedios previewing his 2023 MICCAI work titled "Self-Supervised Super-Resolution for Slice Gap MRI".

August

• Lianrui Zuo's new harmonization paper titled "HACA3: A unified approach for multi-site MR image harmonization" appears in Computerized Medical Imaging and Graphics.  (doi)    HACA3 Code
• A portion of Lianrui Zuo's interview with NeurologyLive is now available, it was recorded at the 2023 Consortium of Multiple Sclerosis Centers (CMSC) Annual Meeting, Aurora, CO, May 31 - June 3, 2023.

July

• As part of our collaboration with Washington Univeristy in St. Louis, Dr. Ruth Okamoto's paper titled "Effect Of Direction And Frequency Of Skull Motion On Mechanical Vulnerability Of The Human Brain" appears in the Journal of Biomechanical Engineering.  (doi)

• IACL papers at Medical Imaging with Deep Learning (MIDL 2023), Nashville, TN, July 10–12, 2023.
  • Zhangxing Bian presented "DRIMET: Deep Registration-based 3D Incompressible Motion Estimation in Tagged-MRI with Application to the Tongue".
  • Savannah Hays presented "Exploring the Optimal Operating MR Contrast for Brain Ventricle Parcellation".

IACL at MIDL 2023
Zhangxing Bian presenting "DRIMET: Deep Registration-based 3D Incompressible Motion Estimation in Tagged-MRI with Application to the Tongue".				Savannah Hays with previous lab member Chenyu Gao.

• Lianrui Zuo is interviewed by the Video Journal of Neurology. Discussing the following topics:
  • Fixing inconsistent MRI data using image harmonization
  • Impact of image harmonization on MS imaging practice
  • Future of MS image standardization
  • Different approaches to improving MS image standardization

June

Savannah Hays, Lianrui Zuo, and Samuel Remedios at the 2023 Consortium of Multiple Sclerosis Centers (CMSC) Annual Meeting, Aurora, CO, May 31 - June 3, 2023..

• IACL papers at the 2023 Consortium of Multiple Sclerosis Centers (CMSC) Annual Meeting, Aurora, CO, May 31 - June 3, 2023.
  • Dr. Blake Dewey presented "Compliance with CMSC MRI Guidelines in a Multi-Center, Pragmatic, Randomized Clinical Trial: Improvements over Time" and "Measuring MRIs Differences Between Sites: Design of a Traveling Subject Study in MS".
  • Lianrui Zuo presented Dr. Shuwen Wei's work titled "Retinal layer thickness comparison between the UK BioBank and people with multiple sclerosis" and "Synthesizing Missing MRI Sequences to Improve Processing Images in Multiple Sclerosis", and his own work "Inconsistent MR acquisition in longitudinal volumetric analysis: Impacts and solutions".
  • Samuel Remedios presented "Cautions in Anisotropy: Thick Slices and Slice Gaps in 2D MR Acquisition Tarnish Volumetrics".
  • Savannah Hays presented "Quantifying contrast differences among MR images used in clinical studies".

IACL at CMSC 2023
Dr. Blake Dewey between his two posters "Compliance with CMSC MRI Guidelines in a Multi-Center, Pragmatic, Randomized Clinical Trial: Improvements over Time" and "Measuring MRIs Differences Between Sites: Design of a Traveling Subject Study in MS".		Samuel Remedios presenting "Cautions in Anisotropy: Thick Slices and Slice Gaps in 2D MR Acquisition Tarnish Volumetrics".
Savannah Hays presenting "Quantifying contrast differences among MR images used in clinical studies".		Lianrui Zuo presenting "Inconsistent MR acquisition in longitudinal volumetric analysis: impacts and solutions".

May

Dr. Muhan Shao being hooded by Prof. J.L. Prince.

• Congratulations to Muhan Shao on receiving her PhD.
• Congratulations to Anqi "Amy" Feng on receiving her masters, she will be staying at Hopkins and joining the PhD program.

April

• Savannah Hays receives an NSF Fellowship.

Savannah Hays presenting "Rapid brain meninges surface reconstruction with layer topology guarantee" at ISBI 2023 in Cartagena de Indias, Colombia.

• IACL papers at the 20^th IEEE International Symposium on Biomedical Imaging (ISBI 2023), Cartagena de Indias, Colombia, April 18-21, 2023.
  • Savannah Hays' paper titled "Optimal operating MR contrast for brain ventricle parcellation".
  • Yuli Wang's paper titled "Automated ventricle parcellation and Evan’s ratio computation in pre- and post-surgical ventriculomegaly".
  • Peiyu Duan's paper titled "Rapid brain meninges surface reconstruction with layer topology guarantee".
  • Anqi Feng's paper titled "Label propagation via random walk for training robust thalamus nuclei parcellation model from noisy annotations".

IACL at ISBI 2023
IACL Posters at ISBI 2023 in Cartagena de Indias, Colombia.
Savannah Hays pulling triple poster duty at ISBI 2023.

• Dr. Yufan He's paper titled "Longitudinal deep network for consistent OCT layer segmentation" appears in Biomedical Optics Express.  (doi)

February

Zhangxing Bian wins a Best Paper at SPIE-MI 2023.

• Congratulations to Zhangxing Bian on winning a Best Paper Award at the Proceedings of SPIE Medical Imaging (SPIE-MI 2023), San Diego, CA, February 19–23, 2023.
• IACL papers at the Proceedings of SPIE Medical Imaging (SPIE-MI 2023), San Diego, CA, February 19–23, 2023.
  • Jinglun Yu presented "New starting point registration method for tagged MRI tongue motion estimation".
  • Lianrui Zuo presented Pouria Tohidi's work titled "Joint synthesis of WMn MPRAGE and parameter maps using deep learning and an imaging equation".
  • Yuli Wang presented "Investigation of probability maps in deep-learning-based brain ventricle parcellation".
  • Chang Yan's work titled "Segmenting thalamic nuclei from manifold projections of multi-contrast MRI".
  • Samuel Remedios presented "A deep generative prior for high-resolution isotropic MR head slices".
  • Zhangxing Bian presented "FastCod: Fast Brain Connectivity in Diffusion Imaging".
  • Zhangxing Bian presented "DrDisco: Deep Registration for Distortion Correction of Diffusion MRI with single phase-encoding".
  • Lianrui Zuo presented "A latent space for unsupervised MR image quality control via artifact assessment".

• Other accepted papers at SPIE-MI 2023 coming from collaborations with IACL.
  • Allen Hong from The College of New Jersey, presented "Investigating the effect of cerebral atrophy on brain deformation using subject-specific models".
  • Xiaofeng Liu from Massachusetts General Hospital, presented "Synthesizing audio from tongue motion during speech using tagged MRI via transformer".

IACL at SPIE-MI 2023
Lianrui Zuo presenting Pouria Tohidi's work titled "Joint synthesis of WMn MPRAGE and parameter maps using deep learning and an imaging equation".			Zhangxing Bian presenting "DrDisco: Deep Registration for Distortion Correction of Diffusion MRI with single phase-encoding".
Samuel Remedios presenting "A deep generative prior for high-resolution isotropic MR head slices".			Lianrui Zuo presenting "A latent space for unsupervised MR image quality control via artifact assessment".
Allen Hong presenting "Investigating the effect of cerebral atrophy on brain deformation using subject-specific models".			Jinglun Yu presenting "New starting point registration method for tagged MRI tongue motion estimation".

• Dr. Muhan Shao's paper titled "Analysis of Tongue Muscle Strain During Speech From Multimodal Magnetic Resonance Imaging" appears in Journal of Speech, Language, and Hearing Research.  (doi)  (PubMed)

January

• Shuo Han's paper titled "ESPRESO: An algorithm to estimate the slice profile of a single magnetic resonance image" appears in Magnetic Resonance Imaging.  (doi)  (PubMed)

2022

December

• Yihao Liu's paper titled "Disentangled Representation Learning for OCTA Vessel Segmentation with Limited Training Data" appears in IEEE Trans. on Medical Imaging.  (doi)  (PubMed)

November

• The lab visited the Corradetti Glass Studio to do some glass blowing.

IACL at Corradetti Glass

September

Lianrui Zuo wins the Best Paper at DALI 2022.

Sam Remedios presenting his poster at MICCAI 2022 titled "Deep filter bank regression for super-resolution of anisotropic MR brain images".

• IACL papers at the 25^th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2022), Singapore, September 18–22, 2022.
  • Samuel W. Remedios presented "Deep filter bank regression for super-resolution of anisotropic MR brain images", 25^th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2022), Singapore, September 18–22, 2022. (doi)  
  • Xiaofeng Liu presented "Tagged-MRI2Audio with Attention Guided Heterogeneous Translator", 25^th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2022), Singapore, September 18–22, 2022. 
  • Lianrui Zuo's presented "Disentangling from A Single MR Modality", 2^nd Workshop on Data Augmentation, Labeling, and Imperfections (DALI 2022) in conjunction with the 25^th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2022), Singapore, September 18–22, 2022.  
  • Yihao Liu presented "Coordinate Translator for Learning Deformable Medical Image Registration", 3^rd Multiscale Multimodal Medical Imaging (MMMI 2022) in conjunction with the 25^th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2022), Singapore, September 18–22, 2022.  
  • Germain Morilhat presented "Deep Learning-based Segmentation of Pleural Effusion From Ultrasound Using Coordinate Convolutions", 2^nd workshop on aFfordable AI and healthcare for Resource diverse global health (FAIR 2022) in conjunction with the 25^th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2022), Singapore, September 18–22, 2022.  

August

• Allen Hong gave his REU presentation titled "Investigating the effects of cerebral atrophy on brain biomechanics using subject specific models".

Allen Hong REU Presentation

July

• Brain Biomechanics Imaging Resources now has 100 datasets available for download.
  • 30 subjects from the Henry Jackson Foundation, imaged with tagged magnetic resonance.
  • 36 subjects from the University of Delaware, imaged with high resolution magnetic resonance elastography at multiple frequencies (30Hz, 50Hz, 70Hz).
  • 34 subjects from Washington University in St. Louis, imaged with magnetic resonance elastography at multiple frequencies (20Hz, 30Hz, 50Hz, 70Hz, 90Hz).
  • All data includes structural magnetic resonance images (T1-w, T2-w) and diffusion weighted images.
  • The structural images have been processed with SLANT-MACRUISE. The diffusion images with TORTOISE.
  • Site information and subject details can be found in the available BBIR documents.
  • Additional information is available in our related publications:
    • "Integrating Linear Viscoelastic Material Properties Derived from Magnetic Resonance Elastography into Subject-Specific Brain Models"  (doi)
    • "MR imaging of human brain mechanics in vivo: New measurements to facilitate the development of computational models of brain injury"  (doi)

June

• Brain Biomechanics Imaging Resources now has 56 datasets available for download.
  • 10 subjects from the Henry Jackson Foundation, imaged with tagged magnetic resonance.
  • 36 subjects from the University of Delaware, imaged with high resolution magnetic resonance elastography at multiple frequencies (30Hz, 50Hz, 70Hz).
  • 10 subjects from Washington University in St. Louis, imaged with magnetic resonance elastography at multiple frequencies (20Hz, 30Hz, 50Hz, 70Hz, 90Hz).
  • All data includes structural magnetic resonance images (T1-w, T2-w) and diffusion weighted images.
  • The structural images have been processed with SLANT-MACRUISE. The diffusion images with TORTOISE.
  • Site information and subject details can be found in the available BBIR documents.
  • Additional information is available in our related publications:
    • "Integrating Linear Viscoelastic Material Properties Derived from Magnetic Resonance Elastography into Subject-Specific Brain Models"  (doi)
    • "MR imaging of human brain mechanics in vivo: New measurements to facilitate the development of computational models of brain injury"  (doi)

May

Drs. Blake E. Dewey and Yufan He flank Prof. J.L. Prince after their hooding ceremony.

• Congratulations to Blake. E. Dewey, Shuo Han, and Yufan He on receiving their PhDs.
• Congratulations to Peiyu "Camille" Duan and Chenyu Gao on receiving their masters. Peiyu Duan is joining a PhD program at Yale University. Chenyu Gao is joining a PhD at Vanderbilt University.

February

• Congratulations to Pouria Tohidi on winning a Best Poster Award at the Proceedings of SPIE Medical Imaging (SPIE-MI 2022), San Diego, CA, February 20–24, 2022.
• IACL papers at the Proceedings of SPIE Medical Imaging (SPIE-MI 2022), San Diego, CA, February 20–24, 2022.
  • Muhan Shao presented "Evaluating the impact of MR image harmonization on thalamus deep network segmentation".
  • Savannah Hays presented "Evaluating the Impact of MR Image Contrast on Whole Brain Segmentation".
  • Peiyu "Camille" Duan presented "Cranial Meninges Reconstruction Based on Convolutional Networks and Deformable Models: Applications to Longitudinal Study of Normal Aging".
  • Ahmed Alshareef presented "Investigating the Effect of Ventricle Size on Brain Deformation using Computational Models" and "Correlation of Cerebral Vasculature to Brain Stiffness Using MRE".
  • Chenyu Gao presented "Effects of Defacing Whole Head MRI on Neuroanalysis".
  • Pouria Tohidi presented "Multiple Sclerosis Brain Lesion Segmentation with Different Architecture Ensembles".

IACL at SPIE-MI 2022
IACL Lab members (and friend) at SPIE-MI 2022 in San Diego.
Ahmed Alshareef presenting his talk titled "Investigating the Effect of Ventricle Size on Brain Deformation using Computational Models".
Peiyu "Camille" Duan presented "Cranial Meninges Reconstruction Based on Convolutional Networks and Deformable Models: Applications to Longitudinal Study of Normal Aging".
Savannah Hays preparing for her presentation titled "Evaluating the Impact of MR Image Contrast on Whole Brain Segmentation".
IACL lab members presenting posters (and winning awards!!).

2021

October

• Brain Biomechanics Imaging Resources now has 30 datasets available for download.
  • 10 subjects from the Henry Jackson Foundation, imaged with tagged magnetic resonance.
  • 10 subjects from the University of Delaware, imaged with high resolution magnetic resonance elastography at multiple frequencies (30Hz, 50Hz, 70Hz).
  • 10 subjects from Washington University in St. Louis, imaged with magnetic resonance elastography at multiple frequencies (20Hz, 30Hz, 50Hz, 70Hz, 90Hz).
  • All data includes structural magnetic resonance images (T1-w, T2-w) and diffusion weighted images.
  • The structural images have been processed with SLANT-MACRUISE. The diffusion images with TORTOISE.
  • Individual subjects can be downloaded or complete site sets.
  • Site information and subject details can be found in the available BBIR documents.
  • Additional information is available in our related publications:
    • "Integrating Linear Viscoelastic Material Properties Derived from Magnetic Resonance Elastography into Subject-Specific Brain Models"  (doi)
    • "MR imaging of human brain mechanics in vivo: new measurements to facilitate the development of computational models of brain injury"  (doi)

• Ahmed Alshareef's paper titled "Integrating Linear Viscoelastic Material Properties Derived from Magnetic Resonance Elastography into Subject-Specific Brain Models" appears in Brain Multiphysics.  (doi)
• Ahmed Alshareef presented "Integrating Linear Viscoelastic Material Properties Derived from Magnetic Resonance Elastography into Subject-Specific Finite Element Brain Models" at the Biomedical Engineering Society (BMES) Annual Meeting, Orlando, FL, October 6-9, 2021.
• Jerry L. Prince delivered a keynote at the DALI MICCAI Workshop.

September

• Samuel W. Remedios presented "Joint Image and Label Self-Super-Resolution" at the Simulation and Synthesis in Medical Imaging (SASHIMI 2021) in conjunction with the 24^th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2021), Strasbourg, France, September 27 – October 1, 2021.  (doi)
• Jacob C. Reinhold presented "A Structural Causal Model for MR Images of Multiple Sclerosis" at the 24^th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2021), Strasbourg, France, September 27 – October 1, 2021.  (doi)
• Lianrui Zuo's paper titled "Unsupervised MR harmonization by learning disentangled representations using information bottleneck theory" appears in NeuroImage.  (doi)

August

• Yufan He successfully defends his thesis titled "Retinal OCT Image Analysis Using Deep Learning".

July

• A paper on our Brain Biomechanics project titled "MR imaging of human brain mechanics in vivo: new measurements to facilitate the development of computational models of brain injury" appears in Annals of Biomedical Engineering.  (doi)

June

• Yufan He's paper titled "Autoencoder Based Self-Supervised Test-Time Adaptation for Medical Image Analysis" appears in Medical Image Analysis.  (doi)
• Congratulations to Lianrui Zuo on winning the Best Poster Award at the 27^th Conference on Information Processing in Medical Imaging (IPMI 2021), Virtually in Bornholm, Denmark, June 28 - July 2, 2021.
• IACL papers at the 27^th Conference on Information Processing in Medical Imaging (IPMI 2021), Virtually in Bornholm, Denmark, June 28 - July 2, 2021.
  • Lianrui Zuo presents his poster teaser for "Information-based Disentangled Representation Learning for Unsupervised MR Harmonization".
  • Shuo Han presents his poster teaser for "MR Slice Profile Estimation by Learning to Match Internal Patch Distributions".

April

• IACL papers at the 18^th IEEE International Symposium on Biomedical Imaging (ISBI 2021), Nice, France, April 13-16, 2021.
  • Shuo Han presented "Slice profile estimation from 2D MRI acquisition using generative adversarial networks".
  • Our collaborator, Xiaofeng Liu at Massachusetts General Hospital, presented "Dual-Cycle constrained bijective VAE-GAN for Tagged-to-Cine magnetic resonance image synthesis".

March

• Can Zhao's paper titled "SMORE: A Self-supervised Anti-aliasing and Super-resolution Algorithm for MRI Using Deep Learning" appears in IEEE Trans. on Medical Imaging.  (doi)
  • The related software can be downloaded from our page about SMORE.

February

• IACL members papers from the Proceedings of SPIE Medical Imaging (SPIE-MI 2021), San Diego, CA, February 14–18, 2021.
  • ShangXian Wang presented "Thalamus Segmentation Using Convolutional Neural Network".  (doi)
  • Mallika Singh presented "Accurate Estimation of Total Intracranial Volume in MRI using a Multi-tasked Image-to-Image Translation Network".  (doi)
  • Di Liu presented "Label super resolution for 3D Magnetic Resonance Images using Deformable U-net".  (doi)
  • Muhan Shao presented "Reconstruction and refinement of crossing muscle fibers in the human tongue".  (doi)
  • Muhan Shao presented "Dynamic palatogram generation from Cine MRI for normalized speech assessment".  (doi)

January

• Jerry L. Prince presented the Medical Imaging keynote at NeurIPS "New Approaches for Magnetic Resonance Image Harmonization", the video is now on YouTube .

2020

December

• Yufan He's paper titled "Structured layer surface segmentation for retina OCT using fully convolutional regression networks" appears in the MICCAI Special Issue of Medical Image Analysis.  (doi).

October

• IACL members present papers at the 23^rd International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2020), Lima, Peru, October 4 - 8, 2020.
  • Yufan He presented "Self domain adapted network".  (doi)
  • Blake Dewey presented "A Disentangled Latent Space for Cross-Site MRI Harmonization".  (doi)

• IACL members had the following presentations at MICCAI 2020 Workshops:
  • Lianrui Zuo presented "Synthesize Realistic MR Images with Noise Control" at SASHIMI 2020.  (doi)
  • Shuo Han presented "Inhomogeneity Correction in Magnetic Resonance Images Using Deep Image Priors" at MLMI 2020.  (doi)
  • Muhan Shao presented "Direct reconstruction of crossing muscle fibers in the human tongue using a deep neural network" at CDMRI 2020.

August

• From our collaboration with Xi’an Jiaotong University, the paper "Unsupervised MR-to-CT Synthesis using Structure-Constrained CycleGAN" appears in IEEE Trans. on Medical Imaging.  (doi)

July

• Shuo Han's paper "Longitudinal analysis of regional cerebellum volumes during normal aging" appears in NeuroImage.  (doi)  (PubMed)

June

• Brain Biomechanics Imaging Resources releases more data.
  • Data is from University of Delaware and Washington University in St. Louis.
  • Includes five new subjects (Two from University of Delaware and three from Washington University in St. Louis).
  • The data is magnetic resonance elastography at multiple frequencies (20Hz through 90Hz).
• Christian Barillot passed away on June 14, he was a well known and liked researcher in the Medical Imaging Community. There is a memorial page for him at IRISA.

May

• The paper "Evaluating White Matter Lesion Segmentations with Refined Sørensen-Dice Analysis" appears in the journal Nature Scientific Reports.  (doi)  (PubMed)
• Shuo Han's paper "Automatic Cerebellum Anatomical Parcellation using U-Net with Locally Constrained Optimization" appears in NeuroImage.  (doi)

April

• Brain Biomechanics Imaging Resources releases updated version of data on NITRC.
  • This release includes MR tagged images of six subjects.
  • Three subjects undergoing rotational motion.
  • Three subjects undergoing head drop.

Jacob Reinhold's presentation from ISBI 2020.

• Jacob C. Reinhold participates in the first virtual ISBI presenting his work titled "Validating uncertainty in medical image translation" .

February

• IACL members present papers at the SPIE Medical Imaging (SPIE-MI 2020) meeting in Houston, TX, February 15 - 20, 2020.
  • Prof. J.L. Prince presented work by Yufan He "Adversarial domain adaptation for multi-device retinal OCT segmentation".
  • Jacob Reinhold presented "Finding novelty with uncertainty".
  • Yihao Liu presented "Variational intensity cross channel encoder for unsupervised vessel segmentation on OCT angiography".
  • Shuo Han presented "Reflection-equivariant convolutional neural networks improve segmentation over reflection augmentation".
  • Yihao Liu presented work by Yufan He "Segmenting retinal OCT images with inter-B-scan and longitudinal information".
• Other accepted papers at SPIE-MI 2020 coming from collaborations with IACL.
  • With Jonghye Woo from Harvard Medical School "Identifying the common and subject-specific functional units of speech movements via a joint sparse non-negative matrix factorization framework".

IACL at SPIE 2020
Shuo Han presenting his poster titled "Reflection-equivariant convolutional neural networks improve segmentation over reflection augmentation".
Jacob Reinhold enjoying a plenary talk.	Yihao Liu presenting a poster.

2019

December

• Can Zhao's paper titled "Applications of a deep learning method for anti-aliasing and super-resolution in MRI" appears in Magnetic Resonance in Medicine  (doi)  (PubMed)
• Blake Dewey's paper titled "DeepHarmony: A deep learning approach to contrast harmonization across scanner changes" also appears in the same special issue of Magnetic Resonance in Medicine  (doi)  (PubMed)

November

IACL wins the 2019 ECE Pumpkin Carving Contest!!

• IACL members win the 2019 ECE Pumpkin Carving Contest!!
  This is our second consecutive Pumpkin Carving Contest win, and our third win in five years.

October

IACL at MICCAI 2019

Can Zhao wins best paper at the SASHIMI Workshop at MICCAI 2019.

• Can Zhao wins best paper at the SASHIMI Workshop at MICCAI 2019, for her paper titled "iSMORE: An iterative self super-resolution algorithm".
• Yufan He wins a MICCAI Young Scientist Award at MICCAI 2019.

• IACL members present papers at the 22^nd International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2019), Shenzhen, China, October 13 - 17, 2019.
  • Can Zhao presented "iSMORE: An iterative self super-resolution algorithm" at the SASHIMI Workshop.
  • Yufan He presented "Fully Convolutional Boundary Regression for Retina OCT Segmentation".
  • Shuo Han presented "Hierarchical Parcellation of the Cerebellum".

Jeffrey Glaister celebrating the defense of his PhD titled "Brain structure segmentation using multiple MRI pulse sequences", pictured with Dr. Jerry L. Prince.

• Dr. Jeffrey Glaister successfully defends his thesis titled "Brain structure segmentation using multiple MRI pulse sequences".

April

Shuo Han presenting the poster "A resolution measurement algorithm for MRI".

• IACL activity at ISBI 2019:
  • The IACL team finishes second at the CHAOS Challenge at ISBI 2019. We competed in Tasks 3 and 5 as team mountain. See the leaderboard for complete results.
  • Yihao Liu presented "Projection Artifact Suppression for Inner Retina in OCT Angiography".
  • Shuo Han presented "A resolution measurement algorithm for MRI".

March

• Yihao Liu's paper titled "Layer boundary evolution method for macular OCT layer segmentation" appears in Biomedical Optics Express.  (doi)  (PubMed)  (PMCID 6420297)

February

• IACL members present papers at the SPIE Medical Imaging (SPIE-MI 2019) meeting in San Diego, CA, February 15 - 20, 2019.
  • Shuo Han presented "Cerebellum parcellation with convolutional neural networks".
  • Lianrui Zuo presented "Automatic Quality Control Using Hierarchical Shape Analysis".
  • Jacob Reinhold presented "Evaluating the impact of intensity normalization on MR Image Synthesis".

• Yufan He's paper "Retinal layer parcellation of optical coherence tomography images: Data resource for Multiple Sclerosis and Healthy Controls"' appears in Data in Brief.  (doi)  (PubMed)  (PMCID 6327073)

January

• The paper "Dual Level-Set Framework for 3D Coronary Artery Wall Segmentation from Coronary CT Angiography" appears in the journal Nature Scientific Reports.  (doi)

2018

December

• The paper "Comparing fully automated state-of-the-art cerebellum parcellation from magnetic resonance imaging" appears in NeuroImage.  (doi)  (PubMed)
• The paper "Why rankings of biomedical image analysis competitions should be interpreted with care" appears in the journal Nature Communications.  (doi)  (PubMed)  (PMCID 6284017)

November

IACL wins the 2018 ECE Pumpkin Carving Contest!!

• IACL members win the 2018 ECE Pumpkin Carving Contest!!

September

Can Zhao presenting her work titled "A Deep Learning based Anti-aliasing Self Super-resolution Algorithm for Magnetic Resonance Imaging" to Dr. Michael Guttman at MICCAI 2018. Dr. Guttman was the first graduate student to ever work in IACL.

• IACL members present papers at the 21^st International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2018), Granada, Spain, September 16 - 20, 2018.
  • Dr. A.D. Gomez presented "Quantifying Tensor Field Similarity With Global Distributions and Optimal Transport".
  • Can Zhao presented "A Deep Learning based Anti-aliasing Self Super-resolution Algorithm for Magnetic Resonance Imaging".
• We also had presentations at several MICCAI workshops.
  • Dr. A.D. Gomez presented "Quantitative validation of MRI-based motion estimation for brain impact biomechanics" at Computational Biomechanics for Medicine (CBM XIII).
  • At Simulation and Synthesis in Medical Imaging (SASHIMI 2018), Blake Dewey presented "Deep Harmonization of Inconsistent MR Data for Consistent Volume Segmentation" and Yuta Hiasa presented "Crossmodality image synthesis from unpaired data using CycleGAN: Effects of gradient consistency loss and training data size".
  • Dr. J.L. Prince presented "Shortcomings of Ventricle Segmentation Using Deep Convolutional Networks" at the Deep Learning Fails Workshop and also "Unpaired Brain MR-to-CT Synthesis using a Structure-Constrained CycleGAN" at the 4^th Workshop on Deep Learning in Medical Image Analysis (DLMIA 2018).
  • In collaboration with Univ. of Pennsylvania, Dr. Min Chen presented "2D Modeling and Correction of Fan-beam Scan Geometry in OCT" at 5^th Workshop on Ophthalmic Medical Image Analysis (MW-OMIA5). Dr. Chen also won the Best Poster prize at MW-OMIA5.

August

• The paper "Preoperative mapping of the supplementary motor area in brain tumor patients using resting-state fMRI with seed based analysis" appears in the American Journal of Neuroradiology.  (doi)  (PubMed)

April

• IACL members present papers at the International Symposium on Biomedical Imaging (ISBI 2018) meeting in Washington, DC, April 4 - 7, 2018.
  • Can Zhao presented "Self Super-Resolution for Magnetic Resonance Images Using Deep Networks".
  • Yihao Liu presented "Multi-Layer Fast Level Set Segmentation for Macular OCT".

IACL at ISBI 2018
Can Zhao presenting her poster titled "Self Super-Resolution for Magnetic Resonance Images Using Deep Networks".			Yihao Liu presenting his poster titled "Multi-Layer Fast Level Set Segmentation for Macular OCT".

February

• IACL members present papers at the SPIE Medical Imaging (SPIE-MI 2018) meeting in Houston, TX, February 10 - 15, 2018.
  • Lianrui Zuo presented "Automatic outlier detection using hidden Markov model for cerebellar lobule segmentation".
  • Muhan Shao presented "Multi-atlas segmentation of the hydrocephalus brain using an adaptive ventricles atlas".
  • Jeffrey Glaister presented "Deformable model reconstruction of the subarachnoid space".
  • Xiaokai Wang presented "A novel filtering approach for 3D harmonic phase analysis of tagged MRI".
• Other accepted papers at SPIE-MI 2018 coming from collaborations with IACL.
  • With Sachin Goyal from IIT Bombay presented "Improving Self Super Resolution in Magnetic Resonance Images".
  • With Aniket Tolpadi from Rice University "Inverse biomechanical modeling via machine learning and synthetic training data".
  • With Sureerat Reaungamornrat from Mahidol University "Inter-scanner Variation Independent Descriptors for Constrained Diffeomorphic Demons Registration of Retinal OCT".

IACL at SPIE 2018
Muhan Shao presenting her talk titled "Multi-atlas segmentation of the hydrocephalus brain using an adaptive ventricles atlas".
Jeffrey Glaister presenting his poster "Deformable model reconstruction of the subarachnoid space".	Aniket Tolpadi presenting his talk "Inverse biomechanical modeling via machine learning and synthetic training data".

January

• Andrew Lang's paper "Intensity inhomogeneity correction of SD-OCT data using macular flatspace" appears in Medical Image Analysis.  (doi)  (PubMed)

2017

September

Yufan He with his awarding winning poster at the OMIA Workshop, held in conjunction with MICCAI 2017.

• Jeffrey Glaister presented "Falx Cerebri Segmentation via Multiatlas Boundary Fusion" at the 20^th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2017), Quebec, Canada, September 10 - 14, 2017.  (doi)
• Presenting during Workshops at the 20^th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2017), Quebec, Canada, September 10 - 14, 2017.
  • Lotta M. Ellingsen presented "Automated Parcellation of the Ventricular System: Validation Study on Normal Pressure Hydrocephalus".  (doi)
  • Can Zhao presented "Whole brain segmentation and labeling from CT using synthetic MR images"  (doi) and "A super-voxel based random forest synthesis framework for bidirectional MR/CT synthesis".
  • Yufan He presented "Towards topological correct segmentation of macular OCT from cascaded FCNs" and won the Best Poster Prize as part of the OMIA Workshop.  (doi)
  • Dr. Jerry L. Prince presented "Group Patterns of Acceleration-Induced Brain Deformation in Vivo".
• Dr. Jerry L. Prince presnted a keynote at Brain Lesion Workshop entitled "Dice overlap measures for multiple objects: Application to lesion segmentation".

July

• The paper "Automated segmentation of mouse OCT volumes (ASiMOV): Validation & clinical study of a light damage model" appears in PLoS ONE  (doi)  (PubMed)
• Jeffrey Glaister's paper "Thalamus segmentation using multi-modal feature classification: Validation and pilot study of an age-matched cohort" appears in NeuroImage.  (doi)  (PubMed)

May

• Dr. Lang and Dr. Bilgel receive their PhDs from Electrical & Computer Engineering and Biomedical Engineering, respectively. Lab alumni Yeyi Yun graduates with a BA, triple majoring in Electrical & Computer Engineering, Economics, and Mathematics.

Dr. Prince collecting his award for promoting diversity.

• Dr. Jerry L. Prince wins the 2017 Diversity Recognition Award from the Johns Hopkins Diversity Leadership Council (DLC).
• The paper "Longitudinal multiple sclerosis lesion segmentation data resource",  (doi) is published.

April

• Johns Hopkins Magazine features an article titled "The CEO who learned to ask" about IACL colaborator David Narrow, the CEO of Sonavex.

March

• The 2017 ENIGMA Cerebellum Challenge and Workshop website launches. The Challenge and Workshop is a collaboration between IACL, the MASI Lab at Vanderbilt, and the IGC Lab at the Univ. of Southern California. The one day Challenge and Workshop is a satellite event of MICCAI 2017, which will be held in Quebec, Canada.

February

Dr. Prince after meeting with students from the "Discovery to Market" class from The Johns Hopkins Carey Business School.

• Dr. Jerry L. Prince is working with students from Dr. Nayoung Louie's "Discovery to Market" class from The Johns Hopkins Carey Business School.

Dr. Prince presenting the poster "Improving graph-based OCT segmentation for severe pathology in Retinitis Pigmentosa patients" at SPIE-MI 2017.

• IACL members present papers at the SPIE Medical Imaging (SPIE-MI 2017) meeting in Orlando, FL, February 11 - 16 2017.
  • Dr. Jerry L. Prince presents "Test-suite for image-based motion estimation of the brain and tongue", "Longitudinal Analysis of Mouse OCT Volumes", "Improving graph-based OCT segmentation for severe pathology in Retinitis Pigmentosa patients", and "Collaborative SDOCT Segmentation and Analysis Software".
  • Blake E. Dewey presents "Efficient Multi-Atlas Registration using an Intermediate Template Image".
  • Jeffrey Glaister presents "Automatic falx cerebri and tentorium cerebelli segmentation from Magnetic Resonance Images".
  • Junghoon Lee presents "Multi-atlas-based CT synthesis from conventional MRI with patch-based refinement for MRI-based radiotherapy planning".
• Other accepted papers at SPIE-MI 2017 coming from collaborations with IACL.
  • With colleagues at MGH "A four-dimensional motion field atlas of the tongue from tagged and cine magnetic resonance imaging".

IACL at SPIE 2017

January

• The papers "Random forest regression for magnetic resonance image synthesis",  (doi) (PubMed),"Longitudinal Multiple Sclerosis Lesion Segmentation: Resource and Challenge",  (doi) (PubMed), and "Cross contrast multi-channel image registration using image synthesis for MR brain images",  (doi) (PubMed) are published.

2016

December

• The paper "MIND Demons: Symmetric Diffeomorphic Deformable Registration of MR and CT for Image-Guided Spine Surgery", IEEE Trans. on Medical Imaging, 35(11):2413-2424, 2016 (doi) (PubMed) is published.

October

Dr. A. David Gomez collecting the best paper prize at the Computational Biomechanics for Medicine XI Workshop at the 19^th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2016), Athens, Greece, October 17 - 21, 2016.

• Dr. A. David Gomez wins the best paper prize at the Computational Biomechanics for Medicine XI Workshop at the 19^th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2016), Athens, Greece, October 17 - 21, 2016.
• IACL members present papers at the 19^th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2016), Athens, Greece, October 17 - 21, 2016.
  • Dr. Amod Jog presented "Self Super-resolution for Magnetic Resonance Images", as part of the main conference (doi) and "Patch Based Synthesis of Whole Head MR Images: Application to EPI Distortion Correction", at the SASHIMI: Simulation and Synthesis in Medical Imaging Workshop.
  • Dr. A. David Gomez presented "Motion Estimation with Finite-Element Biomechanical Models and Tracking Constraints from Tagged MRI", at the Computational Biomechanics for Medicine XI Workshop and "Incompressible Phase Registration for Motion Estimation from Tagged Magnetic Resonance Images", Reconstruction and Analysis of Moving Body Organs‎ (RAMBO 2016) Workshop.
  • Dr. Jerry L. Prince presented the keynote lecture "Patches and pulse sequences for MR image intensity normalization", at the 2nd International Workshop on Patch-based Techniques in Medical Imaging (Patch-MI).

September

• The papers "Temporal filtering of longitudinal brain magnetic resonance images for consistent segmentation", NeuroImage: Clinical, 11:264-275, 2016 (doi) and "Consistent Cortical Reconstruction and Multi-atlas Brain Segmentation", NeuroImage, 138:197-210, 2016 (doi) are published.

August

• The paper "Estimation of fiber orientations using neighborhood information", Medical Image Analysis, 32:243-256, 2016 (doi) is published.

July

• The paper "A multivariate nonlinear mixed effects model for longitudinal image analysis: Application to amyloid imaging", NeuroImage, 134:658-670, 2016 (doi) is published.

May

Drs. Yang, Xing, and Jog celebrate receiving their PhDs with Jerry L. Prince.

• Drs. Zhen Yang, Fangxu Xing, and Amod Jog celebrate their hooding ceremony as part of receiving their PhDs with Jerry L. Prince.
• Paper submission for the MICCAI Workshop SASHIMI: Simulation and Synthesis in Medical Imaging is open. The workshop is focussed on the development of synthetic data with known ground truth to help develop, evaluate, and validate image analysis and reconstruction algorithms.

April

Andrew Lang presenting his poster "Intensity inhomogeneity correction of macular OCT using N3 and retinal flatspace" at the 13^th IEEE International Symposium on Biomedical Imaging (ISBI 2016), Prague, Czech Republic, April 13 - 16, 2016.

• Andrew Lang presents his paper titled "Intensity inhomogeneity correction of macular OCT using N3 and retinal flatspace" at the 13^th IEEE International Symposium on Biomedical Imaging (ISBI 2016), Prague, Czech Republic, April 13 - 16, 2016.

March

Jeff Glaister presenting his poster "Thalamus parcellation using multi-modal feature classification and thalamic nuclei priors" at SPIE Medical Imaging (SPIE-MI 2016) in San Diego.

• Andrew Lang is short-listed for the Robert F. Wagner All Conference Best Student Paper for his work titled "Combined registration and motion correction of longitudinal retinal OCT data" at SPIE Medical Imaging (SPIE-MI 2016).
• IACL members present papers at the SPIE Medical Imaging (SPIE-MI 2016) meeting in San Diego, CA, February 27 - March 3, 2016.
  • Andrew Lang presented "Combined registration and motion correction of longitudinal retinal OCT data".
  • Ke Li presented "Quality Assurance using Outlier Detection on an Automatic Segmentation Method for the Cerebellar Peduncles".
  • Mazy Abulnaga presented "A toolbox to visually explore cerebellar sub-structure shape changes in cerebellar ataxia".
  • Zhen Yang presented "Landmark Based Shape Analysis for Cerebellar Ataxia Classification and Structural Change Pattern Visualization".
  • Can Zhao presented "Effects of Spatial Resolution on Image Registration".
  • Jeff Glaister presented "Thalamus parcellation using multi-modal feature classification and thalamic nuclei priors".
  • Bhavna Antony presented "Voxel Based Morphometry in Optical Coherence Tomography: Validation & Core Findings" and "Simultaneous Segmentation of Retinal Surfaces and Microcystic Macular Edema in SDOCT Volumes".
  • Lotta M. Ellingsen presented "Segmentation and labeling of the ventricular system in normal pressure hydrocephalus using patch-based tissue classification and multi-atlas labeling"
• Other accepted papers at SPIE-MI 2016 coming from collaborations with IACL.
  • With colleagues at Hopkins "Segmentation of Thalamus from MR images via Task-Driven Dictionary Learning".
  • With colleagues at Vanderbilt "Combining Multi-atlas Segmentation with Brain Surface Estimation" and "Improving cerebellar segmentation with statistical fusion".

February

Jerry L. Prince delivers a memorial for Dr. Lee Rosen at SPIE 2016.

• Jerry L. Prince delivers a memorial for Dr. Lee Rosen at SPIE 2016. Dr. Lee Allen Rosen passed away in October 2015.

Medical Image Recognition, Segmentation and Parsing edited by S. Kevin Zhou is published by Elsevier.

• Medical Image Recognition, Segmentation and Parsing edited by S. Kevin Zhou is published by Elsevier. It features Chapter 12: An Overview of the Multi-Object Geometric Deformable Model Approach in Biomedical Imaging by Aaron Carass and Jerry L. Prince.

January

Jerry L. Prince to be Inducted into the Medical and Biological Engineering Elite

WASHINGTON, D.C.— The American Institute for Medical and Biological Engineering (AIMBE) has announced the pending induction of Jerry L. Prince, Ph.D., William B. Kouwenhoven Professor, Electrical and Computer Engineering/Whiting School of Engineering, Johns Hopkins University, to its College of Fellows. Dr. Prince was nominated, reviewed, and elected by peers and members of the College of Fellows for outstanding contributions to biomedical imaging and image analysis.

The College of Fellows is comprised of the top two percent of medical and biological engineers in the country. The most accomplished and distinguished engineering and medical school chairs, research directors, professors, innovators, and successful entrepreneurs, comprise the College of Fellows.

A formal induction ceremony will be held during AIMBE’s 25th Annual Meeting at the National Academy of Sciences Great Hall in Washington, DC on April 4, 2016. Dr. Prince will be inducted along with 160 colleagues who make up the AIMBE College of Fellows Class of 2016.

2015

December

Lab photo from the glass ornament blowing at Corradetti Glass Studio.

• The lab celebrates the Holiday Season by blowing some glass ornaments.

Glass Blowing Christmas Ornaments

October

Lab photo saying goodbye to Drs. Xing and Yang.

• Fangxu Xing defends his thesis titled "Three Dimensional Tissue Motion Analysis from Tagged Magnetic Resonance Imaging". Dr. Xing will be joining Massachusetts General Hospital in Boston, Massachusetts, starting December 15th.
• Zhen Yang defends her thesis titled "Cerebellar Structure Segmentation and Shape Analysis with Application to Cerebellar Ataxia". Dr. Yang will be joining Google in Menlo Park, California, starting November 1st.
• Murat Bilgel's paper "Deformation field correction for spatial normalization of PET images" appears in NeuroImage.  (doi)
• Aaron Carass presents "Longitudinal Patch-Based Segmentation of Multiple Sclerosis White Matter Lesions" at the Machine Learning in Medical Imaging (MLMI 2015) workshop in Munich, Germany.

September

• The paper "MRBrainS challenge: Online Evaluation Framework for Brain Image Segmentation in 3T MRI Scans" appears in Computational Intelligence and Neuroscience.  (doi)

June

Jerry L. Prince presenting a poster at IPMI 2015.

• Jerry Prince presented "Temporal trajectory and progression score estimation from voxelwise longitudinal imaging measures: Application to amyloid imaging" at IPMI 2015.
• An article describing the EchoSure Project developed by Sonavex (appears in the JHU Engineering Magazine).

May

Andrew Lang presenting a poster at ARVO 2015.

• Andrew Lang presented his poster "Automated segmentation of macular SD-OCT scans of retinitis pigmentosa patients shows regional patterns of foveal inner retinal thickening that correlate with visual function" at ARVO 2015 in Denver, Colorado.
• Snehashis Roy's paper "Subject Specific Sparse Dictionary Learning for Atlas Based Brain MRI Segmentation" appears in the IEEE Journal of Biomedical and Health Informatics.  (doi)

April

Jeff Glaister presenting a poster at ISBI 2015.

• Jeff Glaister presented "Probabilistic Fiber Tracking using a Modified Lasso Bootstrap Method" at ISBI 2015 in Brooklyn, New York.
• The Longitudinal Multiple Sclerosis Lesion Segmentation Challenge took place as part of ISBI with ten teams presenting their work on the Challenge day.
• The paper S. Roy, W.-T. Wang, A. Carass, J.L. Prince, J.A. Butman, and D.L. Pham, "PET Attenuation Correction Using Synthetic CT from Ultrashort Echo-Time MR Imaging", Jrnl. of Nuclear Medicine, 55:1-7, 2014 (doi) wins the Alavi-Mandell Publication Award from the Society of Nuclear Medicine and Molecular Imaging (SNMMI).

March

The Longitudinal Multiple Sclerosis Lesion Segmentation Challenge takes place on April 16th, 2015.

• Registration for the Longitudinal Multiple Sclerosis Lesion Segmentation Challenge closes. The Challenge is a collaboration between the IACL Lab, the Henry M. Jackson Foundation, the Max Plank Institute, and the University of Iceland, and takes place as part of the 12th IEEE International Symposium on Biomedical Imaging (ISBI 2015) in New York on April 16th, 2015. 34 Teams registered for the Challenge coming from 15 different countries, representing 27 different institutions/universities.

February

IACL at SPIE-MI 2015
Alessandro Asoni's prize winning poster at SPIE-MI.		Andrew Lang presenting his paper "Longitudinal graph-based segmentation of macular OCT using fundus alignment".		Gunnar Sigurdsson presenting his paper "Interpretable exemplar-based shape classification using constrained sparse linear models".
Fangxu Xing presenting his paper "Relating speech production to tongue muscle compressions using tagged and high-resolution magnetic resonance imaging".		Emily Swingle presenting her paper "Segmentation of microcystic macular edema in Cirrus OCT scans with an exploratory longitudinal study".		Amod Jog presenting his paper "Multi-output decision trees for lesion segmentation in multiple sclerosis".

• Alessandro Asoni wins a poster prize at SPIE-MI 2015 in Orlando, Florida.
• IACL members presented papers for the Proceedings of SPIE Medical Imaging (SPIE-MI 2015), Orlando, FL, February 21-26, 2015.
  • Alessandro Asoni presented "B-Mode ultrasound pose recovery via surgical fiducial segmentation and tracking".
  • Andrew Lang presented "Longitudinal graph-based segmentation of macular OCT using fundus alignment".
  • Gunnar Sigurdsson presented "Interpretable exemplar-based shape classification using constrained sparse linear models".
  • Emily Swingle presented "Segmentation of microcystic macular edema in Cirrus OCT scans with an exploratory longitudinal study".
  • Amod Jog presented "Multi-output decision trees for lesion segmentation in multiple sclerosis".
  • Fangxu Xing presented "Relating speech production to tongue muscle compressions using tagged and high-resolution magnetic resonance imaging".
  • Min Chen presented "Using image synthesis for multi-channel registration of different image modalities".

January

• Amod Jog's paper "MR Image Synthesis by Pulse Sequence Information-based Contrast Learning On Neighborhood Ensembles" appears in Medical Image Analysis.  (doi)
• Andrew Lang's paper "Automatic segmentation of microcystic macular edema in OCT" appears in Biomedical Optics Express.  (doi)

2014

December

• Chuyang Ye successfully defends his PhD thesis titled "Fiber Tracking and Fiber Tract Segmentation Using Diffusion Tensor Imaging".
• Min Chen successfully defends his PhD thesis titled "Deformable Image Registration in the Analysis of Multiple Sclerosis".
• Details are made available about the 2015 Longitudinal Multiple Sclerosis Lesion Segmentation Challenge which will be held as part of the International Symposium on Biomedical Imaging. The challenge will involve teams applying their automatic lesion segmentation algorithms to MR neuroimaging data acquired at multiple time points from patients with multiple sclerosis (MS).

November

• Jerry L. Prince will be speaking at the University of Utah on Friday, November 14, 2014. The topic will be "Medical Image Synthesis Methods and Applications".
• 

  Despite having no prior ultrasound experience, Maryland Governor Larry Hogan uses the EchoFind software guidance to successfully navigate the EchoMark in a test phantom.
  The EchoSure team was invited as a featured presenter and exhibitor at TEDCO's 4th annual Maryland Entrepreneur Expo (http://expo.tedco.md/). Conference participants -- including newly elected Maryland Gov. Larry Hogan -- had the opportunity to try the live EchoFind software demo themselves. Even first-time ultrasound users were able to accurately navigate the test phantom and the team received tremendous positive feedback on their successful demonstration.

October

Jonghye Woo on his last day in the IACL Lab with the labs director Jerry L. Prince.

• The IACL Lab in association with collaborators at the Henry M. Jackson Foundation, the Max Plank Institute, and the University of Iceland will be organizing the Longitudinal Multiple Sclerosis Lesion Segmentation Challenge as part of the 12^th IEEE International Symposium on Biomedical Imaging (ISBI 2015), New York, NY, April 16 - 19, 2015.
• Jonghye Woo has his last day in the IACL Lab.

September

• Jonghye Woo presented "Determining Functional Units of Tongue Motion via Graph-regularized Sparse Non-negative Matrix Factorization"' at MICCAI 2014.  (doi)
• Joshua V. Stough presented his collaboration with IACL "Automatic method for thalamus parcellation using multi-modal feature classification" at MICCAI 2014.  (doi)
• Zhen Yang presented "Deep Learning for Cerebellar Ataxia Classification and Functional Score Regression" in the Machine Learning in Medical Imaging workshop at MICCAI 2014.  (doi)
• Snehashis Roy presented "Subject Specific Sparse Dictionary Learning for Atlas Based Brain MRI Segmentation" in the Machine Learning in Medical Imaging workshop at MICCAI 2014.  (doi)
• Murat Bilgel presented "Deformation Field Correction for Spatial Normalization of PET Images Using a Population-Derived Partial Least Squares Model" in the Machine Learning in Medical Imaging workshop at MICCAI 2014.  (doi)
• Chuyang Ye presented "A Bayesian Approach to Distinguishing Interdigitated Muscles in the Tongue from Limited Diffusion Weighted Imaging" as part of the BAMBI Workshop at MICCAI 2014.  (doi)

August

• IACL receives a 2014 NIH Grant for Segmentation and Registration of Macular SD-OCT with applications to Multiple Sclerosis.

June

Jerry L. Prince and Peter A. Calabresi from an article in JHU Engineering.

• JHU Engineering magazine article describing our research understanding multiple sclerosis using optical coherence tomography:
  • Retinal layer segmentation of macular OCT images
  • MGDM segmentation of macular OCT images
  • Analysis of macular OCT images using deformable registration
• Min Chen's paper "Analysis of macular OCT images using deformable registration" appears in Biomedical Optics Express.  (doi)

April

Amod Jog at ISBI 2014 in Beijing.

• Amod Jog presents two talks at the 11th IEEE International Symposium on Biomedical Imaging (ISBI 2014), Beijing, China, April 28 - May 2, 2014.
  • Random Forest FLAIR reconstruction from T1, T2, and PD-weighted MRI
  • Improving Magnetic Resonance Resolution with Supervised Learning

March

• Jerry L. Prince's book Medical Imaging Signals and Systems 2/E is released.
• The video and presentation from Fangxu Xing's 2013 MICCAI talk, titled "3D Tongue Motion from Tagged and Cine MR Images", is now available.
• Aaron Carass' paper "Multiple-object geometric deformable model for segmentation of macular OCT" appears in Biomedical Optics Express.  (doi)

February

• IACL members presented papers for the Proceedings of SPIE Medical Imaging (SPIE-MI 2014), San Diego, CA, February 15-20, 2014.
  • Andrew Lang presented "An adaptive grid for graph-based segmentation in macular cube OCT".
  • Gunnar Sigurdsson presented "Smoothing fields of weighted collections with applications to diffusion MRI processing".
  • Emily Swingle presented "Microcystic macular edema detection in retina OCT images".
  • Snehashis Roy presented "MR to CT registration of brains using image synthesis" and "Example based lesion segmentation".

2013

December

• Min Chen's paper "Automatic Magnetic Resonance Spinal Cord Segmentation with Topology Constraints for Variable Fields of View" appears in NeuroImage.  (doi)
• Snehashis Roy's paper "Magnetic Resonance Image Example Based Contrast Synthesis" appears in IEEE Trans. on Medical Imaging.  (doi)

October

• Aaron Carass presents "Atlas Based Intensity Transformation of Brain MR Images" at the MBIA workshop as part of MICCAI 2013.  (doi)
• Fangxu Xing presents "3D Tongue Motion from Tagged and Cine MR Images" at MICCAI 2013.  (doi) The video and presentation of his talk are available here.

July

• Andrew Lang's paper "Retinal layer segmentation of macular OCT images using boundary classification" appears in Biomedical Optics Express.  (doi)

June

• John Bogovic presented his paper "Automated Segmentation of the Cerebellar Lobules Using Boundary Specific Classification and Evolution" at the 23rd International Conference on Information Processing in Medical Imaging (IPMI).

April

Chuyang Ye discussing his poster at ISBI 2013.	Junghoon Lee presenting his paper at ISBI 2013.	Joshua Stough at ISBI 2013.
Min Chen discussing his poster at ISBI 2013.	Snehashis Roy waiting to discuss his poster at ISBI 2013.

• IACL members presented papers at the Tenth IEEE International Symposium on Biomedical Imaging (ISBI 2013), San Francisco, CA, April 7 - 11, 2013.
  • Chuyang Ye presented "Segmentation of the Complete Superior Cerebellar Peduncles using a Multi-object Geometric Deformable Model".
  • Snehashis Roy presented "Patch Based Intensity Normalization of Brain MR Images" and "Longitudinal Intensity Normalization in the presence of Multiple Sclerosis Lesions".
  • Amod Jog presented "Magnetic Resonance Image Synthesis through Patch Regression".
  • Zhen Yang presented "Covariance shrinking in active shape models with application to gyral labeling of the cerebral cortex".
  • Fangxu Xing presented "MRI Analysis of 3D normal and Post-glossectomy Tongue Motion in Speech".

March

• "Computer modeling may help athletes, soldiers avoid concussions", Johns Hopkins Hub news article mentions new NIH grant awarded to Phil Bayly (Wash U), K.T. Ramesh, and Jerry Prince. (Dzung Pham is also a Co-PI on this grant.)

February

• IACL members presented papers for the Proceedings of SPIE Medical Imaging (SPIE-MI 2013), Orlando, FL, February 9-14, 2013.
  • Chuyang Ye presented "Parcellation of the thalamus using diffusion tensor images and a multi-object geometric deformable mode".
  • Zhen Yang presented "Automatic cell segmentation in fluorescence images of confluent cell monolayers using multi-object geometric deformable model".
  • Min Chen presented "Voxel-wise displacement as independent features in classification of multiple sclerosis"
  • Amod Jog presented "Pulse sequence based multi-acquisition MR intensity normalization".
  • Andrew Lang presented "Segmentation of retinal OCT images using a random forest classifier".
  • Murat Bilgel presented "Automated anatomical labeling of the cerebral arteries using belief propagation".
  • Nathanael Kuo presented "An intraoperative dynamic dosimetry guidance system for prostate brachytherapy".
  • Jerry L. Prince presented Snehashis Roy's paper "Longitudinal intensity normalization of magnetic resonance images using patches".

2012

October

• Fangxu Xing presented his paper "Estimating 3D tongue motion with MR images" at the Forty-Sixth Asiolomar Conference on Signals, Systems, and Computers in Monterey, California.
• Jerry L. Prince gave the William B. Kouwenhoven Memorial Lecture entitled "24 Years of Tagged Magnetic Resonance Imaging at Johns Hopkins". He was invited by Jin Kang, Chair of ECE, and introduced by Russell H. Taylor. Watch a video of the talk on YouTube.

September

• Bruno Jedynak presented his work "A time-change method for computing an Alzheimer's disease progression score" at the Novel Imaging Biomarkers for Alzheimer's Disease and Related Disorders (NIBAD'12) workshop at the 15^th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2012), Nice, France, October 1-5, 2012.
• Jerry L. Prince won the "Enduring Impact Award" for 2012 from the MICCAI Society. The award was presented at the MICCAI conference in Nice, France.

May

• Three IACL members presented papers at the Ninth IEEE International Symposium on Biomedical Imaging (ISBI 2012), Barcelona, Spain, May 2 - 5, 2012.
  • Sahar Soleimanifard presented "Vessel centerline tracking and boundary segmentation in coronary MRA with minimal manual interaction".
  • Zhen Yang presented her paper "Automatic sulcal curve extraction with MRI based shape prior".
  • Chuyang Ye presented his work "Fully automated segmentation of the dentate nucleus using diffusion weighted images".

February

• IACL members gave several presentations for the Proceedings of SPIE Medical Imaging (SPIE-MI 2012), San Diego, CA, February 4-9, 2012.
  • Fangxu Xing presented "Finding seeds for segmentation using statistical fusion".
  • Junghoon Lee presented "Incorporation of prior knowledge for region of change imaging from sparse scan data in image-guided surgery".
  • Jonghye Woo presented "Super-resolution reconstruction for tongue MR images".
  • Zhen Yang presented "Simultaneous cortical surface labeling and sulcal curve extraction".
  • Chuyang Ye presented "Labeling of the cerebellar peduncles using a supervised Gaussian classifier with volumetric tract segmentation".

January

• Two IACL members attended the IEEE Workshop on Mathematical Methods in Biomedical Image Analysis (MMBIA 2012), Breckenridge, CO, January 9, 2012.
  • Xinyang Liu presented "Topology preserving brain tissue segmentation using graph cuts".
  • Chuyang Ye presented "A fiber tracking method guided by volumetric tract segmentation".

2011

September

• Jerry Prince was honored as a "Fellow of the MICCAI Society", which he received at the MICCAI Conference in Toronto, Canada.

July

• Snehashis Roy wins the best poster award at the 22^nd Conference on Information Processing in Medical Imaging (IPMI 2011), Monastery Irsee, Germany, July 3-8, 2011.

May

Harsh Agarwal after being hooded by Jerry L. Prince.

• Harsh Agarwal earned his Ph.D. and is hooded by Jerry L. Prince.

April

• Yuanming Suo wins the Northern Digital Inc. Excellence Awards for his work on Semiautomatic segmentation of speech articulators using MRI.
• At the Eighth IEEE International Symposium on Biomedical Imaging (ISBI 2011), Chicago, IL, March 30 - April 2, 2011.

• Min Chen presented the talk Topology Preserving Automatic Segmentation of the Spinal Cord in Magnetic Resonance Images .
• Navid Shiee presented the poster Fiber tractography and tract segmentation in multiple sclerosis lesions .
• Snehashis Roy presented the poster Compressed Sensing Based Intensity Non-Uniformity Correction .

February

• At the Proceedings of SPIE Medical Imaging (SPIE-MI 2011), Orlando, FL, February 12-17, 2011.

• Min Chen presented the talk Distance Transforms in Multi Channel MR Image Registration.
• Jerry L. Prince presented the talk Intensity Inhomogeneity Correction of Magnetic Resonance Images using Patches.

2010

June

• Min Chen recently attended the NAMIC 2010 summer project week to help integrate SPECTRE as a Slicer3 extension.
• John Bogovic presented "Topology-Preserving STAPLE" at the IEEE Workshop on Mathematical Methods in Biomedical Image Analysis (MMBIA 2010), San Francisco, California, June 14, 2010.
• Min Chen presented several posters from the lab at the 16th Annual Meeting of the Organization for Human Brain Mapping (HBM 2010), Barcelona, Spain, June 6-10, 2010.
• Jerry Prince gave three 2-hour lectures at the IEEE EMBS International Summer School on Biomedical Imaging in Berder, France, 18-26 June 2010.