My Bibliography

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Extracting meaning from biological imaging data. Molecular biology of the cell. . NIHMSID: NIHMS639422.

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Extracting meaning from biological imaging data. Molecular biology of the cell. . NIHMSID: NIHMS639422.

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Wait, Eric, Winter, Mark, Song, Shihao, Monteleone, David, Stern, Josh, Bjornsson, Chris, Goderie, Susan, Temple, Sally, Cohen, Andrew. Collaborative Visualization in the Browser for Segmentation, Tracking, and Lineaging with 5-D Biological Microscopy Images. .

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Joshi, Rohini, Swaminathan, Sundar Ram, Winter, Mark, Saini, Janmeet S, Blenkinsop, Timothy A, Stern, Jeffrey, Temple, Sally, Cohen, Andrew R. Measuring visual structure in phase and fluorescence microscopy using image compression. .

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Wait, Eric, Mankowski, Walter, Winter, Mark, Kan, Andrey, Heinzel, Susanne, Oostindie, Simone, Hodgkin, Philip D, Goderie, Susan, Apostolopoulou, Maria, Bjornsson, Chris S, others. Segmentation, Tracking and Lineaging of Proliferating Cells from 2-D to 5-D. .

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Roysam, Badrinath, Cohen, Andrew, Getto, Philip, Boyce, Peter. A numerical approach to the computation of light propagation through turbid media: Application to the evaluation of lighted exit signs. 1991 IEEE Industry Application Society Annual Meeting. 1991; c1991.

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Roysam, Badrinath, Cohen, AR, Getto, PH, Boyce, PR. A numerical approach to the computation of light propagation through turbid media: Application to the evaluation of lighted exit signs. IEEE transactions on industry applications. 1993; 29(3):661--669.

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Roysam, B, Bhattacharjya, AK, Ancin, H, Cohen, AR. Intelligent computational 3-D microscopy: New results in segmentation, noise removal, cell counting, and automated neuron tracing. PROCEEDINGS OF THE ANNUAL MEETING-ELECTRON MICROSCOPY SOCIETY OF AMERICA; 1993; c1993.

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Roysam, Badrinath, Bhattacharjya, Anoop K., Ancin, Hakan, Cohen, Andrew R., Mackin, Robert W., Becker, Douglas E., Rodriguez, Carlos. Intelligent computational 3-D microscopy: new results in segmentation, noise removal, cell counting, and automated neuron tracing. Proceedings - Annual Meeting, Microscopy Society of America. 1993; c1993.

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Roysam B, Cohen A, Getto P, Boyce P. A numerical approach to the computation of light propagation through turbid media: application to the evaluation of lighted exit signs. IEEE Transactions on Industry Applications. 1993-Ma; 29(3):661-669. doi: 10.1109/28.222442.

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Cohen, AR, Roysam, B, Turner, JN. Automated tracing and volume measurements of neurons from 3-D confocal fluorescence microscopy data. Journal of microscopy. 1994; 173(2):103--114.

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COHEN A, ROYSAM B, TURNER J. Automated tracing and volume measurements of neurons from 3-D confocal fluorescence microscopy data. Journal of Microscopy. 1994 February; 173(2):103-114. doi: 10.1111/j.1365-2818.1994.tb03433.x.

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He, Wenyun, Hamilton, Thomas A, Cohen, Andrew R, Holmes, Timothy J, Pace, Christopher, Szarowski, Donald H, Turner, James N, Roysam, Badrinath. Automated three-dimensional tracing of neurons in confocal and brightfield images. Microscopy and microanalysis. 2003; 9(4):296--310.

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He W, Hamilton TA, Cohen AR, Holmes TJ, Pace C, Szarowski DH, Turner JN, Roysam B. Automated three-dimensional tracing of neurons in confocal and brightfield images. Microsc Microanal. 2003 Aug;9(4):296-310. doi: 10.1017/S143192760303040X. PubMed PMID: 12901764.

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He W, Hamilton T, Cohen A, Holmes T, Pace C, Szarowski D, Turner J, Roysam B. Automated Three-Dimensional Tracing of Neurons in Confocal and Brightfield Images. Microscopy and Microanalysis. 2003 August; 9(4):296-310. doi: 10.1017/S143192760303040X.

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Cohen, Andrew, Crouch, Scott. System and method for caching and rendering images. 2005 March.

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Cohen, Andrew, Crouch, Scott. System and method for caching and rendering images. 2005 March.

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Cohen, Andrew R. A Generalized Architecture for Unsupervised Summarization of Change in Image Sequences Via Algorithmic Complexity, 2006. Research Thrust R2 Presentations. 2007; :2.

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Cohen, Andrew R. A Generalized Architecture for Unsupervised Summarization of Change in Image Sequences Via Algorithmic Complexity, 2006--REMOVED FROM VIEW AT THE DISCRETION OF NORTHEASTERN UNIVERSITY LIBRARIES-12/11/07. 2007.

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Cohen, Andrew R, Bjornsson, Christopher, Chen, Ying, Banker, Gary, Ladi, Ena, Robey, Ellen, Temple, Sally, Roysam, Badrinath. Automatic summarization of changes in image sequences using algorithmic information theory. Biomedical Imaging: From Nano to Macro, 2008. ISBI 2008. 5th IEEE International Symposium on; 2008; c2008.

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Cohen, Andrew R. Summarizing changes in image sequences using algorithmic information theory. 2008.

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Cohen A, Bjornsson C, Ying Chen, Banker G, Ladi E, Robey E, Temple S, Roysam B. Automatic summarization of changes in image sequences using algorithmic information theory. 2008 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro. 2008 5th IEEE International Symposium on Biomedical Imaging (ISBI 2008); ; Paris, France. IEEE; c2008.

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Mukherjee, Amit, Cohen, Andrew, Roysam, Badrinath, Jenkins, Brian, Fang, Cheng, Petrie, S Kaech, Banker, Gary. Automated methods for profiling the axonal transport of secretory bdnf granules in live cultured neurons from time-lapse microscopy data. Microscopy and Microanalysis. 2009; 15(S2):832.

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Cohen, Andrew R, Bjornsson, Christopher S, Temple, Sally, Banker, Gary, Roysam, Badrinath. Automatic summarization of changes in biological image sequences using algorithmic information theory. IEEE transactions on pattern analysis and machine intelligence. 2009; 31(8):1386--1403.

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Mukherjee A, Cohen A, Roysam B, Jenkins B, Fang C, Petrie S, Banker G. Automated Methods for Profiling the Axonal Transport of Secretory BDNF Granules in Live Cultured Neurons from Time-lapse Microscopy Data. Microscopy and Microanalysis. 2009 July; 15(S2):832-833. doi: 10.1017/S1431927609096809.

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Cohen AR, Bjornsson CS, Temple S, Banker G, Roysam B. Automatic summarization of changes in biological image sequences using algorithmic information theory. IEEE Trans Pattern Anal Mach Intell. 2009 Aug;31(8):1386-403. doi: 10.1109/TPAMI.2008.162. PubMed PMID: 19542574.

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Cohen A, Bjornsson C, Temple S, Banker G, Roysam B. Automatic Summarization of Changes in Biological Image Sequences Using Algorithmic Information Theory. IEEE Transactions on Pattern Analysis and Machine Intelligence. 2009 August; 31(8):1386-1403. doi: 10.1109/TPAMI.2008.162.

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Cohen, Andrew R, Gomes, Francisco LAF, Roysam, Badrinath, Cayouette, Michel. Computational prediction of neural progenitor cell fates. Nature methods. 2010; 7(3):213--218.

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Cohen A, Gomes F, Roysam B, Cayouette M. Computational prediction of neural progenitor cell fates. Nature Methods. 2010-2-; 7(3):213-218. doi: 10.1038/nmeth.1424.

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Cohen AR, Gomes FL, Roysam B, Cayouette M. Computational prediction of neural progenitor cell fates. Nat Methods. 2010 Mar;7(3):213-8. doi: 10.1038/nmeth.1424. Epub 2010 Feb 7. PubMed PMID: 20139969.

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Clark, Brian S, Winter, Mark, Cohen, Andrew R, Link, Brian A. Generation of Rab-based transgenic lines for in vivo studies of endosome biology in zebrafish. Developmental dynamics. 2011; 240(11):2452--2465.

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Winter, Mark, Wait, Eric, Roysam, Badrinath, Goderie, Susan K, Ali, Rania Ahmed Naguib, Kokovay, Erzsebet, Temple, Sally, Cohen, Andrew R. Vertebrate neural stem cell segmentation, tracking and lineaging with validation and editing. Nature Protocols. 2011; 6(12):1942--1952.

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Clark BS, Winter M, Cohen AR, Link BA. Generation of Rab-based transgenic lines for in vivo studies of endosome biology in zebrafish. Dev Dyn. 2011 Nov;240(11):2452-65. doi: 10.1002/dvdy.22758. Epub 2011 Oct 4. PubMed PMID: 21976318; PubMed Central PMCID: PMC3197968.

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Clark B, Winter M, Cohen A, Link B. Generation of Rab-based transgenic lines for in vivo studies of endosome biology in zebrafish. Developmental Dynamics. 2011 November; 240(11):2452-2465. doi: 10.1002/dvdy.22758.

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Winter M, Wait E, Roysam B, Goderie SK, Ali RA, Kokovay E, Temple S, Cohen AR. Vertebrate neural stem cell segmentation, tracking and lineaging with validation and editing. Nat Protoc. 2011 Nov 17;6(12):1942-52. doi: 10.1038/nprot.2011.422. PubMed PMID: 22094730; PubMed Central PMCID: PMC3313840.

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Winter M, Wait E, Roysam B, Goderie S, Ali R, Kokovay E, Temple S, Cohen A. Vertebrate neural stem cell segmentation, tracking and lineaging with validation and editing. Nature Protocols. 2011 November; 6(12):1942-1952. doi: 10.1038/nprot.2011.422.

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Winter M, Fang C, Banker G, Roysam B, Cohen A. Axonal transport analysis using Multitemporal Association Tracking. International Journal of Computational Biology and Drug Design. 2012; 5(1):35-. doi: 10.1504/IJCBDD.2012.045950.

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Winter, Mark R, Fang, Cheng, Banker, Gary, Roysam, Badrinath, Cohen, Andrew R. Axonal transport analysis using multitemporal association tracking. International journal of computational biology and drug design. 2012; 5(1):35--48.

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Winter MR, Fang C, Banker G, Roysam B, Cohen AR. Axonal transport analysis using Multitemporal Association Tracking. Int J Comput Biol Drug Des. 2012;5(1):35-48. doi: 10.1504/IJCBDD.2012.045950. Epub 2012 Mar 21. PubMed PMID: 22436297; PubMed Central PMCID: PMC3380808.

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Cohen, Andrew R, Vit\'anyi, Paul MB. Normalized Google Distance of Multisets with Applications. arXiv preprint arXiv:1308.3177. 2013.

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Mankowski WC, Winter MR, Wait E, Lodder M, Schumacher T, Naik SH, Cohen AR. Segmentation of occluded hematopoietic stem cells from tracking. Annu Int Conf IEEE Eng Med Biol Soc. 2014;2014:5510-3. doi: 10.1109/EMBC.2014.6944874. PubMed PMID: 25571242; PubMed Central PMCID: PMC4324458.

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Koerner M, Wait E, Winter M, Bjornsson C, Kokovay E, Wang Y, Goderie SK, Temple S, Cohen AR. Multisensory interface for 5D stem cell image volumes. Annu Int Conf IEEE Eng Med Biol Soc. 2014;2014:1178-81. doi: 10.1109/EMBC.2014.6943806. PubMed PMID: 25570174; PubMed Central PMCID: PMC4321857.

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Cohen, Andrew R. Extracting meaning from biological imaging data. Molecular biology of the cell. 2014; 25(22):3470--3473.

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Koerner, Michael, Wait, Eric, Winter, Mark, Bjornsson, Chris, Kokovay, Erzsebet, Wang, Yue, Goderie, Susan K, Temple, Sally, Cohen, Andrew R. Multisensory interface for 5D stem cell image volumes. Engineering in Medicine and Biology Society (EMBC), 2014 36th Annual International Conference of the IEEE; 2014; c2014.

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Chenouard, Nicolas, Smal, Ihor, De Chaumont, Fabrice, Ma\vska, Martin, Sbalzarini, Ivo F, Gong, Yuanhao, Cardinale, Janick, Carthel, Craig, Coraluppi, Stefano, Winter, Mark, others. Objective comparison of particle tracking methods. Nature methods. 2014; 11(3):281--289.

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Mankowski, Walter C, Winter, Mark R, Wait, Eric, Lodder, Mels, Schumacher, Ton, Naik, Shalin H, Cohen, Andrew R. Segmentation of occluded hematopoietic stem cells from tracking. Engineering in Medicine and Biology Society (EMBC), 2014 36th Annual International Conference of the IEEE; 2014; c2014.

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Alagoz, Celal, Cohen, Andrew R, Guez, Allon, Bullinga, John. Spiral wave clustering using normalized compression distance. Computing in Cardiology Conference (CinC), 2014; 2014; c2014.

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Alagoz, C., Cohen, A.R., Guez, A., Bullinga, J.. Spiral wave clustering using normalized compression distance. Computing in Cardiology. Computing in Cardiology; 2014; c2014.

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Koerner, M., Wait, E., Winter, M., Cohen, A.R., Dion, G.. The exo-skin soft haptic exoskeletal interface. Fiber Society 2014 Fall Meeting and Technical Conference: Fibers for the Future. Fiber Society 2014 Fall Meeting and Technical Conference: Fibers for the Future; 2014; c2014.

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Wait, Eric, Winter, Mark, Bjornsson, Chris, Kokovay, Erzsebet, Wang, Yue, Goderie, Susan, Temple, Sally, Cohen, Andrew R. Visualization and correction of automated segmentation, tracking and lineaging from 5-D stem cell image sequences. BMC bioinformatics. 2014; 15(1):328.