Publications
*indicates Equal Contribution
Review Paper
1). 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).
Journal Publications
41) Isha Munjal, and Jaya Prakash, "Deep-Learning based deconvolution for correcting spatial impulse response of transducer in optoacoustic tomography," IEEE Transactions on Instrumentation and Measurements 2024 (in press).
40) Kaustav Roy, Akshay Kumar, Vijayendra Shastri, Isha Munjal, Kritank Kalyan, Anuj Ashok, Antony Jeyaseelan, Jaya Prakash, and Rudra Pratap, "PMUT-Powered Photoacoustic Detection: Revolutionizing Microfluidic Concentration Measurements," IEEE Transactions on Instrumentation and Measurements 2024 (in press).
39) 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 2024 (in press).
38) Yash S. Dravid, and Jaya Prakash, "Frequency domain photoacoustic signal analysis for temperature sensing," IEEE Sensors Journal 24(1) 877-884 (2024).
37) Madhavi Tripathi*, Swathi Padmanabhan*, Jaya Prakash, and Ashok Raichur, "Seed mediated galvanic synthesis of ultrasmall CuS-Au nanohybrids for photo-theranostic applications," ACS Applied Nano Materials 6, 14861-14875 (2023). [Was covered by news outlets like IISc, Phys.org, EurekAlert, Bioengineer.org, Sciencemag, NDTV, News18, India Today, The Hindu, ToI, Deccan Herald, The New Indian Express, Hindustan Times, Telegraph, Tribune, PharmaBiz, Eenadu, Udayavani, etc https://acs.altmetric.com/details/154024893/news] https://doi.org/10.1021/acsanm.3c02405
36) Hemanth S. Nakshatri, and Jaya Prakash, "Complex valued long short term memory based architecture for frequency domain photoacoustic imaging," IEEE Transactions on Computational Imaging 9, 551-564 (2023). DOI: 10.1109/TCI.2023.3281192
35) Arumugaraj M, Vipul Gujrati, Vasilis Ntziachristos, and Jaya Prakash, "Deep learning methods hold promise for light fluence compensation in three-dimensional optoacoustic imaging," Journal of Biomedical Optics 27(10), 106004 (2022). DOI: https://doi.org/10.1117/1.JBO.27.10.106004
34) Hemanth S. Nakshatri, and Jaya Prakash, "Model resolution matrix based deconvolution improves over non-quadratic penalization in frequency-domain photoacoustic tomography," The Journal of the Acoustical Society of America 152(3), 1345-1356 (2022). DOI: 10.1121/10.0013829
33) 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). DOI: 10.1109/TIP.2022.3172211
32) Marwan Muhammad, Jaya Prakash, Evangelos Liapis, Vasilis Ntziachristos, and Dominik Juestel, "Weighted model-based optoacoustic reconstruction for partial-view geometries," Journal of Biophotonics e202100334, 1-12 (2022). DOI: https://doi.org/10.1002/jbio.202100334
31) Misun Yun, Sung-Hwan You, Vu Hong Nguyen, Jaya Prakash, Sarah Glasl, Vipul Gujrati, Hyon E. Choy, Andre C. Stiel, Jung-Joon Min and Vasilis Ntziachristos, "Reporter Gene-Based Optoacoustic Imaging of E. coli Targeted Colon Cancer In vivo," Scientific Reports 11, 24430 (2021). DOI: https://doi.org/10.1038/s41598-021-04047-4
30). 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, 18536 (2021). DOI: https://doi.org/10.1038/s41598-021-97833-z
29). 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
28). Nian Liu, Vipul Gujrati, Jaber Malekzadeh-Najafabadi, Juan Pablo Fuenzalida Werner, Uwe Klemm, Longguang Tang, Zhenyue Chen, Jaya Prakash, Yuanhui Huang, Andre Stiel, Gabriele Mettenleiter, Michaela Aichler, Andreas Blutke, Axel Walch, Karin Kleigrewe, Daniel Razansky, Michael Sattler, and Vasilis Ntziachristos, "Croconaine based nanoparticles enable efficient optoacoustic imaging of murine brain tumours," Photoacoustics 22, 100263 (2021). DOI: https://doi.org/10.1016/j.pacs.2021.100263
27). 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 32(3), 932-946 (2021). [Was covered by news outlets like IISc, TechXplore, The Hindu, Times of India, Times Now, Deccan Herald, The New Indian Express, Eenadu, PharmaBiz, Business Standard, etc https://ieee.altmetric.com/details/99566510/news]. DOI: 10.1109/TNNLS.2021.3054746
26). 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, e202000191 (2021). DOI: 10.1002/jbio.202000191
25). Kaushik Basak Chowdhury, Jaya Prakash, Angelos Karlas, Dominik Juestel, and Vasilis Ntziachristos, "A synthetic total impulse response characterization method for correction of hand-held optoacoustic images," IEEE Transactions on Medical Imaging 39(10), 3218 - 3230 (2020). DOI: 10.1109/TMI.2020.2989236.
24). Tong Lu, Yihan Wang, Jiao Li, Jaya Prakash, Feng Gao, and Vasilis Ntziachristos, "Full-frequency correction of spatial impulse response in back-projection scheme using space-variant filtering for optoacoustic mesoscopy," Photoacoustics 19, 100193 (2020). DOI: 10.1016/j.pacs.2020.100193.
23). Hong Yang, Dominik Juestel, Jaya Prakash, Angelos Karlas, Anne Helfen, Masthoff Max, Moritz Wildgruber, and Vasilis Ntziachristos, "Soft ultrasound priors in optoacoustic reconstruction: improving clinical vascular imaging," Photoacoustics 19, 100172 (2020). DOI: 10.1016/j.pacs.2020.100172
22). Jiao Li, Andrei Chekkoury, Jaya Prakash, Sarah Glasl, Paul Vetschera, Benno Koberstein-Schwarz, Ivan Olefir, Vipul Gujrati, and Murad Omar, and Vasilis Ntziachristos, "Spatial heterogeneity of oxygenation and hemodynamics in breast cancer resolved in vivo by conical multispectral optoacoustic mesoscopy," Light: Science & Applications 9, 57 (2020). [Was covered by news outlets like TechnologyNetworks, EurekAlert, Medicalpress, The Medical News, Imaging Technology News, MTA Dialog, TUM etc https://nature.altmetric.com/details/79734018]. DOI: 10.1038/s41377-020-0295-y
21). Jaya Prakash*, Mir Mehdi Seyedebrahimi*, Ara Ghazaryan*, Jaber Malekzadeh-Najafabadi, Vipul Gujrati, and Vasilis Ntziachristos, "Short wavelength optoacoustic spectroscopy based on water muting," Proceedings of the National Academy of Sciences 117(8), 4007-4014 (2020). DOI: 10.1073/pnas.1910597117 [Research Highlight IISc]
20). Jaya Prakash*, Subhamoy Mandal*, Daniel Razansky, and Vasilis Ntziachristos, ''Maximum entropy based non-negative optoacoustic tomographic image reconstructions,'' IEEE Transactions on Biomedical Engineering 66(9), 2604-2616 (2019). DOI: 10.1109/tbme.2019.2892842
19). Vipul Gujrati*, Jaya Prakash*, Jaber Malekzadeh-Najafabadi, Andre Stiel, Uwe Klemm, Ruth Hillermann, Gabriele Mettenleiter, Michaela Aichler, Axel Walch, Vasilis Ntziachristos, "Bioengineered bacterial vesicles as biological nano-heaters for optoacoustic imaging" Nature Communications 10(1), 1114, (2019). [Was covered by news outlets like Phys.org, EurekAlert, AzoNano, NanoWerk, ScienceDaily, The Medical News, ArzteZeitung, TUM/HMGU etc https://nature.altmetric.com/details/56675636/news]. DOI: 10.1038/s41467-019-09034-y
18). Jaya Prakash*, Dween Sanny*, 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). DOI: 10.1109/TMI.2018.2889314
17). Dween R. Sanny, Jaya Prakash, Sandeep K Kalva, Manojit Pramanik, 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
16). Volker Neuschmelting, Kwanghee Kim, Jaber Malekzadeh-Najafabadi, Sylvia Jebiwott, Jaya Prakash, Avigdor Scherz, Jonathan A Coleman, Moritz F. Kircher, and Vasilis Ntziachristos, ''WST11 vascular targeted photodynamic therapy effect monitoring using multispectral optoacoustic tomography (MSOT) in mice,'' Theranostics 8(3), 723 (2018). DOI: 10.7150/thno.20386
15). Jaber Malekzadeh-Najafabadi*, Jaya Prakash*, and Vasilis Ntziachristos, ''Nonlinear optoacoustic readings from diffusive media at near infrared wavelengths,'' Journal of Biophotonics 11(1), e201600310 (2018). DOI: 10.1002/jbio.201600310
14). Yiyong Han, Lu Ding, Xose Luis Dean Ben, Daniel Razansky, Jaya Prakash, and Vasilis Ntziachristos, ''Three-dimensional optoacoustic reconstruction using fast sparse representation,'' Optics Letters 42(5), 979-982 (2017) (Also selected for publication in Virtual Journal of Biomedical Optics, 12(5)). DOI: 10.1364/OL.42.000979
13). Almut Glinzer*, Xiaopeng Ma*, Jaya Prakash, Melanie Kimm, Fabian Lohöfer, Katja Kosanke, Jaroslav Pelisek, Moritz Thon, Hans-Henning Eckstein, Michael Gee, Vasilis Ntziachristos, Alma Zernecke, and Moritz Wildgruber, ''Targeting elastase for molecular imaging of early atherosclerotic lesion,'' Arteriosclerosis, Thrombosis, and Vascular Biology 37(3), 525-533, (2017). DOI: 10.1161/atvbaha.116.308726
12). Xiaopeng Ma*, Valerie Phi Van*, Melanie Kimm, Jaya Prakash, Horst Kessler, Katja Kosanke, Annettee Feuchtinger, Michaela Aichler, Aayush Gupta, Ernst Rummeny, Michel Eisenblaetter, Jens Siveke, Axel Walch, Rickmet Braren, Vasilis Ntziachristos, and Moritz Wildgruber, ''Hybrid fluorescence molecular tomography/x-ray computed tomography for imaging integrin expression in non-small cell lung cancer,'' Neoplasia 19(1), 8-16 (2017). DOI: 10.1016/j.neo.2016.11.009
11). Hailong He*, Jaya Prakash*, Andreas Bühler, and Vasilis Ntziachristos, ''Optoacoustic tomography using accelerated sparse recovery and coherence factor weighting,'' Tomography: A journal for imaging research 2(2), 138-145 (2016). DOI: 10.18383/j.tom.2016.00148
10). Xiaopeng Ma, Jaya Prakash, Francesca Ruscitti, Sarah Glash, Fabio Franco Stellari, Gino Villetti, and Vasilis Ntziachristos, "Assessment of asthmatic inflammation using hybrid fluorescence molecular tomography- x-ray computed tomography," Journal of Biomedical Optics 21(1), 15009 (2016). DOI: 10.1117/1.jbo.21.1.015009
9). 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 (2015). DOI: 10.1118/1.4934829
8). Jaya Prakash, Aditi Subramani 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). [Top Downloads from Biomedical optics Express for Image Reconstruction and Inverse Problems]. DOI: 10.1364/BOE.5.001363
7). 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). DOI: 10.1109/TMI.2013.2297691
6). Nick Todd, Jaya Prakash, Henrik Odeen, Joshua de Bever, Allison Payne, Phaneendra Yalavarthy, and Dennis Parker, "Towards real-time availability of 3-D temperature maps created with temporally constrained reconstruction," Magnetic Resonance in Medicine 71(4), 1394-1404 (2014). DOI: 10.1002/mrm.24783
5). 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). DOI: 10.1109/jstqe.2013.2278218
4). Calvin B. Shaw, Jaya Prakash, Manojit Pramanik, and Phaneendra K. Yalavarthy, "LSQR-based decomposition provides an efficient way of computing optimal regularization parameter in photoacoustic tomography," Journal of Biomedical Optics 18(8), 080501 (2013). DOI: 10.1117/1.JBO.18.8.080501
3). 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). DOI: 10.1118/1.4792459
2). 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) (Also selected for publication in Virtual Journal of Biomedical Optics, 8(2)). DOI: 10.1364/OL.38.000088
1). 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). DOI: 10.1117/1.3506216
Conferences
21) I. Munjal, and J. Prakash, "Multi-Encoder Deep Learning improves Computed Tomography," IEEE Symposium on Biomedical Imaging, Athens, Greece, May 2024.
20) H. Nakshatri, and J. Prakash, "Complex valued long short term memory based architecture for frequency domain photoacoustic imaging," IEEE Symposium on Biomedical Imaging, Athens, Greece, May 2024.
19) I. Munjal, and J. Prakash, "Spatial Impulse Response of Ultrasound Transducer Correction Using Deep Learning in Photoacoustic Tomography," Optica Biophotonics Congress: Biomedical Optics, Florida, USA, April 2024.
18) S. Padmanabhan, and J. Prakash, "Approaching Optical Rotation Through the Lens of Near-InfraRed-II Photoacoustics," Optica Biophotonics Congress: Biomedical Optics, Florida, USA, April 2024.
17) I. Munjal, and J. Prakash, "Spatial Impulse Response of Ultrasound Transducer Correction Using Deep Learning in Photoacoustic Tomography," IEEE South Asian Conference on Ultrasonics, IIT Gandhinagar, March 2024.
16) S. Padmanabhan, and J. Prakash, "Exploring Photoacoustics from Optical Activity: A Perspective for Biomolecular Sensing," IEEE South Asian Conference on Ultrasonics, IIT Gandhinagar, March 2024.
15) I. Munjal, Arumugaraj, and J. Prakash, "Deep learning methods for correcting fluence effects in photoacoustic tomography," Photonics, IISc, Bengaluru, July 2023.
14) S. Padmanabhan, and J. Prakash, "Development of Polarisation based Photoacoustic Sensing System and Appropriate models to enable the Propagation of Polarized Light in Tissues," Photonics, IISc, Bengaluru, July 2023.
13) K. Roy, V. Shastri, A. Kumar, J. Rout, Isha, K. Kalyan, J. Prakash, R. Pratap, ''A PMUT based photoacoustic system as a microfluidic concentration detector,'' SPIE Photonics West, California, February 2022.
12) J. Prakash*, D. Sanny*, S. K. Kalva, M. Pramanik, and P. K. Yalavarthy, ''Fractional regularization to improve photoacoustic tomographic image reconstruction,” SPIE Photonics West, California, March 2021.
11) J. Prakash*, MM Seyedebrahimi*, A. Ghazaryan*, J. Malekzadeh-Najafabadi, V. Gujrati, and V. Ntziachristos, "Cooled Infrared Optoacoustic Spectroscopy (CIROAS) for accurate sensing based on water muting," SPIE Photonics West, California, March 2021.
10) N. Liu, V. Gujrati, et. al., "Croconaine-derived CR780 nanoparticles enable efficient optoacoustic imaging of deep brain tumor," PS 15-04 EMIM Meeting, Virtual Meeting, 2020.
9) H. Yang, J. Prakash, and V. Ntziachristos, "Modeling the variation in speed-of-sound between couplant and tissue improves the spectral accuracy of multispectral optoacoustic tomography ," SPIE Photonics West, California, February 2019.
8) L. Prade, J. Prakash, and V. Ntziachristos, ''Optoacoustic imaging utilizing diode lasers in frequency domain,'' SPIE Photonics West, California, February 2017.
7) H. He*, J. Prakash*, A. Bühler, and V. Ntziachristos, ''Optoacoustic tomography using accelerated sparse recovery and coherence factor weighting,'' SPIE Photonics West, California, February 2017.
6) J. Malekzadeh*, J. Prakash*, and V. Ntziachristos, ''Enabling accurate quantitative optoacoustic tomography by correcting non-linear effects,'' ESMI- TOPIM TECH, Multiparametric Imaging, Crete, July 2016.
5) 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, April 2016.
4) J. Prakash, ''Model Resolution Matrix based Deconvolution for Biomedical Optical Imaging,'' Fifth Electrical Sciences Divisional Symposium, Faculty Hall, IISc Bangalore, Feb 20- 21, 2014 (www.ece.iisc.in/~divsymposium).
3) 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, May 12-16, 2013, Munich, Germany.
2). N. Todd, J. Prakash, H. Odeen, J. d. Bever, A. Payne, P. Yalavarthy, and D. Parker, "Towards real-time availability of 3-D temperature maps created with temporally constrained reconstruction," ISMRM 20th Annual Meeting, Australia, May 2012, [Top-10 Posters of ISMRM].
1). V. Chandrasekharan, J. Prakash,K. Rajamani, M. Gopal, R. K. Balkrishna, Nitin B. S., Nitin M., K. Achyutan, and B. Bijlani, "Virtual Soldering environment using touch and gesture for engineering labs education," Proc. of IEEE Students Technology Symposium (TechSym), IIT-Kharagpur, 206-210 (2010).
© Jaya Prakash, 2020
Disclaimer:
Copyright and all rights therein are maintained by the authors or by other copyright holders, notwithstanding that they have offered their works here electronically. These articles may be downloaded for personal use only. Any other use requires prior permission of the author and/or publisher.
Image downloaded from net