Pitkäaho, Tomi, Manninen, Aki and Naughton, Thomas J. (2019) Focus prediction in digital holographic microscopy using deep convolutional neural networks. Applied Optics, 58 (5). A202-A208. ISSN 0003-6935

Pitkäaho, Tomi, Pitkäkangas, Ville, Niemelä, Mikko, Rajput, Sudheesh K., Nishchal, Naveen K. and Naughton, Thomas J. (2018) Space-variant video compression and processing in digital holographic microscopy sensor networks with application to potable water monitoring. Applied Optics, 57 (22). E190-E198. ISSN 1559-128X

Pitkäaho, Tomi, Manninen, Aki and Naughton, Thomas J. (2018) Classification of Digital Holograms with Deep Learning and Hand-Crafted Features. In: Digital Holography and Three- Dimensional Imaging 2018 (part of Imaging and Applied Optics 2018), 2018.

Pitkäaho, Tomi, Manninen, Aki and Naughton, Thomas J. (2018) Detecting the presence of a transparent object in off-axis digital holograms. Digital Holography and Three- Dimensional Imaging 2018 (part of Imaging and Applied Optics 2018).

Pitkäaho, Tomi, Manninen, Aki and Naughton, Thomas J. (2018) Principal component analysis on time-lapse captured digital holograms of cell clusters. In: Biophotonics Congress: Biomedical Optics Congress 2018, 2018.

Pitkäaho, Tomi, Manninen, Aki and Naughton, Thomas J. (2018) Temporal Deep Learning Classification of Digital Hologram Reconstructions of Multicellular Samples. In: Biophotonics Congress: Biomedical Optics Congress 2018, 2018.

Lehtimäki, Taina M., Reilly, Ronan and Naughton, Thomas J. (2018) Towards Perception-Inspired Numerical Measures of Compression Error in Digital Holograms of Natural Three-Dimensional Scenes. In: 40th European Conference on Visual Perception ECVP 2017, 27–31 Aug 2017, Berlin, Germany.

Qaiser, Talha, Mukherjee, Abhik, Reddy P.B., Chaitanya, Munugoti, Sai D., Tallam, Vamsi, Pitkäaho, Tomi, Lehtimäki, Taina M., Naughton, Thomas J., Berseth, Matt, Pedraza, Aníbal, Mukundan, Ramakrishnan, Smith, Matthew, Bhalerao, Abhir, Rodner, Erik, Simon, Marcel, Denzler, Joachim, Huang, Chao-Hui, Bueno, Gloria, Snead, David, Ellis, Ian O., Ilyas, Mohammad and Rajpoot, Nasir (2017) HER2 challenge contest: a detailed assessment of automated HER2 scoring algorithms in whole slide images of breast cancer tissues. Histopathology, 72 (2). pp. 227-238. ISSN 1365-2559

Huo, Yongkai, Kovács, Péter Tamás, Naughton, Thomas J. and Hanzo, Lajos (2017) Wireless Holographic Image Communications Relying on Unequal Error Protected Bitplanes. IEEE Transactions on Vehicular Technology, 66 (8). pp. 7136-7148. ISSN 0018-9545

Pitkäaho, Tomi, Manninen, Aki and Naughton, Thomas J. (2017) Focus classification in digital holographic microscopy using deep convolutional neural networks. In: Advances in Microscopic Imaging. Proceedings of SPIE-OSA (10414). SPIE, Bellingham, WA, 104140K. ISBN 9781510612860

Pitkäaho, Tomi, Manninen, Aki and Naughton, Thomas J. (2017) Deep convolutional neural networks and digital holographic microscopy for in-focus depth estimation of microscopic objects. In: Irish Machine Vision and Image Processing Conference Proceedings 2017. Irish Pattern Recognition & Classification Society, pp. 52-59. ISBN 978-0-9934207-2-6

Pitkäaho, Tomi, Pitkäkangas, Ville, Niemelä, Mikko, Rajput, Sudheesh K., Nishchal, Naveen K. and Naughton, Thomas J. (2017) Digital holographic microscopy in remote potable water monitoring. In: Digital Holography and Three-Dimensional Imaging, 29 May – 1 Jun 2017, JeJu Island, South Korea.

Pitkäaho, Tomi, Pitkäkangas, Ville, Niemelä, Mikko, Rajput, Sudheesh, Nishchal, Naveen K. and Naughton, Thomas J. (2017) Digital holographic sensor network and image analyses for distributed potable water monitoring. In: Irish Machine Vision and Image Processing Conference Proceedings 2017. Irish Pattern Recognition & Classification Society, pp. 221-224. ISBN 978-0-9934207-2-6

Pitkäaho, Tomi, Manninen, Aki and Naughton, Thomas J. (2017) Performance of autofocus capability of deep convolutional neural networks in digital holographic microscopy. In: Digital Holography and Three-Dimensional Imaging, 29 May – 1 Jun 2017, JeJu Island, South Korea.

Zhang, Lingfei and Naughton, Thomas J. (2017) Study of imperfect keys to characterise the security of optical encryption. In: Irish Machine Vision and Image Processing Conference Proceedings 2017. Irish Pattern Recognition & Classification Society, pp. 202-210. ISBN 978-0-9934207-2-6

Huo, Yongkai, Naughton, Thomas J. and Hanzo, Lajos (2017) Unequal Error Protected Bitplanes Improve the Robustness of Wireless Holographic Image Communications. In: Digital Holography and Three-Dimensional Imaging, 29 May – 1 Jun 2017, JeJu Island, South Korea.

Pitkäaho, Tomi, Naughton, Thomas J. and Manninen, Aki (2016) Monitoring MDCK cell vesicles by digital holographic microscopy and image processing. In: 2016 Imaging and Applied Optics Congress, 2016.

Lehtimäki, Taina M., Niemelä, Mikko, Näsänen, Risto, Reilly, Ronan and Naughton, Thomas J. (2016) Using traditional glass plate holograms to study visual perception of future digital holographic displays. In: Optics InfoBase Conference Papers, 2016.

Kujawinska, Malgorzata, Kozacki, Tomasz, Falldorf, Claas, Meeser, Thomas, Hennelly, Bryan M., Garbat, Piotr, Zaperty, Weronica, Niemelä, Mikko, Finke, Grzegorz, Kowiel, Marcin and Naughton, Thomas J. (2014) Multiwavefront digital holographic television. Optics Express, 22 (3). pp. 2324-2336. ISSN 1094-4087

Mooney, Aidan, Duffin, Joe, Naughton, Thomas J., Monahan, Rosemary, Power, James F. and Maguire, Phil (2014) PACT: An initiative to introduce computational thinking to second-level education in Ireland. In: International Conference on Engaging Pedagogy 2014 (ICEP), 5th December 2014, Athlone Institute of Technology.

Pitkäaho, Tomi and Naughton, Thomas J. (2014) Speckle Noise Reduction in Michelson Digital Holography Using Known or Unknown Reference Linear Phases and Image Processing. In: Fringe 2013. Springer, pp. 649-652. ISBN 9783642363580

Woods, Damien and Naughton, Thomas J. (2012) Optical computing: Photonic neural networks. Nature Physics, 8 (4). pp. 257-259. ISSN 1745-2473

Nishchal, Naveen K. and Naughton, Thomas J. (2011) Flexible optical encryption with multiple users and multiple security levels. Optics Communications, 284 (3). pp. 735-739. ISSN 0030-4018

Naughton, Thomas J., Falldorf, Claas, Onural, Levent, Ferraro, Pietro, Depeursinge, Christian, Krueger, Sven, Emery, Yves, Hennelly, Bryan M. and Kujawiñska, Małgorzata (2011) 3D capture, processing, display, and perception with digital holography: results from a European-funded project. In: Digital Holography and Three-Dimensional Imaging, May 2011, Japan.

Pitkäaho, Tomi and Naughton, Thomas J. (2011) Calculating depth maps from digital holograms using stereo disparity. Optics Letters, 36 (11). pp. 2035-2037. ISSN 0146-9592

Näsänen, Risto, Colomb, Tristan, Emery, Yves and Naughton, Thomas J. (2011) Enhancement of three-dimensional perception of numerical hologram reconstructions of real-world objects by motion and stereo. Optics Express, 19 (17). pp. 16075-16086. ISSN 1094-4087

Näsänen, Risto, Naughton, Thomas J., Colomb, Tristan and Emery, Yves (2010) 3D perception of numerical hologram reconstructions enhanced by motion and stereo. Information Optics (WIO) 2010 9th Euro-American Workshop. pp. 1-3.

Naughton, Thomas J., Falldortt, Claas, Onural, Levent and Ferraro, Pietro (2010) Capture, processing, and display of real-world 3D objects using digital holography. Information Optics (WIO) 2010 9th Euro-American Workshop. p. 1.

Lehtimaki, Taina M., Saaskilahti, Kirsti, Kowiel, Marcin and Naughton, Thomas J. (2010) Displaying digital holograms of real-world objects on a mobile device using tilt-based interaction. Information Optics (WIO) 2010 9th Euro-American Workshop. pp. 1-3.

Lehtimaki, Taina M., Saaskilahti, Kirsti, Pitkaaho, Tomi and Naughton, Thomas J. (2010) Evaluation of perceived quality attributes of digital holograms viewed with a stereoscopic display. Information Optics (WIO) 2010 9th Euro-American Workshop. pp. 1-3.

Pitkäaho, Tomi and Naughton, Thomas J. (2010) Numerical reconstruction of digital holograms for conventional 3D display. Information Optics (WIO) 2010 9th Euro-American Workshop.

Page, Andrew J., Keane, Thomas M. and Naughton, Thomas J. (2010) Multi-heuristic dynamic task allocation using genetic algorithms in a heterogeneous distributed system. Journal of Parallel and Distributed Computing, 70 (7). pp. 758-766. ISSN 0743-7315

Naughton, Thomas J. (2010) Phase in Optical Image Processing. In: International Conference on Advanced Phase Measurement Methods in Optics and Imaging, Monte Verità, Ascona, Switzerland, 16-21 May 2010. American Institute of Physics, Melville, N.Y. , pp. 235-240. ISBN 9780735407831

Paturzo, Melania, Memmolo, Pasquale, Finizio, Andrea, Näsänen, Risto, Naughton, Thomas J. and Ferraro, Pietro (2010) Synthesis and display of dynamic holographic 3D scenes with real-world objects. Optics Express, 19 (9). pp. 8806-8815.

Lehtimäki, Taina M., Sääskilahti, Kirsti, Pitkäaho, Tomi and Naughton, Thomas J. (2010) Comparing numerical error and visual quality in reconstructions from compressed digital holograms. SPIE Proceedings, 7690 (769012).

Darakis, Emmanouil, Khanam, Taslima, Rajendran, Arvind, Kariwala, Vinay, Naughton, Thomas J. and Asundi, Anand K. (2010) Microparticle characterization using digital holography. Chemical Engineering Sciences, 65 (2). pp. 1037-1044. ISSN 0009-2509

Lehtimäki, Taina M., Sääskilahti, Kirsti, Näsänen, Risto and Naughton, Thomas J. (2010) Visual perception of digital holograms on autostereoscopic displays. SPIE Proceedings, 7329. 73290C-1-73290C-7.

Nishchal, Naveen K., Pitkäaho, Tomi and Naughton, Thomas J. (2010) Digital Fresnel Hologram Watermarking. In: 2010 9th Euro-American Workshop on Information Optics (WIO). IEEE, pp. 1-3. ISBN 9781424482269

Paturzo, Melania, Memmolo, Pasquale, Finizio, Andrea, Näsänen, Risto, Naughton, Thomas J. and Ferraro, Pietro (2010) Holographic Display of synthetic 3D dynamic scene. 3D Research, 1 (2). pp. 31-35. ISSN 2092-6731

Molony, Karen M., Hennelly, Bryan M., Kelly, Damien P. and Naughton, Thomas J. (2010) Reconstruction algorithms applied to in-line Gabor digital holographic microscopy. Optics Communications, 283. pp. 903-909. ISSN 0030-4018

Lehtimäki, Taina M., Sääskilahti, Kirsti, Näsänen, Risto and Naughton, Thomas J. (2010) Stereo perception of reconstructions of digital holograms of real-world objects. Journal of Physics: Conference Series, 206 (012030). ISSN 1742-6588

Pitkäaho, Tomi and Naughton, Thomas J. (2010) Using disparity in digital holograms for three-dimensional object segmentation. SPIE Proceedings, 7690. 769004-1-769004-8.

Darakis, Emmanouil, Kowiel, Marcin, Näsänen, Risto and Naughton, Thomas J. (2010) Visually lossless compression of digital hologram sequences. SPIE Proceedings , 7529. 752912-1-752912-8.

Woods, Damien and Naughton, Thomas J. (2009) Optical computing. Applied Mathematics and Computation, 215 (4). pp. 1417-1430. ISSN 0096-3003

Näsänen, Risto, Metso, A., Lehtimäki, Taina M. and Naughton, Thomas J. (2009) Perceptual quality of reconstructions of digital holograms: extending depth of focus by binocular fusion. In: European Conference on Visual Perception, August 24th - 28th 2009, Regensburg, Germany.

Pandey, Nitesh, Hennelly, Bryan M., Kelly, Damien P. and Naughton, Thomas J. (2009) Speed up of Fresnel transforms for Digital holography using pre-computation. Proceedings of the China-Ireland Information and Communications Technology Conference (CIICT 2009). ISBN 9780901519672. pp. 234-236.

Kelly, Damien P., Pandey, Nitesh, Hennelly, Bryan M. and Naughton, Thomas J. (2009) Quantization noise: An additional constraint for the extended sampling theorem. OpticsInfoBase.

Darakis, Emmanouil, Kempkes, Michel, Khanam, Taslima, Rajendran, Arvind, Kariwala, Vinay, Naughton, Thomas J., Mazzotti, Marco and Asundi, Anand K. (2009) Localization of Microfibers within Volumes Using Digital Holographic Video. In: DTuB6, 26-30 April 2009, Vancouver, Canada.

Molony, Karen M. and Naughton, Thomas J. (2009) Segmentation and three-dimensional visualisation of digital in-line holographic microscopy data. In: CIICT 2009 : proceedings of the China-Ireland information and communications technologies conference. Dept. of Computer Science, National University of Ireland, Maynooth, Co. Kildare, Ireland, pp. 227-233. ISBN 9780901519672

Monaghan, David S., Situ, Guohai, Gopinathan, Unnikrishnan, Naughton, Thomas J. and Sheridan, John T. (2009) Analysis of phase encoding for optical encryption. Optics Communications, 282 (4). pp. 482-492. ISSN 0030-4018

Monaghan, David S., Gopinathan, Unnikrishnan, Kelly, Damian P., Naughton, Thomas J. and Sheridan, John T. (2009) Systematic errors of an optical encryption system due to the discrete values of a spatial light modulator. Optical Engineering, 48 (2). 027001.1-027001.7. ISSN 0091-3286

Kempkes, Michel, Darakis, Emmanouil, Khanam, Taslima, Rajendran, Arvind, Kariwala, Vinay, Mazzotti, Marco, Naughton, Thomas J. and Asundi, Anand K. (2009) Three dimensional digital holographic profiling of micro-fibers. Optics Express, 17 (4). pp. 2938-2943. ISSN 1094-4087

Darakis, Emmanouil and Naughton, Thomas J. (2009) Compression of digital hologram sequences using MPEG-4. Proceedings of SPIE, 7358.

Ryle, James P., Molony, Karen M., McDonnell, Susan, Naughton, Thomas J. and Sheridan, John T. (2009) Multispectral lensless digital holographic microscope: imaging MCF-7 and MDA-MB-231 cancer cell cultures. Proceedings of SPIE, 7442 (744206). pp. 1-11. ISSN 0277-786X

Naughton, Thomas J., Kreis,, Thomas, Onural, Levent and Ferraro, Pietro (2009) Processing of optically-captured digital holograms for three-dimensional display. SPIE Proceedings, 7329 (7329A). pp. 1-11.

Kelly, Damien P., Hennelly, Bryan M., Pandey, Nitesh, Naughton, Thomas J. and Rhodes, William T. (2009) Resolution limits in practical digital holographic systems. Optical Engineering, 48 (095801). pp. 1-13. ISSN 0091-3286

Molony, Karen M., Ryle, James P., McDonnell, Susan, Sheridan, John T. and Naughton, Thomas J. (2009) Segmentation and visualization of digital in-line holographic microscopy of three-dimensional scenes using reconstructed intensity images. Proceedings of SPIE, 7443 (74431F). pp. 1-10. ISSN 0277-786X

Pandey, Nitesh, Hennelly, Bryan M., Kelly, Damien P. and Naughton, Thomas J. (2009) Speed up of Fresnel transforms for Digital holography using pre-computed chirp and GPU processing. SPIE Proceedings, 7442.

Naughton, Thomas J., Monaghan, David S., Gopinathan, Unnikrishnan, Situ, Guohai and Sheridan, John T. (2009) Statistical investigation of the double random phase encoding technique. Journal of the Optical Society of America A., 26 (9). pp. 2033-2042. ISSN 1084-7529

Pitkäaho, Tomi and Naughton, Thomas J. (2009) Stereo vision based approach for extracting features from digital holograms. In: Fringe 2009 6th International Workshop on Advanced Optical Metrology. Springer, Berlin, pp. 562-567. ISBN 978-3-642-03050-5

Nishchal, Naveen K. and Naughton, Thomas J. (2009) Three-Dimensional Image Watermarking Using Fractional Fourier Transform. In: ICOP 2009-International Conference on Optics and Photonics CSIO, 30 October-1 November 2009, Chandigarh, India. (Unpublished)

McElhinney, Conor P., Hennelly, Bryan M., Ahrenberg, Lukas and Naughton, Thomas J. (2008) Removing the twin image in digital holography by segmented filtering of in-focus twin image. Optics & Photonics for Information Processing, 7072. pp. 707208-1.

Kelly, D.P., Hennelly, Bryan M., McElhinney, Conor P. and Naughton, Thomas J. (2008) A Practical Guide to Digital Holography and Generalized Sampling. Proceedings of SPIE, 7072. 707215.1-707215.11. ISSN 0277-786X

Gopinathan, Unnikrishnan, Monaghan, David S., Hennelly, Bryan M., McElhinney, Conor P., Kelly, Damien P., McDonald, John, Naughton, Thomas J. and Sheridan, John T. (2008) A Projection System for Real World Three-Dimensional Objects Using Spatial Light Modulators. Journal of Display Technology, 4 (2). pp. 254-261. ISSN 1551-319X

Page, Andrew J., Ahrenberg, Lukas and Naughton, Thomas J. (2008) Low memory distributed reconstruction of large digital holograms. Optics Express, 16 (3). pp. 1990-1995.

Situ, Guohai, Monaghan, David S., Naughton, Thomas J., Sheridan, John T., Pedrini, Giancarlo and Osten, Wolfgang (2008) Collision in double random phase encoding. Optics Communications, 281 (20). pp. 5122-5125. ISSN 0030-4018

Molony, Karen M., Maycock, Jonathan, McDonald, John B, Hennelly, Bryan M. and Naughton, Thomas J. (2008) A Comparison of Wavelet Analysis Techniques in Digital Holograms. Proceedings of SPIE - The International Society for Optical Engineering 6994, 6994.

Monaghan, David S., Gopinathan, Unnikrishnan, Situ, Guohai, Naughton, Thomas J. and Sheridan, John T. (2008) Cost Function Statistical Analysis in Double Random Phase Encoding. Proceedings of SPIE, 7072. 70720Z-1-70720Z-8. ISSN 0277-786X

McElhinney, Conor P., Hennelly, Bryan M. and Naughton, Thomas J. (2008) Extended focused imaging for digital holograms of macroscopic three-dimensional objects. Applied Optics, 47 (19). D71-D79. ISSN 0003-6935

McElhinney, Conor P., Hennelly, Bryan M. and Naughton, Thomas J. (2008) Focused image creation approaches for macroscopic objects encoded in digital holograms. Proceedings of SPIE, 6994. 69940U. ISSN 0277-786X

Naughton, Thomas J., Hennelly, Bryan M. and Dowling, Tom (2008) Introducing secure modes of operation for optical encryption. Journal of the the Optical Society of America A, 25 (10). pp. 2608-2617. ISSN 1084-7529

Gopinathan, Unnikrishnan, Situ, Guohai, Naughton, Thomas J. and Sheridan, John T. (2008) Noninterferometric phase retrieval using a fractional Fourier system. Journal of the Optical Society of America A, 25 (1). pp. 108-115. ISSN 1084-7529

Woods, Damien and Naughton, Thomas J. (2008) Optical Computing. In: CDMTCS Research Report Series. Centre for Discrete Mathematics and Theoretical Computer Science, pp. 307-330.

Woods, Damien and Naughton, Thomas J. (2008) Parallel and sequential optical computing. Lecture Notes in Computer Science, 5172. pp. 70-86. ISSN 0302-9743

Monaghan, David S., Situ, Guohai, Gopinathan, Unnikrishnan, Naughton, Thomas J. and Sheridan, John T. (2008) Role of phase key in the double random phase encoding technique: an error analysis. Applied Optics, 47 (21). pp. 3808-3816. ISSN 0003-6935

Page, Andrew J., Keane, Thomas M. and Naughton, Thomas J. (2008) Scheduling in a dynamic heterogeneous distributed system using estimation error. Journal of Parallel and Distributed Computing, 68 (11). pp. 1452-1462. ISSN 0743-7315

Rogers, Alan, Shorten, Robert N., Heffernan, Daniel and Naughton, Thomas J. (2008) Synthesis of piecewise-linear chaotic maps: Invariant densities, autocorrelations and switching. International Journal of Bifurcation and Chaos in Applied Sciences and Engineering, 18 (8). pp. 2169-2189. ISSN 0218-1274

McElhinney, Conor P., Hennelly, Bryan M. and Naughton, Thomas J. (2008) Twin-image Reduction in Inline Digital Holography using an Object Segmentation Heuristic. Journal of Physics: Conference Series, 139 (1). 012014-1-012014-5. ISSN 1742-6588

Keane, Thomas M., Naughton, Thomas J. and McInerney, James O. (2007) MultiPhyl: a high-throughput phylogenomics webserver using distributed computing. Nucleic Acids Research, 35 (Web Server Issue). W33-W37. ISSN 0305-1048

Shortt, Alison E., Naughton, Thomas J. and Javidi, Bahram (2007) Histogram Approaches for Lossy Compression of Digital Holograms of Three-Dimensional Objects. IEEE Transactions on Image Processing, 16 (6). pp. 1548-1556. ISSN 1057-7149

Darakis, Emmanouil, Naughton, Thomas J. and Soraghan, John J. (2007) Compression defects in different reconstructions from phase-shifting digital holographic data. Applied Optics, 46 (21). pp. 4579-4586. ISSN 1559-128X

McElhinney, Conor P., McDonald, John, Castro, Albertina, Frauel, Yann, Javidi, Bahram and Naughton, Thomas J. (2007) Depth-independent segmentation of macroscopic three-dimensional objects encoded in single perspectives of digital holograms. Optics Letters, 32 (10). pp. 1229-1231. ISSN 0146-9592

Hennelly, Bryan M., Naughton, Thomas J. and McDonald, John (2007) Digital Holographic Superresolution by Rotating the Object Wavefield. In: B. M. Hennelly, T. J. Naughton, and J. McAdaptive Optics: Analysis and Methods/Computational Optical Sensing and Imaging/Information Photonics/Signal Recovery and Synthesis Topical Meetings on CD-ROM. Optical Society of America, DTuD5. ISBN 1557528381

Murphy, Niall, Naughton, Thomas J., Woods, Damien, Henley, Beverley, McDermott, Kieran, Duffy, Elaine, van der Burgt, Peter J.M. and Woods, Niamh (2007) Implementations of a model of physical sorting. International Journal of Unconventional Computing, 4 (1). pp. 3-12. ISSN 1548-7199

Monaghan, David S., Gopinathan, Unnikrishnan, Naughton, Thomas J. and Sheridan, John T. (2007) Key-space analysis of double random phase encryption technique. Applied Optics, 26. pp. 6641-6647. ISSN 0003-6935

Maycock, Jonathan, Hennelly, Bryan M., McDonald, John, Frauel, Yann, Castro, Albertina, Javidi, Bahram and Naughton, Thomas J. (2007) Reduction of speckle in digital holography by discrete Fourier filtering. Journal of the Optical Society of America, 24 (6). pp. 1617-1622. ISSN 1084-7529

Frauel, Yann, Castro, Albertina, Naughton, Thomas J. and Javidi, Bahram (2007) Resistance of the double random phase encryption against various attacks. Optics Express, 15 (16). pp. 10253-10265. ISSN 1094-4087

McElhinney, Conor P., McDonald, John, Castro, Albertina, Frauel, Yann, Javidi, Bahram and Naughton, Thomas J. (2007) Segmentation of three-dimensional objects from background in digital holograms. In: IMVIP 2007. International Machine Vision and Image Processing Conference, 2007. IEEE, pp. 41-46. ISBN 0769528872

Maycock, Jonathan, Hennelly, Bryan M., McDonald, John, Frauel, Yann, Castro, Albertina, Javidi, Bahram and Naughton, Thomas J. (2007) Speckle Reduction Using the Discrete Fourier Filtering Technique. In: IMVIP 2007. International Machine Vision and Image Processing Conference, 2007. IEEE, p. 201. ISBN 0769528872

Hennelly, Bryan M., Naughton, Thomas J., McDonald, John, Sheridan, J. T., Unnikrishnan, G., Kelly, D.P. and Javidi, B. (2007) Spread-space spread-spectrum technique for secure multiplexing. Optics Letters, 32 (9). pp. 1060-1062. ISSN 0146-9592

Lehtimäki, Taina M. and Naughton, Thomas J. (2007) Stereoscopic viewing of digital holograms of real-world objects. In: 3DTV Conference, 2007. IEEE, pp. 1-4. ISBN 9781424407217

Keane, Thomas, Creevey, Christopher, Pentony, Melissa, Naughton, Thomas J. and McInerney, James (2006) Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC Evolutionary Biology, 6. pp. 29-46.

Murphy, Niall, Woods, Damien and Naughton, Thomas J. (2006) Bio-Computation using Holliday junctions. In: Information-MFCSIT'06 : Fourth International Conference on Information, Information'06, and the Fourth Irish Conference on the Mathematical Foundations of Computer Science and Information Technology'06, August 1-5, 2016, University College Cork. (Unpublished)

Keane, Thomas, Page, Andrew, Naughton, Thomas J., Travers, Simon and McInerney, James (2006) Building Large Phylogenetic Trees on Coarse-Grained Parallel Machines. Algorithmica, 45 (3). pp. 285-300.

Gopinathan, Unnikrishnan, Monaghan, David S., Shortt, Alison, Naughton, Thomas J., Sheridan, John T. and Javidi, Bahram (2006) Capture, encryption, compression, and display of digital holograms of three-dimensional objects. In: SPIE Proceedings. SPIE, 62521F.

Shortt, Alison, Naughton, Thomas J. and Javidi, Bahram (2006) Compression of Optically Encrypted Digital Holograms Using Artificial Neural Networks. Journal of Display Technology, 2 (4). pp. 401-410. ISSN 1551-319X

Page, Andrew J., Coyle, Shirley, Keane, Thomas M., Naughton, Thomas J., Markham, Charles and Ward, Tomas E. (2006) Distributed Monte Carlo Simulation of Light Transportation in Tissue. In: IPDPS 2006. 20th International Parallel and Distributed Processing Symposium, 2006. IEEE, pp. 1-4. ISBN 1424400546

Coyle, Shirley, Keane, Thomas M., Naughton, Thomas J., Markham, Charles and Ward, Tomas E. (2006) Distributed Monte Carlo simulation of light transportation in tissue. In: Parallel and Distributed Processing Symposium. International Parallel and Distributed Processing Symposium, Rhodes Island. ISBN 1424400546

McElhinney, Conor P., Maycock, Jonathan, Hennelly, Bryan M., Naughton, Thomas J., McDonald, John and Javidi, Bahram (2006) Extraction and reconstruction of shape information from a digital hologram of three-dimensional objects. In: IMVIP 2006 : Proceedings of the Irish Machine Vision and Image Processing Conference 2006. Vision System Group, DCU, pp. 76-83. ISBN 9780955388507

Monaghan, David S., Gopinathan, Unnikrishnan, Naughton, Thomas J. and Sheridan, J. T. (2006) A Numerical analysis of double random phase encryption. In: SPIE Proceedings. SPIE, 63110P.

Monaghan, David S., Gopinathan, Unnikrishnan, Kelly, Damien P., Naughton, Thomas J. and Sheridan, J. T. (2006) Numerical analysis of systematic errors in an optical encryption system. In: SPIE Proceedings. SPIE, 61870X.

Gopinathan, Unnikrishnan, Naughton, Thomas J. and Sheridan, John T. (2006) Polarization encoding and multiplexing of two-dimensional signals: Application to image encryption. Applied Optics, 45 (22). pp. 5693-5700. ISSN 0003-6935

Maycock, Jonathan, McElhinney, Conor P., Hennelly, Bryan M., Naughton, Thomas J., McDonald, John and Javidi, Bahram (2006) Reconstruction of partially occluded objects encoded in three-dimensional scenes by using digital holograms. Applied Optics, 45 (13). pp. 2975-2985. ISSN 0003-6935

Frauel, Yann, Naughton, Thomas J., Matoba, Osamu, Tajahuerce, Enrique and Javidi, Bahram (2006) Three-Dimensional Imaging and Processing Using Computational Holographic Imaging. Proceedings of the IEEE, 94 (3). ISSN 0018-9219

Shortt, Alison, Naughton, Thomas J. and Javidi, Bahram (2006) A companding approach for nonuniform quantization of digital holograms of three-dimensional objects. Optics Express, 14 (12). pp. 5129-5134. ISSN 1094-4087

Gopinathan, Unnikrishnan, Monaghan, David S., Naughton, Thomas J. and Sheridan, John T. (2006) A known-plaintext heuristic attack on the Fourier plane encryption algorithm. Optics Express, 14 (8). pp. 3181-3186. ISSN 1094-4087

Page, Andrew J. and Naughton, Thomas J. (2005) Framework for task scheduling in heterogeneous distributed computing using genetic algorithms. Artificial Intelligence Review, 24 (3-4). pp. 415-429.

Shortt, Alison, Naughton, Thomas J. and Javidi, Bahram (2005) Compression of encrypted digital holograms using artificial neural networks. Optics in Information Systems, 16 (2). 1, 8.

Keane, Thomas M., Page, Andrew J., McInerney, James O. and Naughton, Thomas J. (2005) A high-throughput bioinformatics distributed computing platform. In: Proceedings. 18th IEEE Symposium on Computer-Based Medical Systems, 2005. IEEE, pp. 377-382. ISBN 0769523552

Woods, Damien and Naughton, Thomas J. (2005) An optical model of computation. Theoretical Computer Science, 334. pp. 227-258.

Monaghan, David S., Gopinathan, Unnikrishnan, Hennelly, Bryan M., Kelly, Damien P., Naughton, Thomas J. and Sheridan, J. T. (2005) Applications of Spatial Light Modulators in Optical Signal Processing Systems. In: Proceedings of SPIE: Opto-Ireland 2005: Photonic Engineering, 358. SPIE Press.

Page, Andrew J., Keane, Thomas M. and Naughton, Thomas J. (2005) Bioinformatics on a Heterogeneous Java Distributed System. In: Proceedings. 19th IEEE International Parallel and Distributed Processing Symposium, 2005. IEEE Computer Society. ISBN 0769523129

Keane, T.M., Page, A.J., Naughton, Thomas J., Travers, S.A.A. and McInerney, J.O. (2005) Building large phylogenetic trees on coarse-grained parallel machines. Algorithmica. (In Press)

Shortt, Alison, Naughton, Thomas J. and Javidi, Bahram (2005) Compression of digital holograms of three-dimensional objects using the wavelet transform. Optics Express, 14 (7). pp. 2625-2630. ISSN 1094-4087

Keane, T.M., Naughton, Thomas J., Travers, S.A.A., McInerney, J.O. and McCormack, G.P. (2005) DPRml: Distributed Phylogeny Reconstruction by Maximum Likelihood. Bioinformatics, 21. pp. 969-974.

Keane, T.M., Naughton, Thomas J., Travers, S.A.A., McInerney, J.O. and McCormack, G.P. (2005) DPRml: distributed phylogeny reconstruction by maximum likelihood. Bioinformatics, 21 (7). pp. 969-974.

Keane, T.M. and Naughton, Thomas J. (2005) DSEARCH: sensitive database searching using distributed computing. Bioinformatics, 21. pp. 1705-1706.

Page, Andrew J. and Naughton, Thomas J. (2005) Dynamic task scheduling using genetic algorithms for heterogeneous distributed computing. In: IPDPS '05 Proceedings of the 19th IEEE International Parallel and Distributed Processing Symposium (IPDPS'05) - Workshop 6. IEEE, 189.1-189.8. ISBN 0769523129

Page, Andrew J. and Naughton, Thomas J. (2005) Framework for task scheduling in heterogeneous distributed computing using genetic algorithms. Artificial Intelligence Review, 24 (3-4). pp. 415-429.

Maycock, Jonathan, McElhinney, Conor P., Shortt, Alison, Naughton, Thomas J., McDonald, John, Hennelly, Bryan M., Gopinathan, Unnikrishnan, Monaghan, David S., Sheridan, John T. and Javidi, Bahram (2005) Holographic image processing of three-dimensional objects. In: Three-Dimensional TV, Video, and Display IV, Proceedings of SPIE 6016. SPIE Press.

Javidi, Bahram, Tajahuerce, Enrique, Martinez-Corral, Manuel, Naughton, Thomas J. and Frauel, Yann (2005) New developments in active and passive 3D image sensing, visualization, and processing. Proceedings of SPIE, 5986 (598601). pp. 1-11. ISSN 0277-786X

Frauel, Yann, Castro, Albertina, Naughton, Thomas J. and Javidi, Bahram (2005) Security analysis of optical encryption. Proceedings of SPIE, 5986 (598603). pp. 1-10. ISSN 0277-786X

Gopinathan, Unnikrishnan, Monaghan, David S., Naughton, Thomas J., Sheridan, J. T. and Javidi, Bahram (2005) Strengths and weaknesses of optical encryption algorithms. In: LEOS 2005. The 18th Annual Meeting of the IEEE Lasers and Electro-Optics Society, 2005. IEEE Press, New York, pp. 951-952. ISBN 0780392175

Page, Andrew, Keane, Thomas and Naughton, Thomas J. (2004) Adaptive Scheduling Across a Distributed Computation Platform. Proceedings Third International Symposium on Parallel and Distributed Computing.

Naughton, Thomas J. and Javidi, Bahram (2004) Compression of encrypted three-dimensional objects using digital holography. Optical Engineering, 43. pp. 2233-2238.

Naughton, Thomas J., McDonald, John and Javidi, Bahram (2004) Efficient Compression of Digital Holograms for Internet Transmission of Three-Dimensional Images. LEOS Newsletter: special issue on hot topics in electro-optical sensors and systems, 18 (1). pp. 9-10.

Page, Andrew J. and Naughton, Thomas J. (2004) Framework for task scheduling in heterogeneous distributed computing using genetic algorithms. In: 15th Artificial Intelligence and Cognitive Science Conference, 2004, Castlebar, Co. Mayo, Ireland.

Naughton, Thomas J., Tajahuerce, Enrique, McDonald, John and Javidi, Bahram (2004) Three-dimensional image sensing, encryption, compression, and transmission using digital holography. SPIE Proceedings, 5611. pp. 24-32.

Naughton, Thomas J., McDonald, John and Javidi, Bahram (2003) Efficient compression of Fresnel fields for Internet transmission of three-dimensional images. Applied Optics, 42 (23). pp. 4758-4764.

Keane, Thomas M., Allen, Richard, Naughton, Thomas J., McInerney, James O. and Waldron, John (2003) Distributed Java Platform with Programmable MIMD Capabilities. In: FIDJI 2002: Scientific Engineering for Distributed Java Applications. Lecture Notes in Computer Science (LNCS) (2604). Springer, pp. 122-131. ISBN 3540006796

Page, Andrew, Keane, Thomas, Allen, Richard, Naughton, Thomas J. and Waldron, John (2003) Multi-tiered distributed computing platform. In: UNSPECIFIED.

Naughton, Thomas J., Frauel, Yann, Javidi, Bahram and Tajahuerce, Enrique (2002) Compression of digital holograms for three-dimensional object reconstruction and recognition. Applied Optics, 41 (20). pp. 4124-4132.

Keane, Thomas M., Allen, Richard, Naughton, Thomas J., McInerney, James O. and Waldron, John (2002) Distributed computing for DNA analysis. In: PPPJ '02/IRE '02 Proceedings of the inaugural conference on the Principles and Practice of programming, 2002 and Proceedings of the second workshop on Intermediate representation engineering for virtual machines, 2002. National University of Ireland Maynooth, pp. 65-70. ISBN 0901519871

Delaney, Aidan and Naughton, Thomas J. (2002) Emulation of an unconventional model of computation in Java. In: PPPJ '02/IRE '02 Proceedings of the inaugural conference on the Principles and Practice of programming, 2002 and Proceedings of the second workshop on Intermediate representation engineering for virtual machines, 2002. National University of Ireland Maynooth, pp. 1-6. ISBN 0901519871

Matoba, Osamu, Naughton, Thomas J., Frauel, Yann, Bertaux, Nicolas and Javidi, Bahram (2002) Real-time three-dimensional object reconstruction by use of a phase-encoded digital hologram. Applied Optics, 41 (29). pp. 6187-6192. ISSN 1559-128X

Matoba, Osamu, Naughton, Thomas J., Frauel, Yann, Bertaux, Nicolas and Javidi, Bahram (2002) Three-dimensional object reconstruction using phase-only information from a digital hologram. Proceedings of SPIE, 4864. pp. 122-128. ISSN 0277-786X

Naughton, Thomas J. and Woods, Damien (2001) On the Computational Power of a Continuous-Space Optical Model of Computation. In: MCU 2001: Machines, Computations, and Universality. Lecture Notes in Computer Science book series (LNCS) (2055). Springer, pp. 288-299. ISBN 3540421211

Naughton, Thomas J. (2000) Continuous-space model of computation is Turing universal. Proceedings of SPIE, 4109. pp. 121-128. ISSN 0277-786X

Naughton, Thomas J. (2000) Fourier optical limits of coherent acousto-optic matrix-vector processor. Proceedings of SPIE, 4089. pp. 181-190. ISSN 0277-786X

Naughton, Thomas J. (2000) Model of computation for Fourier optical processors. Proceedings of SPIE, 4089. pp. 24-34. ISSN 0277-786X

Naughton, Thomas J., Javadpour, Zohreh, Keating, John, Klima, Milos and Rott, Jiri (1999) General-purpose acousto-optic connectionist processor. Optical Engineering, 38 (7). pp. 1170-1177. ISSN 0091-3286

Klima, Milos, Rott, Jiri, Naughton, Thomas J. and Keating, John (1997) Joint transform correlation in security applications. In: Proceedings. The Institute of Electrical and Electronics Engineers 31st Annual 1997 International Carnahan Conference on Security Technology, 1997. IEEE, pp. 77-81. ISBN 0780339134