Publications

  • Edwards K, Chhabra A, Dormer J, Jones P, Boutin RD, Lenchik L, Fei BW (Corresponding author). Abdominal muscle segmentation from CT using a convolutional neural network. Medical Imaging 2020: Biomedical Applications in Molecular, Structural, and Functional Imaging; 11317(113170L). International Society for Optics and Photonics,
    Edwards_2020_SPIE [PubMed] [PDF] [DOI]
  • Halicek M, Dormer JD, Little JV, Chen AY, Fei BW (Corresponding author). Tumor detection of the thyroid and salivary glands using hyperspectral imaging and deep learning. Biomedical Optics Express; 11(3):1383-400.
    Halicek_2020_BOE_2 [PubMed] [PDF] [DOI]
  • Ma L, Liu X, Fei BW. A multi-level similarity measure for the retrieval of the common CT imaging signs of lung diseases. Medical & Biological Engineering & Computing; 2020:1-15.
    Ma_2020_MBEC [PubMed] [PDF] [DOI]

  • Bangalore Yogananda CG, Shah BR, Vejdani-Jahromi M, Nalawade SS, Murugesan GK, Yu FF, Pinho MC, Wagner BC, Mickey B, Patel TR, Fei BW (Corresponding author). A novel fully automated MRI-based deep-learning method for classification of IDH mutation status in brain gliomas. Neuro-oncology; 22(3):402-11.

    Yogananda_2020_NeuroOnc [PubMed] [PDF] [DOI]

  • Shahedi M, Halicek M, Dormer JD, Fei BW (Corresponding author). Incorporating minimal user input into deep learning based image segmentation. Medical Imaging 2020: Image Processing; 11313(1131313). International Society for Optics and Photonics,

    Shahedi_2020_SPIE_2 [PubMed] [PDF] [DOI]

  • Mavuduru A, Halicek M, Shahedi M, Little JV, Chen AY, Myers LL, Fei BW (Corresponding author). Using a 22-layer U-Net to perform segmentation of squamous cell carcinoma on digitized head and neck histological images. Medical Imaging 2020: Digital Pathology; 11320(113200C). International Society for Optics and Photonics,

    Mavuduru_2020_SPIE [PubMed] [PDF] [DOI]

  • Shahedi M, Dormer JD, TT AD, Do QN, Xi Y, Lewis MA, Madhuranthakam AJ, Twickler DM, Fei BW (Corresponding author). Segmentation of uterus and placenta in MR images using a fully convolutional neural network. Medical Imaging 2020: Computer-Aided Diagnosis; 11314(113141R). International Society for Optics and Photonics,

    Shahedi_2020_SPIE [PubMed] [PDF] [DOI]

  • Vargas J, Le P, Shahedi M, Gahan J, Johnson B, Dormer JD, Shahub S, Pfefferle M, Judson BO, Alshara Y, Li Q. A complex dual-modality kidney phantom for renal biopsy studies. Medical Imaging 2020: Ultrasonic Imaging and Tomography; 11319(113190J). International Society for Optics and Photonics,

    Vargas_2020_SPIE [PubMed] [PDF] [DOI]

  • Mahajan A, Dormer J, Li Q, Chen D, Zhang Z, Fei BW (Corresponding author). Siamese neural networks for the classification of high-dimensional radiomic features. Medical Imaging 2020: Computer-Aided Diagnosis; 11314(113143Q). International Society for Optics and Photonics,

    Mahajan_2020_SPIE [PubMed] [PDF] [DOI]

  • Ortega S, Halicek M, Fabelo H, Guerra R, Lopez C, Lejeune M, Godtliebsen F, Callico GM, Fei BW (Corresponding author). Hyperspectral imaging and deep learning for the detection of breast cancer cells in digitized histological images. Medical Imaging 2020: Digital Pathology; 11320(113200V). International Society for Optics and Photonics,

    Ortega_2020_SPIE [PubMed] [PDF] [DOI]

  • Bettati P, Chalian M, Huang J, Dormer J, Shahedi M, Fei BW (Corresponding author). Augmented reality-assisted biopsy of soft tissue lesions. Medical Imaging 2020: Image-Guided Procedures, Robotic Interventions, and Modeling; 11315(113150W). International Society for Optics and Photonics,

    Bettati_2020_SPIE [PubMed] [PDF] [DOI]

  • Halicek M, Ortega S, Fabelo H, Lopez C, Lejeune M, Callico GM, Fei BW (Corresponding author). Conditional generative adversarial network for synthesizing hyperspectral images of breast cancer cells from digitized histology. Medical Imaging 2020: Digital Pathology; 11320(113200U). International Society for Optics and Photonics,

    Halicek_2020_SPIE [PubMed] [PDF] [DOI]

  • Ma L, Halicek M, Zhou X, Dormer J, Fei BW (Corresponding author). Hyperspectral microscopic imaging for automatic detection of head and neck squamous cell carcinoma using histologic image and machine learning. Medical Imaging 2020: Digital Pathology; 11320(113200W). International Society for Optics and Photonics,

    Ma_2020_SPIE [PubMed] [PDF] [DOI]

  • Dormer J, Bhuiyan M, Rahman N, Deaton N, Sheng J, Padala M, Desai J, Fei BW (Corresponding author). Image guided mitral valve replacement: registration of 3D ultrasound and 2D x-ray images. Medical Imaging 2020: Image-Guided Procedures, Robotic Interventions, and Modeling; 11315(113150Z). International Society for Optics and Photonics,

    Dormer_2020_SPIE [PubMed] [PDF] [DOI]

  • Pfefferle M, Shahub S, Shahedi M, Gahan J, Johnson B, Le P, Vargas J, Judson B, Alshara Y, Fei BW (Corresponding author). Renal biopsy under augmented reality guidance. Medical Imaging 2020: Image-Guided Procedures, Robotic Interventions, and Modeling; 11315(113152W). International Society for Optics and Photonics,

    Pfefferle_2020_SPIE [PDF] [DOI]

  • Huang J, Halicek M, Shahedi M, Fei BW (Corresponding author). Augmented reality visualization of hyperspectral imaging classifications for image-guided brain tumor resection. Medical Imaging 2020: Image-Guided Procedures, Robotic Interventions, and Modeling; 11315(113150U). International Society for Optics and Photonics,

    Huang_2020_SPIE [PubMed] [PDF] [DOI]

  • Selim M, Zhang J, Fei BW, Zhang GQ, Chen J. STAN-CT: Standardizing CT Image using Generative Adversarial Network. arXiv preprint; arXiv: 2004.01307.

    Selim_2020_arXiv [PubMed] [PDF]

  • Hao D, Ding S, Qiu L, Lv Y, Fei BW, Zhu Y, Qin B. Sequential vessel segmentation via deep channel attention network. Neural Networks.

    Hao_2020_NeuralN [PubMed] [PDF] [DOI]

  • Ortega S, Halicek M, Fabelo H, Callico GM, Fei BW (Corresponding author). Hyperspectral and multispectral imaging in digital and computational pathology: a systematic review. Biomedical Optics Express; 11(6): 3195-3233.

    [PubMed] [PDF] [DOI]

  • Twickler DM, Do QN, Yin Xi, Shahedi M, Dormer J, Devi TT A, Lewis MA, Spong CY, Dashe JS, Madhuranthakam A, Fei BW (Corresponding author). 228: Automated segmentation of the human placenta and uterus with MR imaging using artificial intelligence (AI). American Journal of Obstetrics & Gynecology; 222(1): S158-S159.

    [PDF]

  • Abiodun-Ojo OA, Akintayo AA, Akin-Akintayo O, Tade FI, Nieh PT, Master VA, Alemozaffar M, Osunkoya AO, Goodman MM, Fei BW (Corresponding author). 18F-Fluciclovine parameters on targeted prostate biopsy associated with true positivity in recurrent prostate cancer. Journal of Nuclear Medicine; 60(11): 1531-1536.

    AbiodunOjo_2019_JNM [PubMed] [DOI]

  • Qin BJ, Jin MX, Hao DD, Lv Y, Liu QG, Zhu YQ, Ding S, Zhao J, Fei BW (Corresponding author). Accurate vessel extraction via tensor completion of background layer in X-ray coronary angiograms. Pattern Recognition;87:38-54.

    Qin_2019_PatternRec [PubMed] [PDF] [DOI]

  • Ma L, Lu G, Wang D, Qin X, Chen ZG, Fei BW (Corresponding author). Adaptive deep learning for head and neck cancer detection using hyperspectral imaging. Visual Computing for Industry, Biomedicine, and Art; 2(1): 1-12.

    Ling_2019_VisualComputing [PubMed] [PDF] [DOI]

  • Shahedi M, Halicek M, Li QM, Lizhi L, Zhang ZF, Verma S, Schuster DM, Fei BW (Corresponding author). A semiautomatic approach for prostate segmentation in MR images using local texture classification and statistical shape modeling. Proceedings of SPIE Medical Imaging 2019: Image-Guided Procedures, Robotic Interventions, and Modeling.

    Shahedi_2019_SPIE [PubMed] [PDF] [DOI]

  • Halicek M, Himar F, Ortega S, Little JV, Wang X, Chen AY, Callicó GM, Myers LL, Sumer BD, Fei BW (Corresponding author). Cancer detection using hyperspectral imaging and evaluation of the superficial tumor margin variance with depth. Proceedings of SPIE Medical Imaging 2019: Image-Guided Procedures, Robotic Interventions, and Modeling.

    Halicek_2019_SPIE_1 [PubMed] [PDF] [DOI]

  • Nalawade SS, Muregesan GK, Vejdani-Jahromi M, Fisicaro RA, Yogananda CGB, Wagner B, Mickey B, Maher E, Pinho MC, Fei BW. Classification of Brain Tumor IDH Status using MRI and Deep Learning. bioRxiv (2019):757344.

    Nalawade_2019_bioRxiv [PDF]

  • Nalawade S, Murugesan GK, Vejdani-Jahromi M, Fisicaro RA, Yogananda GCB, Wagner B, Mickey B, Maher E, Pinho MC, Fei BW, Madhuranthakam AJ, Maldjian JA. Classification of brain tumor isocitrate dehydrogenase status using MRI and deep learning. Journal of Medical Imaging; 6(4): 046003.

    Nalawade_2019_SPIE [PubMed] [PDF] [DOI]

  • Brown K, Dormer JD, Fei BW, Hoyt K, Ruiter NV, Byram BC. Deep 3D convolutional neural networks for fast super-resolution ultrasound imaging. Proceedings of SPIE Medical Imaging 2019: Ultrasonic Imaging and Tomography.

    Brown_2019_MedImaging [PubMed] [PDF] [DOI]

  • Fabelo H, Halicek M, Ortega S, Shahedi M, Szolna A, Pineiro JF, Sosa C, O’Shanahan AJ, Bisshopp S, Espino C, Marquez M, Hernandez M, Carrera D, Morera J, Callicó GM, Sarmiento R, Fei BW (Corresponding author). Deep learning-based framework for in-vivo identification of glioblastoma tumor using hyperspectral images of human brain. Sensors;19(4).

    Fabelo_2019_Sensors [PubMed] [PDF] [DOI]

  • Shahedi M, Halicek M, Dormer JD, Schuster DM, Fei BW (Corresponding author). Deep learning-based three-dimensional segmentation of the prostate on computed tomography images. Journal of Medical Imaging;6(2):025003.

    Shahedi_2019_MedImaging [PubMed] [PDF] [DOI]

  • Halicek M, Shahedi M, Little JV, Chen AY, Myers LL, Sumer BD, Fei BW, Tomaszewski JE, Ward AD. Detection of squamous cell carcinoma in digitized histological images from the head and neck using convolution neural networks. Proceedings of SPIE Medical Imaging 2019: Digital Pathology.

    Halicek_2019_SPIE [PubMed] [PDF] [DOI]

  • Yogananda CGB, Nalawade SS, Murugesan GK, Wagner B, Pinho MC, Fei BW, Madhuranthakam AJ, Maldjian JA. Fully Automated Brain Tumor Segmentation and Survival Prediction of Gliomas using Deep Learning and MRI. bioRxiv (2019):760157.

    Yogananda_2019_bioRxiv [PubMed] [PDF]

  • Lu G, Wang D, Qin X, Muller S, Little JV, Wang X, Chen AY, Chen G, Fei BW (Corresponding author). Histopathology feature mining and association with hyperspectral imaging for the detection of squamous neoplasia. Scientific reports; 9(1): 1-13.

    Lu_2019_SR [PubMed] [PDF] [DOI]

  • Halicek M, Fabelo H, Ortega S, Little JV, Wang X, Chen AY, Callico GM, Myers L, Sumer BD, Fei BW (Corresponding author). Hyperspectral imaging for head and neck cancer detection: specular glare and variance of the tumor margin in surgical specimens. Journal of Medical Imaging;6(3):035004.

    Halicek_2019_JMI [PubMed] [PDF] [DOI]

  • Halicek M, Dormer J, Little JV, Chen AY, Myers L, Sumer BD, Fei BW (Corresponding author). Hyperspectral Imaging of Head and Neck Squamous Cell Carcinoma for Cancer Margin Detection in Surgical Specimens from 102 Patients Using Deep Learning. Cancers (2019);11(9):1367.

    Halicek_2019_Cancers_1 [PubMed] [PDF] [DOI]

  • Halicek M, Fabelo H, Ortega S, Callicó GM, Fei BW (Corresponding author). In-vivo and ex-vivo tissue analysis through hyperspectral imaging techniques: Revealing the invisible featuers of cancer. Cancers;11(6).

    Halicek_2019_Cancers [PubMed] [PDF] [DOI]

  • Halicek M, Dormer J, Pham M, Little JV, Chen AY, Myers L, Sumer BD, Fei BW (Corresponding author). Label-Free, Noncontact Hyperspectral Imaging for Classification of Histologic Grade in Gross Specimens of Squamous Cell Carcinoma Using Deep Learning. Medical Physics;46(6):E462-E463.

  • Halicek M, Little JV, Wang X, Chen AY, Fei BW (Corresponding author). Optical biopsy of head and neck cancer using hyperspectral imaging and convolution neural networks. Journal of Biomedical Optics;24(3):1-9.

    Halicek_2019_JBO [PubMed] [PDF] [DOI]

  • Mei K, Hu B, Fei BW, Qin B. Phase asymmetry ultrasound despeckling with fractional anisotropic diffusion and total variation. IEEE Transactions on Image Processing (2019); 29: 2845-2859.

    Mei_2019_IEEE [PubMed] [PDF] [DOI]

  • Li QM, Dormer JD, Daryani P, Chen D, Zhang ZF, Fei BW, Hahn HK, Mori K. Radiomics analysis of MRI for predicting molecular subtypes of breast cancer in young women. Proceedings of SPIE Medical Imaging 2019: Computer-Aided Diagnosis.

    Li_2019_MedImaging [PubMed] [PDF] [DOI]

  • Fei BW, Callicó GM, Morera J, Szolna A, Sarmiento R, Ortega S, Halicek M, Himar F. Surgical aid visualization system for glioblastoma tumor identification based on deep learning and in-vivo hyperspectral images of human patients. Proceedings of SPIE 2019: Image-Guided Procedures, Robotic Interventions, and Modeling.

    Fabelo_2019_SPIE [PubMed] [PDF] [DOI]

  • Wirkert SJ, Isensee F, Vemuri AS, Ayala, LA, Maier-Hein KH, Fei BW, Maier-Hein L. Task-specific multispectral band selection. arXiv: 1905.11297;1.

    Wirkert_2019_arXiv [PDF]

  • Shahedi M, Ma L, Halicek M, Guo R, Zhang G, Schuster DM, Nieh P, Master VA, Fei BW (Corresponding author). A semiautomatic algorithm for three-dimensional segmentation of the prostate on CT images using shape and local texture characteristics. Proceedings of SPIE: The Internation Society for Optical Engineering;10576.

    Shahedi_2018_MedImaging [PubMed] [PDF] [DOI]

  • Shahedi M, Halicek M, Liu L, Zhang Z, Schuster DM, Fei BW (Corresponding author). A semiautomatic segmentation method for the prostate in magnetic resonance images using local texture classification and statistical shape modeling. Medical Physics;45(6):2527-2541.

    Shahedi_2018_MedPhys [PubMed] [PDF] [DOI]

  • Dormer JD, Halicek M, Ma L, Reilly CM, Schreibmann E, Fei BW (Corresponding author). Convolutional neural networks for the detection of diseased hearts using CT images and left atrium patches. Proceedings of SPIE: The International Society for Optical Engineering;10575.

    Dormer_2018_MedImaging_2 [PubMed] [PDF] [DOI]

  • Tian Z, Liu L, Fei BW. Deep convolutional neural network for prostate MR segmentation. International Journal of Computer Assisted Radiology and Surgery;13(11):1687.

    Tian_2018_JCARS [PDF]

  • Halicek M, Little JV, Wang X, Chen ZG, Patel M, Griffith CC, El-Diery MW, Sava NF, Chen AY, Fei BW (Corresponding author). Deformable registration of histological cancer margins to gross hyperspectral images using demons. Proceedings of SPIE: The International Society for Optical Engineering;10581.

    Halicek_2018_MedImaging_1 [PubMed] [PDF] [DOI]

  • Lu G, Wang DS, Qin X, Muller S, Wang X, Chen AY, Chen ZG, Fei BW (Corresponding author). Detection and delineation of squamous neoplasia with hyperspectral imaging in a mouse model of tongue carcinogenesis. Journal of Biophotonics;11(3):e201700078.

    Lu_2018_JBiophotonics [PubMed] [PDF] [DOI]

  • Dormer JD, Ma L, Halicek M, Reilly CM, Schreibmann E, Fei BW (Corresponding author). Heart chamber segmentation from CT using convolutional neural networks. Proceedings of SPIE: The International Society for Optical Engineering;10578.

    Dormer_2018_MedImaging [PubMed] [PDF] [DOI]

  • Watson SR, Dormer JD, Fei BW. Imaging technologies for cardiac fiber and heart failure: A review. Heart failure reviews;23(2):273-289.

    Watson_2018_HeartFailure [PubMed] [PDF] [DOI]

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