Patents

  1. Devices and methods for combined optical and magnetic resonance imaging (US Patent No: US 8886284 B2); Inventors: Pogue, B. W. and Carpenter, C. M. and Davis, S. C. and Paulsen, K. D. and Yalavarthy, P. K. and Dehghani, H.

  2. Methods for perfusion quantification based on oscillatory limited QR deconvolution and analytical spectral filtering (Indian Patent No: 403270); Inventors: Yalavarthy, P. K. and Reddy, K. V. and  Lee, J.
  3. Method and system for stereo-visual localization of object (US Patent No: 11647949 B2); Inventors: Venkatesan, S. M., Yalavarthy, P. K. and Annamalai, T. 
  4. Visual protocol for needle Insertion for aiding in intravenous procedures with a mobile stereo camera Indian Patent Application No: 201741020003); Inventors: Venkatesan, S. M. and Yalavarthy, P. K. 
The copyright of the following publications has been transferred to the publisher. These articles may be downloaded for personal use only. Any other use requires prior permission of the author and/or publisher.

Journals

2025

(86). Venkatesh Vadaddi, Raji S. Mathew, and Phaneendra K. Yalavarthy, "ISDU-QSMNet: Iteration Specific Denoising with Unshared Weights for Improved QSM Reconstruction," NMR in Biomedicine 38(11), e70152 (2025). [Supplementary Information; doi: 10.1002/nbm.70152]PUBMED

(85). Joel Jeffery, Ashwin RajKumar, Sudanshu Pandey, Lokesh Bathala, and Phaneendra K. Yalavarthy, "Inference time correction based on confidence and uncertainty for improved deep-learning model performance and explainability in medical image classification," Computerized Medical Imaging and Graphics (Special issue on Trustworthy Artificial Intelligence for Medical Imaging) 125, 102630 (2025). [doi: 10.1016/j.compmedimag.2025.102630] PUBMED

(84). Adewale K. Ipadeola, Mostafa H. Sliem, Dana Abdeen, Nicholas Laycock, Ashwin RajKumar, Phaneendra K. Yalavarthy, and Aboubakr M. Abdullah, "Integrated Electrochemical and Machine Learning Framework for SiO2/CaCO3 Under-deposits Driven Welded X65 Carbon Steel Corrosion Mitigation in Sour Service Conditions," Petroleum Research 2025 (in press). [Supporting Information; doi: 10.1016/j.ptlrs.2025.09.006]

(83). Adewale K. Ipadeola, Mostafa H. Sliem, Dana Abdeen, Nicholas Laycock, Ashwin RajKumar, Phaneendra K. Yalavarthy, and Aboubakr M. Abdullah, "Unmasking the Hidden Threat: Conductive Under-Deposits and Their Role in Preferential Weldment Corrosion of Carbon Steel under Sour Conditions," Langmuir 41(35), 23632-23651 (2025). [doi: 10.1021/acs.langmuir.5c02733]  [Supporting Information; Coverpage article] PUBMED

(82). Eman M. Fayyad, Adewale K. Ipadeola, Mostafa H. Sliem, Dana Abdeen, Noora Al-Qahtani, Ashwin RajKumar, Joel Jeffrey, Phaneendra K. Yalavarthy, and Aboubakr M. Abdullah, "Interfacial robustness of commercial amine-based inhibitors mitigates under-deposit corrosion of carbon steel in simulated sour conditions: A merged electrochemical and machine learning study," Emergent Materials 2025 (in press). [doi:  10.1007/s42247-025-01196-4]

(81). [Ashwin RajKumar*, Naveen Paluru*], Raji S. Mathew, Prathamesh Shenai, Dana Abdeen, Nicholas Laycock, and Phaneendra K. Yalavarthy, "Unsupervised Machine Learning for Automated Corrosion Staging Using Optical Microscopy Images," npj Materials Degradation 9, 83 (2025). [*Equal Contribution; doi: 10.1038/s41529-025-00635-1] [Media Coverage]

(80). Hariharan Ravishankar, Naveen Paluru, Prasad Sudhakar, and Phaneendra K. Yalavarthy, "Information Geometric Approaches for Patient-Specific Test-Time Adaptation of Deep Learning Models for Semantic Segmentation," IEEE Transactions on Medical Imaging 44(6), 2553-2567 (2025). [doi: 10.1109/TMI.2025.3540546] PUBMED

2024

(79). Naveen Paluru, Raji S. Mathew, and Phaneendra K. Yalavarthy, "DF-QSM: Data Fidelity based Hybrid Approach for Improved Quantitative Susceptibility Mapping of the Brain," NMR in Biomedicine 37(9), e5163 (2024). [doi: 10.1002/nbm.5163] PUBMED

(78). Aditya Rastogi and Phaneendra K. Yalavarthy, "Greybox: A hybrid algorithm for direct estimation of tracer kinetic parameters from undersampled DCE-MRI data," Medical Physics 51(7), 4838-4858 (2024). [doi: 10.1002/mp.16935] PUBMED

(77). Vadaddi Venkatesh, Raji S. Mathew, and Phaneendra K. Yalavarthy, "SpiNet-QSM: Model-based Deep Learning with Schatten p-norm Regularization for Improved Quantitative Susceptibility Mapping," Magnetic Resonance Materials in Physics, Biology and Medicine (Special Issue on The role of artificial intelligence in MRI/MRS acquisition and reconstruction) 37(3), 411-427 (2024). [doi: 10.1007/s10334-024-01158-7] PUBMED

(76). Utkarsh Gupta, Vijitha Periyasamy, Ronny Hofmann, Jaya Prakash, and Phaneendra K. Yalavarthy, "Two-step morphology-based denoising and non local means smoothing improves micro-CT digital rock images," Geophysical Prospecting (Special Issue on Rock Physics Contribution to the Energy Transition Challenge) 72(5), 2049-2063 (2024). [doi:10.1111/1365-2478.13429]

(75). Chitimireddy Sindhura, Mohammad Al Fahim, Phaneendra K. Yalavarthy, and Subrahmanyam Gorthi, "Fully Automated Sinogram-based Deep Learning Model for Detection and Classification of Intracranial Hemorrhage," Medical Physics 51(3), 1944-1956 (2024). [doi:10.1002/mp.16714] PUBMED

(74). Karan R. Gujarati, Lokesh Bathala, Vaddadi Venkatesh, Raji S. Mathew, and Phaneendra K. Yalavarthy, "Transformer-based Automated Segmentation of the Median Nerve in Ultrasound Videos of Wrist-to-Elbow Region," IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control 71(1), 56-69 (2024). [doi: 10.1109/TUFFC.2023.3330539] [Media Coverage] PUBMED

(73). Raji S. Mathew, Naveen Paluru, and Phaneendra K. Yalavarthy, "Model-Resolution based Deconvolution for Improved Quantitative Susceptibility Mapping," NMR in Biomedicine 37(2), e5055 (2024). [doi:10.1002/nbm.5055] PUBMED


2023

(72). Aditya Rastogi, Arindam Dutta, and Phaneendra K. Yalavarthy, "VTDCE-Net: A Time Invariant Deep Neural Network for Direct Estimation of Pharmacokinetic Parameters from Undersampled DCE MRI Data," Medical Physics 50(3), 1560-1572 (2023). [doi:10.1002/mp.16081] PUBMED

(71). Naveen Paluru, Hariharan Ravishankar, Sharat Hegde, and Phaneendra K. Yalavarthy, "Self Distillation for Improving the Generalizability of Retinal Disease Diagnosis using Optical Coherence Tomography Images," IEEE Journal of Selected Topics in Quantum Electronics (Issue on biophotonics) 29(4), 7200812 (2023). [doi:10.1109/JSTQE.2023.3240729]

2022

(70). [Vishal R. Ahuja*, Utkarsh Gupta*, Shivani R. Rapole*], Nishank Saxena, Ronny Hofmann, Ruarri J. Day-Stirrat, Jaya Prakash, and Phaneendra K. Yalavarthy, "Siamese-SR: A Siamese Super-Resolution model for boosting resolution of Digital Rock images for improved petrophysical property estimation," IEEE Transactions on Image Processing 31, 3479-3493 (2022). [Supplementary; *Equal Contribution; doi: 10.1109/TIP.2022.3172211] PUBMED

2021

(69). Jaya Prakash, Umang Agarwal, and Phaneendra K. Yalavarthy, "Multi GPU parallelization of maximum likelihood expectation maximization method for digital rock tomography data," Scientific Reports 11, 18356 (2021). [doi: 10.1038/s41598-021-97833-z] PUBMED

(68). Daniel S. Breland, Aveen Dayal, Ajit Jha, Phaneendra K. Yalavarthy, Om J. Pandey, and Linga R. Cenkeramaddi, "Robust Hand Gestures Recognition using a Deep CNN and Thermal Images," IEEE Sensors Journal 21(23), 26602-26614 (2021). [doi: 10.1109/JSEN.2021.3119977]

(67). Jaya Prakash, Sandeep K. Kalva, Manojit Pramanik, and Phaneendra K. Yalavarthy, "Binary photoacoustic tomography for improved vasculature imaging," Journal of Biomedical Optics 26(8), 086004 (2021). [doi: 10.1117/1.JBO.26.8.086004] PUBMED

(66). Navchetan Awasthi, Aveen Dayal, Linga R. Cenkeramaddi, and Phaneendra K. Yalavarthy, "Mini-COVIDNet : Efficient Light Weight Deep Neural Network for Ultrasound based Point-of-Care Detection of COVID-19," IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control 68(6), 2023-2037 (2021). [doi: 10.1109/TUFFC.2021.3068190; Among Top 3 popular articles for the month of May 2021; Top 2 popular articles for the month of June 2021; Top 20 popular articles for the month of July 2021; Top 10 popular articles for the months of August 2021 and September 2021] [Coverpage article; Media Coverage] PUBMED

(65). Siddharth Gupta, Prabhat K. Rai, Abhinav Kumar, Phaneendra K. Yalavarthy, and Linga R. Cenkeramaddi, "Target Classification by mmWave FMCW Radars using Machine Learning on Range-Angle Images," IEEE Sensors Journal 21(18), 19993-20001 (2021). [doi: 10.1109/JSEN.2021.3092583]

(64). Prabhat K. Rai, Henning Idsøe, Rajesh R. Yakkati, Abhinav Kumar, Mohammed Z. A. Khan, Phaneendra K. Yalavarthy, and Linga R. Cenkeramaddi, "Localization and Activity Classification of Unmanned Aerial Vehicle using mmWave FMCW Radars," IEEE Sensors Journal 21(14), 16043-16053 (2021). [doi: 10.1109/JSEN.2021.3075909]

(63). Aditya Rastogi and Phaneendra K. Yalavarthy, "SpiNet: A Deep Neural Network for Schatten p-norm Regularized Medical Image Reconstruction," Medical Physics 48(5), 2214-2229 (2021). [doi: 10.1002/mp.14744] PUBMED

(62). Daniel S. Breland, Simen B. Skriubakken, Aveen Dayal, Ajit Jha, Phaneendra K. Yalavarthy, and Linga R. Cenkeramaddi, "Deep Learning-Based Sign Language Digits Recognition From Thermal Images with Edge Computing System," IEEE Sensors Journal 21(9), 10445-10453 (2021). [doi: 10.1109/JSEN.2021.3061608]

(61). Naveen Paluru, Aveen Dayal, Havard B. Jenssen, Tomas Sakinis, Linga R. Cenkeramaddi, Jaya Prakash, and Phaneendra K. Yalavarthy, "Anam-Net : Anamorphic Depth Embedding based Light-Weight CNN for Segmentation of Anomalies in COVID-19 Chest CT Images," IEEE Transactions on Neural Networks and Learning Systems (Fast Track: COVID-19 Focused Papers) 32(3), 932-946 (2021). [doi: 10.1109/TNNLS.2021.3054746; Among Top 30 popular articles for the month of February 2021; Top 10 popular articles for the month of March 2021; Top 15 popular articles for the month of April 2021; Top 20 popular articles for the month of May 2021; Top 20 popular articles for the month of June 2021; Top 20 popular articles for the month of July 2021; Top 25 popular articles for the month of August 2021; Top 25 popular articles for the month of September 2021] [Media Coverage] PUBMED

(60). Navchetan Awasthi, Sandeep K. Kalva, Manojit Pramanik, and Phaneendra K. Yalavarthy, "Dimensionality Reduced Plug and Play Priors for Improving Photoacoustic Tomographic Imaging with Limited Noisy Data," Biomedical Optics Express (Feature issue of Translational Photoacoustic Imaging for Disease Diagnosis, Monitoring, and Surgical Guidance) 12(3), 1320-1338 (2021). [doi: 10.1364/BOE.415182] PUBMED

(59). Aveen Dayal, Naveen Paluru, Linga R. Cenkeramaddi, Soumya J, and Phaneendra K. Yalavarthy, "Design and Implementation of Deep Learning Based Contactless Authentication System Using Hand Gestures," Electronics (Artificial Intelligence Circuits and Systems (AICAS) Section) 10(2), 182 (2021). [doi: 10.3390/electronics10020182]

(58). Phaneendra K. Yalavarthy,  Sandeep K. Kalva, Manojit Pramanik, and Jaya Prakash, "Non-local means improves total-variation constrained photoacoustic image reconstruction," Journal of Biophotonics 14(1), e202000191 (2021). [Supplementary; doi: 10.1002/jbio.202000191] PUBMED

(57). Nilesh A. Kande, Rupali Dakhane, Ambedkar Dukkipati, and Phaneendra K. Yalavarthy, "SiameseGAN: A Generative Model for Denoising of Spectral Domain Optical Coherence Tomography Images," IEEE Transactions on Medical Imaging 40(1), 180-192 (2021). [doi: 10.1109/TMI.2020.3024097] PUBMED

2020

(56). [Navchetan Awasthi*, Gaurav Jain*], Sandeep K. Kalva, Manojit Pramanik, and Phaneendra K. Yalavarthy, "Deep Neural Network Based Sinogram Super-resolution and Bandwidth Enhancement for Limited-data Photoacoustic Tomography," IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control (Special issue on Deep Learning in Medical Ultrasound) 67(12), 2660-2673 (2020). [*Equal Contribution; doi: 10.1109/TUFFC.2020.2977210; Among Top 10 popular articles for the month of March 2020; Top 50 popular articles for the month of September 2020; Top 30 popular articles for the month of December 2020; Top 40 popular articles for the month February 2021] PUBMED

(55). Navchetan Awasthi, Prateek Katare, Sai S. Gorthi, and Phaneendra K. Yalavarthy, "Guided filter based image enhancement for focal error compensation in low cost automated histopathology microscopic system," Journal of Biophotonics 13(11), e202000123 (2020).  [doi: 10.1002/jbio.202000123]  PUBMED

(54). Aditya Rastogi and Phaneendra K. Yalavarthy, "Comparison of iterative parametric and indirect deep learning-based reconstruction methods in highly undersampled DCE‐MR Imaging of the breast," Medical Physics 47(10), 4838-4861 (2020). [doi: 10.1002/mp.14447] PUBMED

(53). Anuj Kaushik, Phaneendra K. Yalavarthy, and Ratan K. Saha, ''Convergent Born series improves accuracy of numerical solution of time independent photoacoustic wave equation," Journal of Modern Optics 67(9), 849-855 (2020). [doi: 10.1080/09500340.2020.1777334]

2019

(52). [Dween R. Sanny*, Jaya Prakash*], Sandeep K. Kalva, Manojit Pramanik, and Phaneendra K. Yalavarthy, "Fractional Regularization to Improve Photoacoustic Tomographic Image Reconstruction," IEEE Transactions on Medical Imaging 38(8), 1935-1947 (2019). [*Equal Contribution; doi: 10.1109/TMI.2018.2889314] PUBMED

(51). Navchetan Awasthi, K. Ram Prabhakar, Sandeep Kumar Kalva, Manojit Pramanik, R. Venkatesh Babu, and Phaneendra K. Yalavarthy, "PA-Fuse: A Deep Supervised Approach for Fusion of Photoacoustic Images with Distinct Reconstruction Characteristics," Biomedical Optics Express 10(5), 2227-2243 (2019). [doi: 10.1364/BOE.10.002227] PUBMED

(50). Sreedevi Gutta, Manish Bhatt, Sandeep K. Kalva, Manojit Pramanik, and Phaneendra K. Yalavarthy, "Modeling errors compensation with total least squares for limited data photoacoustic tomography," IEEE Journal of Selected Topics in Quantum Electronics (Issue on biophotonics) 25(1), 6800214 (2019). [doi: 10.1109/JSTQE.2017.2772886]

(49). [Sreedevi Gutta*, Venkata S. Kadimesetty*], Sriram Ganapathy, and Phaneendra K. Yalavarthy, "Convolutional Neural Network based Robust Denoising of Low-Dose Computed Tomography Perfusion Maps," IEEE Transactions on Radiation and Plasma Medical Sciences (Special issue on machine learning methods for image processing and radiomics) 3(2), 137-152 (2019). [*Equal Contribution; doi: 10.1109/TRPMS.2018.2860788; Among Top 25 popular articles for the months of August 2018, March 2019, April 2019, & May 2019] 

2018

(48). Dween R. Sanny, Jaya Prakash, Sandeep K. Kalva, Manojit Pramanik, and Phaneendra K. Yalavarthy, "Spatially variant regularization based on model resolution and fidelity embedding characteristics improves photoacoustic tomography," Journal of Biomedical Optics 23(10), 100502 (2018). [doi: 10.1117/1.JBO.23.10.100502] PUBMED

(47). Sreedevi Gutta, Sandeep K. Kalva, Manojit Pramanik, and Phaneendra K. Yalavarthy, "Accelerated image reconstruction using extrapolated Tikhonov filtering for photoacoustic tomography," Medical Physics 45(8), 3749-3767 (2018). [doi: 10.1002/mp.13023] PUBMED

(46). Navchetan Awasthi, Sandeep K. Kalva, Manojit Pramanik, and Phaneendra K. Yalavarthy, "Image Guided Filtering for Improving Photoacoustic Tomographic Image Reconstruction," Journal of Biomedical Optics 23(9), 091413 (2018). [doi: 10.1117/1.JBO.23.9.091413] PUBMED

(45). Navchetan Awasthi, Sandeep K. Kalva, Manojit Pramanik, and Phaneendra K. Yalavarthy, "Vector Extrapolation Methods for Accelerating Iterative Reconstruction Methods in Limited-Data Photoacoustic Tomography," Journal of Biomedical Optics 23(7), 071204 (2018). [doi: 10.1117/1.JBO.23.7.071204] PUBMED

2017

(44). Sreedevi Gutta, Venkata S. Kadimesetty, Sandeep K. Kalva, Manojit Pramanik, Sriram Ganapathy, and Phaneendra K. Yalavarthy, "Deep Neural Network based Bandwidth Enhancement of Photoacoustic Data," Journal of Biomedical Optics 22(11), 116001 (2017). [doi: 10.1117/1.JBO.22.11.116001] PUBMED

(43). Phaneendra K. Yalavarthy, "Editorial: Special Issue on Applied Computational Science and Engineering," Journal of the Indian Institute of Science 97(3), 311 (2017). [doi: 10.1007/s41745-017-0039-z]

(42). Naren Rao, Haris Jeelani, Rashmin Achalia, Garima Achalia, Arpitha Jacob, Rose dawn Bharath, Shivarama Varambally, Ganesan Venkatasubramanian, and Phaneendra K. Yalavarthy, "Population differences in Brain morphology: Need for population specific Brain template," Psychiatry research: Neuroimaging 265, 1-8 (2017). [doi: 10.1016/j.pscychresns.2017.03.018] PUBMED

2016

(41). Manish Bhatt, Atithi Acharya, and Phaneendra K. Yalavarthy, "Computationally efficient error estimate for evaluation of regularization in photoacoustic tomography," Journal of Biomedical Optics 21(10), 106002 (2016). [doi: 10.1117/1.JBO.21.10.106002] PUBMED

(40). Manish Bhatt, Sreedevi Gutta, and Phaneendra K. Yalavarthy, "Exponential Filtering of Singular Values Improves Photoacoustic Image Reconstruction," Journal of the Optical Society of America A: Optics, Imaging Science, and Vision 33(9), 1785-1792 (2016). [doi: 10.1364/JOSAA.33.001785] PUBMED

(39). Manish Bhatt, Kalyan R. Ayyalasomayajula, and Phaneendra K. Yalavarthy, "A Generalized Beer-Lambert Model for Near Infrared Light Propagation in Thick Biological Tissues," Journal of Biomedical Optics 21(7), 076012 (2016). [doi: 10.1117/1.JBO.21.7.076012] PUBMED

(38). Calvin B. Shaw, Zhiqiu Li, Brian W. Pogue, and Phaneendra K. Yalavarthy, "Direct sensitivity based data-optimization strategy for image-guided diffuse optical tomography," IEEE Journal of Selected Topics in Quantum Electronics (Issue on biophotonics) 22(3), 6803709 (2016). [doi:10.1109/JSTQE.2016.2558178]

2015

(37). Jaya Prakash, Nick Todd, and Phaneendra K. Yalavarthy, “Prior Image based Temporally Constrained Reconstruction (PITCR) algorithm for Magnetic Resonance guided High Intensity Focused Ultrasound," Medical Physics 42(12), 6804-6814 (2015). [doi: 10.1118/1.4934829]  PUBMED

2014

(36). Jaya Prakash, Nick Todd, and Phaneendra K. Yalavarthy, “Advances in Image Reconstruction Methods for Real-Time Magnetic Resonance Thermometry," Journal of the Indian Institute of Science (Issue on Magnetic Resonance Spectroscopy and Imaging) 94(4), 387-406 (2014).

(35). Jaya Prakash, Aditi S. Raju, Calvin B. Shaw, Manojit Pramanik, and Phaneendra K. Yalavarthy, “Basis pursuit deconvolution for improving model-based reconstructed images in photoacoustic tomography,” Biomedical Optics Express 5(5), 1363-1377 (2014). [Featured in Top Downloads from Biomedical Optics Express for Image Reconstruction and Inverse Problems] PUBMED

(34). Calvin B. Shaw and Phaneendra K. Yalavarthy, "Performance evaluation of typical approximation algorithms for non-convex Lp-minimization in diffuse optical tomography," Journal of the Optical Society of America A: Optics, Imaging Science, and Vision 31(4), 852-862 (2014). [CODE] PUBMED

(33). Jaya Prakash, Hamid Dehghani, Brian W. Pogue, and Phaneendra K. Yalavarthy, “Model-Resolution based Basis Pursuit Deconvolution Improves Diffuse Optical Tomographic Imaging,” IEEE Transactions on Medical Imaging 33(4), 891-901 (2014). [CODE] PUBMED  

(32).  Nick Todd, Jaya Prakash, Henrik Odéen, Josh de Bever, Allison Payne, Phaneendra K. Yalavarthy, and Dennis L. Parker, “Toward real-time availability of 3-D temperature maps created with temporally constrained reconstruction," Magnetic Resonance in Medicine 71(4), 1394-1404 (2014). PUBMED

(31). Calvin B. Shaw and Phaneendra K. Yalavarthy, “Incoherence based optimal selection of independent measurements in diffuse optical tomography," Journal of Biomedical Optics 19(3), 036017 (2014). [CODE] PUBMED

(30). [Jaya Prakash*, Calvin B. Shaw*], Rakesh Manjappa, Rajan Kanhirodan, and Phaneendra K. Yalavarthy, “Sparse Recovery Methods Hold Promise for Diffuse Optical Tomographic Image Reconstruction," IEEE Journal of Selected Topics in Quantum Electronics (Issue on biophotonics) 20(2), 6800609 (2014). [CODE] [*Equal Contribution]

2013

(29). Calvin B. Shaw, Jaya Prakash, Manojit Pramanik, and Phaneendra K. Yalavarthy, “Least Squares QR-based decomposition provides an efficient way of computing optimal regularization parameter in photoacoustic tomography," Journal of Biomedical Optics 18(8), 080501 (2013). PUBMED

(28). Ravi P. K. Jagannath and Phaneendra K. Yalavarthy, “Non-Quadratic Penalization Improves Near Infrared Diffuse Optical Tomography," Journal of the Optical Society of America A: Optics, Imaging Science, and Vision 30(8), 1516–1523 (2013). PUBMED

(27). Ravi P. K. Jagannath and Phaneendra K. Yalavarthy, “An Efficient Gradient-Free Simplex Method for Estimation of Optical Properties in Image-Guided Diffuse Optical Tomography," Journal of Biomedical Optics 18(3), 030503 (2013).[CODE] PUBMED

(26). Jaya Prakash and Phaneendra K. Yalavarthy, “A LSQR-type method provides a computationally efficient automated optimal choice of regularization parameter in diffuse optical tomography," Medical Physics 40(3), 033101 (2013). [CODE] PUBMED

(25). Kalyan R. Ayyalasomayajula and Phaneendra K. Yalavarthy, “Analytical Solutions for Diffuse Fluorescence Spectroscopy/Imaging of Biological Tissues in Regular Geometries Part II: Comparison and Validation," Journal of the Optical Society of America A: Optics, Imaging Science, and Vision 30(3), 553-559 (2013).PUBMED

(24). Kalyan R. Ayyalasomayajula and Phaneendra K. Yalavarthy, “Analytical Solutions for Diffuse Fluorescence Spectroscopy/Imaging of Biological Tissues in Regular Geometries Part I: Zero and Extrapolated Boundary Conditions," Journal of the Optical Society of America A: Optics, Imaging Science, and Vision 30(3), 537-552 (2013). PUBMED

(23). Sashikumaar Ganesan and Phaneendra K. Yalavarthy, "Modeling of Terahertz Heating Effects in Realistic Tissues," IEEE Journal of Selected Topics in Quantum Electronics (Issue on current trends in terahertz photonics and applications) 19(1), 8400908 (2013).

(22). Jaya Prakash and Phaneendra K. Yalavarthy, "Data-resolution based optimal choice of minimum required measurements for image-guided diffuse optical tomography," Optics Letters 38(2), 88-90 (2013). PUBMED

2012

(21). Calvin B. Shaw and Phaneendra K. Yalavarthy, "Prior image-constrained L1-norm-based reconstruction method for effective usage of structural information in diffuse optical tomography," Optics Letters 37(20), 4353-4355 (2012). PUBMED

(20). Ravi P. K. Jagannath and Phaneendra K. Yalavarthy, “Minimal Residual Method Provides Optimal Regularization Parameter for Diffuse Optical Tomography," Journal of Biomedical Optics 17(10), 106015:1-7 (2012). [CODE] PUBMED 

(19). Calvin B. Shaw and Phaneendra K. Yalavarthy, "Effective contrast recovery in rapid dynamic near-infrared diffuse optical tomography using L1-norm-based linear image reconstruction method," Journal of Biomedical Optics 17(8), 086009:1-10 (2012). PUBMED

(18). Deepak Karkala and Phaneendra K. Yalavarthy, "Data-Resolution based Optimization of the Data-Collection Strategy for Near Infrared Diffuse Optical Tomography," Medical Physics 39(8), 4715-4725 (2012). PUBMED

(17). Dilip M. Thomas, Phaneendra K. Yalavarthy, Deepak Karkala, and Vijay Natarajan, "Mesh simplification based on edge collapsing could improve computational efficiency in near infrared optical tomographic imaging," IEEE Journal of Selected Topics in Quantum Electronics (Issue on biophotonics) 18(4),  1493-1501 (2012). [CODE]

(16). Sree Harsha Katamreddy and Phaneendra K. Yalavarthy, "Model-Resolution Based Regularization Improves Near Infrared Diffuse Optical Tomography," Journal of the Optical Society of America A: Optics, Imaging Science, and Vision 29(5), 649-656 (2012). [Featured as most downloaded article for October and November months of 2015] PUBMED

2010

(15). Jaya Prakash, Venkittarayan Chandrasekharan, Vishwajith Upendra, and Phaneendra K. Yalavarthy, "Accelerating frequency-domain diffuse optical tomographic image reconstruction using graphics processing units," Journal of Biomedical Optics 15(6), 066009 (2010). [CODE]PUBMED

(14). Ravi P. K. Jagannath and Phaneendra K. Yalavarthy, “Approximation of Internal Refractive Index Variation Improves Image Guided Diffuse Optical Tomography of Breast,” IEEE Transactions on Biomedical Engineering 57(10), 2560-2563 (2010). PUBMED

(13). M. S. Singh, Phaneendra K. Yalavarthy, R. M. Vasu, and K. Rajan,  “Assessment of ultrasound modulation of near infrared light on the quantification of scattering coefficient,” Medical Physics 37(7), 3744-3751 (2010). PUBMED

(12). Manuchehr Soleimani, Phaneendra K. Yalavarthy, and Hamid Dehghani, “Helmholtz-type regularization method for permittivity reconstruction using experimental phantom data of electrical capacitance tomography,” IEEE Transactions on Instrumentation and Measurement 59(1), 78-83 (2010).

2009

(11). Saurabh Gupta, Phaneendra K. Yalavarthy, Debasish Roy, Daqing Piao, and Ram M. Vasu, “Singular Value Decomposition based computationally efficient algorithm for rapid dynamic near-infrared diffuse optical tomography,” Medical Physics 36(12), 5559-5567 (2009). PUBMED

(10). Hamid Dehghani, Mathew. E. Eames, Phaneendra K. Yalavarthy, Scott C. Davis, Subhadra Srinivasan, Colin M. Carpenter, Brian W. Pogue, and Keith D. Paulsen, “Near Infrared Optical Tomography using NIRFAST: Algorithms for Numerical Model and Image Reconstruction Algorithms,” Communications in Numerical Methods in Engineering (Special Issue on Recent Advances in Computational Techniques for Biomedical Imaging) 25(6), 711-732 (2009). PUBMED

2008

(9). Phaneendra K. Yalavarthy, Daniel R. Lynch, Brian W. Pogue, Hamid Dehghani, and Keith D. Paulsen, “Implementation of a computationally efficient least-squares algorithm for highly under-determined three-dimensional diffuse optical tomography problems,” Medical Physics 35(5), 1682-1697 (2008). PUBMED

2007

(8). Subhadra Srinivasan, Brian W. Pogue, Colin M. Carpenter, Phaneendra K. Yalavarthy, and Keith D. Paulsen, “A boundary element approach for image-guided near-infrared absorption and scatter estimation,” Medical Physics 34(11), 4545-4557 (2007). PUBMED

(7). Mathew. E. Eames, Brian W. Pogue, Phaneendra K. Yalavarthy, and Hamid Dehghani, “An efficient Jacobian reduction method for diffuse optical image reconstruction,” Optics Express 15(24), 15908-15919 (2007). PUBMED

(6). Phaneendra K. Yalavarthy, Brian W. Pogue, Hamid Dehghani, Colin M. Carpenter, Shudong Jiang and Keith D. Paulsen, “Structural information within regularization matrices improves near infrared diffuse optical tomography,” Optics Express 15(13), 8043-8058 (2007). PUBMED

(5). Andrew. L. Darling, Phaneendra K. Yalavarthy, Marvin M. Doyley, Hamid Dehghani, and Brian W. Pogue, “Interstitial fluid pressure in soft tissue as a result of externally applied contact pressure,” Physics in Medicine and Biology 52(14), 4121-4136 (2007). PUBMED

(4). Phaneendra K. Yalavarthy, Brian W. Pogue, Hamid Dehghani, and Keith D. Paulsen, “Weight-Matrix Structured Regularization Provides Optimal Generalized Least-Squares Estimate in Diffuse Optical Tomography,” Medical Physics 34(6), 2085-2098 (2007). PUBMED

2006

(3). Phaneendra K. Yalavarthy, Hamid Dehghani, Brian W Pogue, and Keith D Paulsen, "Critical computational aspects of near infrared circular tomographic imaging: Analysis of measurement number, mesh resolution and reconstruction basis," Optics Express 14, 6113-6127 (2006). PUBMED

2005

(2). Phaneendra K. Yalavarthy, Kirtish Karlekar, H S Patel, R M Vasu, Manojit Pramanik, P C Mathias, B Jain and P K Gupta, “Experimental investigation of perturbation Monte-Carlo based derivative estimation for imaging low-scattering tissue," Optics Express 13(3),  985-997 (2005). PUBMED

2004

(1). Phaneendra K. Yalavarthy, and R M Vasu, “Reconstruction of optical properties of low-scattering tissue using derivative estimated through perturbation Monte-Carlo method,” Journal of Biomedical Optics 9(5),  1002-1012 (2004).PUBMED


Conference Proceedings
(31). H. Ravishankar, N. Paluru, P. Sudhakar, and P. K. Yalavarthy, "UATTA-QSM: Uncertainty Aware Test Time Adaptation for Improved Quantitative Susceptibility Mapping," 2025 IEEE 21st International Symposium on Biomedical Imaging (ISBI), Houston, TX, USA, April 14-17, 2025.

(30). H. Ravishankar, N. Paluru, P. Sudhakar, and P. K. Yalavarthy, "Inference Time Adaptation for Improved Retinal Disease Diagnosis Using Optical Coherence Tomography Images," 2025 IEEE 21st International Symposium on Biomedical Imaging (ISBI), Houston, TX, USA, April 14-17, 2025.

(29). H. K. Aggarwal, A. Jerald, P. K. Yalavarthy, and R. Langoju, and B. Das, "Display Field-of-View Agnostic Robust CT Kernel Synthesis Using Model-Based Deep Learning," 2025 IEEE 21st International Symposium on Biomedical Imaging (ISBI), Houston, TX, USA, April 14-17, 2025.

(28). C. Sindhura, P. K. Yalavarthy, and S. Gorthi, "Sino-CT-Fusion-Net: A Lightweight Deep Learning Framework for Detection and Classification of Intracranial Hemorrhages," 2024 IEEE International Conference on Image Processing (ICIP 2024), Abu Dhabi, UAE, October 27-30, 2024.

(27). H. Ravishankar, P. Sudhakar, and P. K. Yalavarthy, "TTA-FM: Patient-Specific Test-Time Adaptation using Foundation Models for Improved Prostate Segmentation In Magnetic Resonance Images," 2024 IEEE 21st International Symposium on Biomedical Imaging (ISBI), Athens, Greece, May 27-30, 2024.

(26). H. K. Aggarwal, P. K. Yalavarthy, and R. Langoju, "Self-supervised Noise-aware Kernel Synthesis for Improved X-ray Computed Tomography Imaging," 2024 IEEE 21st International Symposium on Biomedical Imaging (ISBI), Athens, Greece, May 27-30, 2024.

(25). J. Prakash, D. Sanny, S. Kalva, M. Pramanik, and P. K. Yalavarthy, "Fractional regularization improves photoacoustic image reconstruction," Proc. SPIE 11642, Photons Plus Ultrasound: Imaging and Sensing 2021, 1164236 (5 March 2021).

(24). K. Krishnan, K. V. Reddy, B. Ajani, and P. K. Yalavarthy, "Rapid perfusion quantification using Welch-Satterthwaite approximation and analytical spectral filtering," Paper ID: 101330Q, Proc. SPIE Medical Imaging, Orlando, USA, February 11-16, 2017.

(23). K. V. Reddy, A. Mitra, and and P. K. Yalavarthy, "Fast Analytical Spectral Filtering Methods for Magnetic Resonance Perfusion Quantification," Paper ID: WeCT5.17, Proc. of 2016 38th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), Florida, USA, August 16-20, 2016.

(22). J. Prakash, N. Todd, and P. K. Yalavarthy, "Prior Image based Temporally Constrained Reconstruction for Magnetic Resonance guided HIFU," Abstract ID: 3610, ISMRM 24th Annual Meeting, Singapore, 2016.

(21). P. K. Yalavarthy, K. V. Reddy, and J. Lee, "Magnetic Resonance Perfusion Quantification using QR-based Deconvolution," Abstract ID: 2864, ISMRM 24th Annual Meeting, Singapore, 2016.

(20). R. P. K. Jagannath and P. K. Yalavarthy, "Automated Choice of Regularization Parameter for Spatially Variant Regularization in Diffuse Optical Tomography," SPIE/OSA European Conference on Biomedical Optics (ECBO-2013), May 12-16, 2013, Munich, Germany.

(19). Y. N. Swamy and P. K. Yalavarthy, "Estimation of optimal regularization parameter using Morozov discrepancy principle for Diffuse optical Tomography," SPIE/OSA European Conference on Biomedical Optics (ECBO-2013), May 12-16, 2013, Munich, Germany.

(18). J. Prakash, V. Desai, S. Srinivasan, and P. K. Yalavarthy, "Multi-core computers have high scalability than graphics processing units for diffuse optical tomographic image reconstruction," SPIE/OSA European Conference on Biomedical Optics (ECBO-2013), May 12-16, 2013, Munich, Germany.

(17). C. B. Shaw and P. K. Yalavarthy, "Efficient compound regularization ($\ell_1$-TV) based reconstruction method for rapid dynamic diffuse optical tomography," SPIE/OSA European Conference on Biomedical Optics (ECBO-2013), May 12-16, 2013, Munich, Germany.

(16). P. K. Rakshatha, V. Vijaykumar, N. Sinha, and P. K.  Yalavarthy, "Distinguishing cognitive states using iterative classification," Proceeding of the Eighth Indian Conference on Computer Vision, Graphics and Image Processing (ICVGIP '12), Article No. 21, 2012.

ISMRM(15). N. Todd, J. Prakash, H. Odeen, J. de Bever, A. Payne, P. K. Yalavarthy, and D. L. Parker, "Towards real-time availability of 3-D temperature maps created with temporally constrained reconstruction," ISMRM 20th Annual Meeting 2012 [Top-10 Posters of ISMRM]. 
 

(14). R. P. K. Jagannath, P. K. Yalavarthy, "A semi-analytic method for continuous-wave diffuse optical tomography," SPIE/OSA European Conference on Biomedical Optics, May 22-26, 2011, Munich, Germany.

(13). P. K. Yalavarthy, D. A. Low, C. Noel, Z. Wei, D. Yang, A. Apte, J. Bradley, J. Deasy, and I. El Naqa, “Current role of PET in oncology: Potentials and challenges in the management of non-small cell lung cancer,” Proc. of IEEE 42nd Annual Asilomar Conference on Signals, Systems, and Computers (26-29 October 2008, Pacific Grove, California) 1067–1071 (2008). [invited paper]

(12). M. Soleimani, C. N. Mitchell, J. R. Tong, H. Dehghani, and P. K. Yalavarthy, “Regularization of electrical impedance tomography imaging using Helmholtz operator,” Proc. of Electrical Impedance Tomography Conference 2008 (EIT 2008, 16-18 June 2008, Hanover, New Hampshire), 163–166 (2008).

(11). M. E. Eames, B. W. Pogue, P. K. Yalavarthy, and H. Dehghani, “An efficient Jacobian reduction method for image reconstruction using Diffuse Optical Tomography,” Biomedical Optics Topical Meeting on CD-ROM (The Optical Society of America, Washington, DC), 16-19 March 2008.

(10). P. K. Yalavarthy, R. Langoju, B. Pogue, H. Dehghani, A. Patil, and K. Paulsen, “Cramer-Rao estimation of error limits for diffuse optical tomography with spatial prior information,” Proc. of SPIE 6434 (BiOS-2007 in Photonics West-2007, 20-25 January 2007, San Jose, California), 643403:1-13 (2007).

(9). S. C. Davis, H. Dehghani, P. K. Yalavarthy, B. W. Pogue, K. D. Paulsen, “Comparing two regularization techniques for diffuse optical tomography,” Proc. of SPIE 6434 (BiOS-2007 in Photonics West-2007, 20-25 January 2007, San Jose, California), 64340X:1-12 (2007).

(8). H. Dehghani, C. M. Carpenter, P. K. Yalavarthy, B. W. Pogue, and J. P. Culver, “Structural a-priori Information in near infrared optical tomography,” Proc. of SPIE 6431 (BiOS-2007 in Photonics West-2007, 20-25 January 2007, San Jose, California), 64310B:1-7 (2007).

(7). A. Darling, P. K. Yalavarthy, H. Dehghani, and B. W. Pogue, “Interstitial fluid pressure due to externally applied force in breast tissue,” Proc. of SPIE 6431 (BiOS-2007 in PhotonicsWest-2007, 20-25 January 2007, San Jose, California), 64310Z:1-10 (2007).

(6). Phaneendra K. Yalavarthy, Colin Carpenter, Shudong Jiang, Hamid Dehghani, Brian W. Pogue and Keith D. Paulsen, "Incorporation of MR structural information in diffuse optical tomography using Helmholtz type regularization", Biomedical Optics Topical Meeting on CD-ROM (The Optical Society of America, Washington, DC), March 19-22, 2006.

(5). Colin Carpenter, Brian W. Pogue, Phaneendra Yalavarthy, Scott Davis, Shudong Jiang, Hamid Dehghani and Keith D. Paulsen, "Analysis of 3-dimensional reconstruction in a MR-guided NIR tomography system", Biomedical Optics Topical Meeting on CD-ROM (The Optical Society of America, Washington, DC), March 19-22, 2006.

(4). Phaneendra K. Yalavarthy, Hamid Dehghani, Brian W. Pogue, and Keith D. Paulsen, “Measurement optimization for Near-Infrared optical tomography,” Proc. of SPIE 5693 (BiOS-2005 in Photonics West-2005, 22–27 January 2005, San Jose, California), p. 64-73, 2005.

(3). Daqing Piao, Shudong Jiang, Subhadra Srinivasan, Phaneendra K. Yalavarthy, Xiaomei Song, Brian W. Pogue, “Spectral-encoding for parallel source implementation in NIR tomography,” Proc. of SPIE 5693 (BiOS-2005 in Photonics West-2005, 22–27 January 2005, San Jose, California), p. 129-136, 2005.

(2). Phaneendra K. Yalavarthy, Kirtish Karlekar and R M Vasu, “Perturbation Monte-Carlo based derivative estimation for imaging transport regime tissue optical properties,” Proc. of SPIE 5486, p. 77-84, 2004.

(1). Phaneendra K. Yalavarthy and R M Vasu, “Perturbation Monte-Carlo based derivative estimation for imaging low-scattering inclusions in a heterogeneous tissue,” Proc. IEEE TENCON-2003:Conference on Convergent Technologies for Asia-Pacific Region, p. 529-533, 2003.
Conference Presentations

(12). P. K. Yalavarthy, Z. Wei, J. Wen, P. Parikh, T. Zhao, J. Bradley, and D. A. Low,  "A spatially-based binning method for improving the quantitative accuracy of free-breathing PET/CT images," Int. J. Radiat. Oncol. Biol. Phys. 72 (ASTRO annual meeting 2008, 21-25 September 2008, Boston, Massachusetts), S613-S614 (2008).

(11). T. Zhao, J. Bradley, C. Noel, P. K. Yalavarthy, P. Parikh, T. Yang, D. Yang, S. Mutic, and D. A. Low, “Application of five-dimensional breathing motion model for monitoring radiation damage,”  Med. Phys. 35 (American Association of Physicists in Medicine (AAPM) annual meeting 2008, 27-31 July 2008, Houston, Texas), 2877 (2008).

(10). P. K. Yalavarthy, B. Pogue, and H. Dehghani, “A generalized least-squares minimization method for near infrared diffuse optical tomography,” Department of Defense Era of Hope Meeting, Baltimore, Maryland 25-28 June 2008 (invited presentation).

(9). S. Srinivasan, B. W. Pogue, C. Carpenter, P. K. Yalavarthy, and K. D. Paulsen, “A Boundary Element Approach for Image-guided Near-Infrared Absorption and Scatter Estimation,” Network for Translational Research Optical Imaging Network (NTROI) Retreat, Hyatt Regency Newport Beach, CA, June 28-30, 2007.

(8). B. W. Pogue, C. M. Carpenter, P. K. Yalavarthy, S. C. Davis, J. Wang, and K. D. Paulsen, “Recovery of hemoglobin images from MR-guided NIR spectroscopy,” SPIE Medical Imaging-2007, San Diego, California, 17-22 February 2007.

(7). B. W. Pogue, C. M. Carpenter, P. K. Yalavarthy, H. Dehghani, S. Jiang, X. Wang, W. A. Wells, C. A. Kogel, S. P. Poplack, J. B. Weaver, and K. D. Paulsen, “Proposed methods to improve false positive and false negative rates in MR breast imaging, through combination with NIR broadband spectroscopy/tomography,” BiOS-2007 in Photonics West-2007, San Jose, California, 20-25 January 2007 (invited presentation).

(6). P. K. Yalavarthy, B. W. Pogue, H. Dehghani, S. Jiang, and K. D. Paulsen, “Generalized Least-Squares minimization for Magnetic Resonance guided Diffuse Optical Tomography,” BiOS-2007 in Photonics West-2007, San Jose, California, 20-25 January 2007.

(5). P. K. Yalavarthy, B. W. Pogue, H. Dehghani, S. Jiang, and K. D. Paulsen, “Outline of the Weighted Least-Squares minimization for Diffuse Optical Tomography,” Network for Translational Research Optical Imaging Network (NTROI) Retreat, Hyatt Regency Newport Beach, CA, June 22-24, 2006.

(4). P. K. Yalavarthy, K. Karlekar, and R. M. Vasu, “Design of a time-domain optical tomography imager for imaging tissue with low-scattering coefficient,” Int. Conf. on Laser Applications and Optical Metrology (ICLAOM-03), IIT Delhi, India, Dec. 1-4, 2003.

(3). P. K. Yalavarthy and R. M. Vasu, “Optical inhomogeneity reconstruction in tissue with low scattering inclusions using derivative estimated through perturbation MonteCarlo,” National Symposium on Engg. Optics (NSEO-03), Meerut College, Meerut, India, April-2003.

(2). P. K. Yalavarthy, “Perturbation Monte-Carlo (pMC) Technique: A novel Imaging modality in optical tomography,” Lamp-Workshop, Winter college on bio-photonics, ICTP, Trieste, Italy, February 10-21, 2003.

(1). R. M. Vasu and P. K. Yalavarthy, “Efficient calculation of Jacobian for solving the inverse photon transport problem in the tissue,” Conference on Optics and Photonics in Engineering (COPE-03), New Delhi, India, Jan-2003.
Technical Reports

(4). Colin Carpenter and Phaneendra K. Yalavarthy, “2-D Plotting of Finite Difference or Finite Element Solutions with Tecplot,” NML Lab Report, NML-07-1, Dartmouth College, February 2007.

(3). Phaneendra K. Yalavarthy, “Derivation of an alternative form for generalized least-squares update equation in Diffuse Optical Tomography,” NML Lab Report, NML-06-10, Dartmouth College, July 2006.

(2). Phaneendra K. Yalavarthy and Daniel R. Lynch, “Generalized Least-Squares minimization for Diffuse Optical Tomography: Use of Complex data,” NML Lab Report, NML-06-9, Dartmouth College, July 2006.

(1). Phaneendra K. Yalavarthy, Phillip R. Perrinez, and Keith D. Paulsen, “Integration formulas for tetrahedral element,” NML Lab Report, NML-06-8, Dartmouth College, May 2006.
Theses

(3). Phaneendra K. Yalavarthy, “A generalized least-squares minimization method for near infrared diffuse optical tomography," Ph.D. Thesis, Dartmouth College, Hanover, September 2007.

(2). Phaneendra K. Yalavarthy, “Diffuse optical tomographic reconstruction in low-scattering tissue: development of inversion algorithms based on Monte-Carlo simulation," M.Sc.(Engg.) thesis, Indian Institute of Science, Bangalore, India, January 2004.

(1). Phaneendra K. Yalavarthy, “Precision measurements of energies and intensities of gamma transitions in the electron capture decay of 75Se using large volume HPGe-detector," M.Sc. dissertation, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, India, March 2001.
Letters

(1). Phaneendra K. Yalavarthy, “Ultrasound Imaging: a boon or bane?,” Current Science 88(7), p. 1019, April 10, 2005.

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