TY - JOUR AU - Bissell, M. J. AU - Hines, W. C. PY - 2011 DA - 2011// TI - Why don’t we get more cancer? A proposed role of the microenvironment in restraining cancer progression JO - Nat Med VL - 17 UR - https://doi.org/10.1038/nm.2328 DO - 10.1038/nm.2328 ID - Bissell2011 ER - TY - JOUR AU - Harjanto, D. AU - Zaman, M. H. PY - 2010 DA - 2010// TI - Matrix mechanics and receptor-ligand interactions in cell adhesion JO - Org Biomol Chem VL - 8 UR - https://doi.org/10.1039/B913064K DO - 10.1039/B913064K ID - Harjanto2010 ER - TY - JOUR AU - Sutherland, R. M. PY - 1988 DA - 1988// TI - Cell and environment interactions in tumor microregions: the multicell spheroid model JO - Science VL - 240 UR - https://doi.org/10.1126/science.2451290 DO - 10.1126/science.2451290 ID - Sutherland1988 ER - TY - JOUR AU - Day, R. N. AU - Schaufele, F. PY - 2005 DA - 2005// TI - Imaging molecular interactions in living cells JO - Mol Endocrinol VL - 19 UR - https://doi.org/10.1210/me.2005-0028 DO - 10.1210/me.2005-0028 ID - Day2005 ER - TY - JOUR AU - Ponomarev, V. PY - 2009 DA - 2009// TI - Nuclear imaging of cancer cell therapies JO - J Nucl Med VL - 50 UR - https://doi.org/10.2967/jnumed.109.064055 DO - 10.2967/jnumed.109.064055 ID - Ponomarev2009 ER - TY - JOUR AU - Eliceiri, K. W. AU - Berthold, M. R. AU - Goldberg, I. G. AU - Ibáñez, L. AU - Manjunath, B. S. AU - Martone, M. E. PY - 2012 DA - 2012// TI - Biological imaging software tools JO - Nat Methods VL - 9 UR - https://doi.org/10.1038/nmeth.2084 DO - 10.1038/nmeth.2084 ID - Eliceiri2012 ER - TY - BOOK AU - Pawley, J. PY - 2006 DA - 2006// TI - Handbook of Biological Confocal Microscopy PB - Springer Science+Business Media, LLC CY - New York UR - https://doi.org/10.1007/978-0-387-45524-2 DO - 10.1007/978-0-387-45524-2 ID - Pawley2006 ER - TY - JOUR AU - Lou, X. AU - Kang, M. AU - Xenopoulos, P. AU - Muñoz-Descalzo, S. AU - Hadjantonakis, A. -. K. PY - 2014 DA - 2014// TI - A rapid and efficient 2D/3D nuclear segmentation method for analysis of early mouse embryo and stem cell image data JO - Stem Cell Reports VL - 2 UR - https://doi.org/10.1016/j.stemcr.2014.01.010 DO - 10.1016/j.stemcr.2014.01.010 ID - Lou2014 ER - TY - JOUR AU - Huisken, J. AU - Swoger, J. AU - Bene, F. AU - Wittbrodt, J. AU - Stelzer, E. H. K. PY - 2004 DA - 2004// TI - Optical sectioning deep inside live embryos by selective plane illumination microscopy JO - Science VL - 305 UR - https://doi.org/10.1126/science.1100035 DO - 10.1126/science.1100035 ID - Huisken2004 ER - TY - JOUR AU - Greger, K. AU - Swoger, J. AU - Stelzer, E. H. K. PY - 2007 DA - 2007// TI - Basic building units and properties of a fluorescence single plane illumination microscope JO - Rev Sci Instrum VL - 78 UR - https://doi.org/10.1063/1.2428277 DO - 10.1063/1.2428277 ID - Greger2007 ER - TY - JOUR AU - Stelzer, E. H. K. PY - 2014 DA - 2014// TI - Light-sheet fluorescence microscopy for quantitative biology JO - Nat Methods VL - 12 UR - https://doi.org/10.1038/nmeth.3219 DO - 10.1038/nmeth.3219 ID - Stelzer2014 ER - TY - BOOK AU - Pampaloni, F. AU - Richa, R. AU - Ansari, N. AU - Stelzer, E. H. K. PY - 2015 DA - 2015// TI - Advanced Fluorescence Microscopy, Methods and Protocols PB - Springer Science+Business Media, LLC CY - New York ID - Pampaloni2015 ER - TY - JOUR AU - Strobl, F. AU - Stelzer, E. H. K. PY - 2014 DA - 2014// TI - Non-invasive long-term fluorescence live imaging of Tribolium castaneum embryos JO - Development VL - 141 UR - https://doi.org/10.1242/dev.108795 DO - 10.1242/dev.108795 ID - Strobl2014 ER - TY - JOUR AU - Keller, P. J. AU - Stelzer, E. H. K. PY - 2008 DA - 2008// TI - Quantitative in vivo imaging of entire embryos with digital scanned laser light sheet fluorescence microscopy JO - Curr Opin Neurobiol VL - 18 UR - https://doi.org/10.1016/j.conb.2009.03.008 DO - 10.1016/j.conb.2009.03.008 ID - Keller2008 ER - TY - JOUR AU - Malpica, N. AU - Solórzano, C. O. AU - Vaquero, J. J. AU - Santos, A. AU - Vallcorba, I. AU - García-Sagredo, J. M. PY - 1997 DA - 1997// TI - Applying watershed algorithms to the segmentation of clustered nuclei JO - Cytometry VL - 28 UR - https://doi.org/3.0.CO;2-7 DO - 3.0.CO;2-7 ID - Malpica1997 ER - TY - JOUR AU - Gniadek, T. J. AU - Warren, G. PY - 2007 DA - 2007// TI - WatershedCounting3D: a new method for segmenting and counting punctate structures from confocal image data JO - Traffic VL - 8 UR - https://doi.org/10.1111/j.1600-0854.2007.00538.x DO - 10.1111/j.1600-0854.2007.00538.x ID - Gniadek2007 ER - TY - STD TI - Wählby C, Bengtsson E. Segmentation of cell nuclei in tissue by combining seeded watersheds with gradient information. Springer Verlag Berlin Heidelb. 2003;408–414. ID - ref17 ER - TY - JOUR AU - Al-Kofahi, Y. AU - Lassoued, W. AU - Lee, W. AU - Roysam, B. PY - 2010 DA - 2010// TI - Improved automatic detection and segmentation of cell nuclei in histopathology images JO - IEEE Trans Biomed Eng VL - 57 UR - https://doi.org/10.1109/TBME.2009.2035102 DO - 10.1109/TBME.2009.2035102 ID - Al-Kofahi2010 ER - TY - JOUR AU - Qi, J. PY - 2014 DA - 2014// TI - Dense nuclei segmentation based on graph cut and convexity-concavity analysis JO - J Microsc VL - 253 UR - https://doi.org/10.1111/jmi.12096 DO - 10.1111/jmi.12096 ID - Qi2014 ER - TY - JOUR AU - Sommer, C. AU - Straehle, C. AU - Kothe, U. AU - Hamprecht, F. A. PY - 2011 DA - 2011// TI - Ilastik: Interactive learning and segmentation toolkit JO - IEEE Int Symp Biomed Imaging From Nano to Macro VL - 2011 ID - Sommer2011 ER - TY - STD TI - Chen C, Wang W, Ozolek JA, Lages N, Altschuler SJ, Wu LF, Rohde GK. A template matching approach for segmenting microscopy images. In International Symposium on Biomedical Imaging; 2012:768–771. ID - ref21 ER - TY - JOUR AU - Li, G. AU - Liu, T. AU - Tarokh, A. AU - Nie, J. AU - Guo, L. AU - Mara, A. PY - 2007 DA - 2007// TI - 3D cell nuclei segmentation based on gradient flow tracking JO - BMC Cell Biol VL - 8 UR - https://doi.org/10.1186/1471-2121-8-40 DO - 10.1186/1471-2121-8-40 ID - Li2007 ER - TY - JOUR AU - Delgado-Gonzalo, R. AU - Chenouard, N. AU - Unser, M. PY - 2013 DA - 2013// TI - Spline-based deforming ellipsoids for interactive 3D bioimage segmentation JO - IEEE Trans Image Process VL - 22 UR - https://doi.org/10.1109/TIP.2013.2264680 DO - 10.1109/TIP.2013.2264680 ID - Delgado-Gonzalo2013 ER - TY - CHAP AU - Harder, N. AU - Bodnar, M. AU - Eils, R. AU - Spector, D. L. AU - Rohr, K. PY - 2011 DA - 2011// TI - 3D segmentation and quantification of mouse embryonic stem cells in fluorescence microscopy images BT - Bildverarbeitung für die Medizin PB - Springer CY - Berlin Heidelberg ID - Harder2011 ER - TY - JOUR AU - Yu, D. AU - Pham, T. D. AU - Zhou, X. PY - 2009 DA - 2009// TI - Analysis and recognition of touching cell images based on morphological structures JO - Comput Biol Med VL - 39 UR - https://doi.org/10.1016/j.compbiomed.2008.10.006 DO - 10.1016/j.compbiomed.2008.10.006 ID - Yu2009 ER - TY - JOUR AU - Zhong, Q. AU - Zhou, P. AU - Yao, Q. AU - Mao, K. PY - 2009 DA - 2009// TI - A novel segmentation algorithm for clustered slender-particles JO - Comput Electron Agric VL - 69 UR - https://doi.org/10.1016/j.compag.2009.06.015 DO - 10.1016/j.compag.2009.06.015 ID - Zhong2009 ER - TY - JOUR AU - Chen, L. AU - Chan, L. L. H. AU - Zhao, Z. AU - Yan, H. PY - 2013 DA - 2013// TI - A novel cell nuclei segmentation method for 3D C. elegans embryonic time-lapse images JO - BMC Bioinformatics VL - 14 UR - https://doi.org/10.1186/1471-2105-14-328 DO - 10.1186/1471-2105-14-328 ID - Chen2013 ER - TY - STD TI - Mikula K, Remesiková M, Stasová O, Peyriéras N. Segmentation and analysis of 3D zebrafish cell image data. In International Congress on Image and Signal Processing; 2010:1444–48. ID - ref28 ER - TY - JOUR AU - Keller, P. J. AU - Schmidt, A. D. AU - Wittbrodt, J. AU - Stelzer, E. H. K. PY - 2008 DA - 2008// TI - Reconstruction of zebrafish early light sheet microscopy JO - Science VL - 322 UR - https://doi.org/10.1126/science.1162493 DO - 10.1126/science.1162493 ID - Keller2008 ER - TY - JOUR AU - Indhumathi, C. AU - Cai, Y. Y. AU - Guan, Y. Q. AU - Opas, M. PY - 2011 DA - 2011// TI - An automatic segmentation algorithm for 3D cell cluster splitting using volumetric confocal images JO - J Microsc VL - 243 UR - https://doi.org/10.1111/j.1365-2818.2010.03482.x DO - 10.1111/j.1365-2818.2010.03482.x ID - Indhumathi2011 ER - TY - JOUR AU - Zanella, C. AU - Campana, M. AU - Rizzi, B. AU - Melani, C. AU - Sanguinetti, G. AU - Bourgine, P. PY - 2009 DA - 2009// TI - Cells segmentation from 3-D confocal images of early zebrafish embryogenesis JO - IEEE Trans Image Process VL - 19 UR - https://doi.org/10.1109/TIP.2009.2033629 DO - 10.1109/TIP.2009.2033629 ID - Zanella2009 ER - TY - JOUR AU - Bashar, M. K. AU - Yamagata, K. AU - Kobayashi, T. J. PY - 2014 DA - 2014// TI - Improved and robust detection of cell nuclei from four dimensional fluorescence images JO - PLoS One VL - 9 UR - https://doi.org/10.1371/journal.pone.0101891 DO - 10.1371/journal.pone.0101891 ID - Bashar2014 ER - TY - JOUR AU - Bilgin, C. C. AU - Kim, S. AU - Leung, E. AU - Chang, H. AU - Parvin, B. PY - 2013 DA - 2013// TI - Integrated profiling of three dimensional cell culture models and 3D microscopy JO - Bioinformatics VL - 29 UR - https://doi.org/10.1093/bioinformatics/btt535 DO - 10.1093/bioinformatics/btt535 ID - Bilgin2013 ER - TY - STD TI - Lien J, Amato NM. Approximate convex decomposition of polyhedra. In ACM symposium on Solid and physical modeling; 2006:121–131. ID - ref34 ER - TY - JOUR AU - Attene, M. AU - Mortara, M. AU - Spagnuolo, M. AU - Falcidieno, B. PY - 2008 DA - 2008// TI - Hierarchical convex approximation of 3D shapes for fast region selection JO - Comput Graph Forum VL - 27 UR - https://doi.org/10.1111/j.1467-8659.2008.01271.x DO - 10.1111/j.1467-8659.2008.01271.x ID - Attene2008 ER - TY - JOUR AU - Asafi, S. AU - Goren, A. AU - Cohen-Or, D. PY - 2013 DA - 2013// TI - Weak Convex Decomposition by Lines-of-sight JO - Comput Graph Forum VL - 32 UR - https://doi.org/10.1111/cgf.12169 DO - 10.1111/cgf.12169 ID - Asafi2013 ER - TY - JOUR AU - Ward, J. J. H. PY - 1963 DA - 1963// TI - Hierarchical Grouping to Optimize an Objective Function JO - J Am Stat Assoc VL - 58 UR - https://doi.org/10.1080/01621459.1963.10500845 DO - 10.1080/01621459.1963.10500845 ID - Ward1963 ER - TY - STD TI - Plugin for auto local threshold (ImageJ). [http://fiji.sc/wiki/index.php/Auto_Local_Threshold] UR - http://fiji.sc/wiki/index.php/Auto_Local_Threshold ID - ref38 ER - TY - STD TI - Physikalische Biologie. [https://www.physikalischebiologie.de/downloads] UR - https://www.physikalischebiologie.de/downloads ID - ref39 ER - TY - STD TI - FARSight. [http://www.farsight-toolkit.org] UR - http://www.farsight-toolkit.org ID - ref40 ER - TY - STD TI - 3D ImageJ Suite. [http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:3d_ij_suite:start] UR - http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:3d_ij_suite:start ID - ref41 ER - TY - JOUR AU - Ollion, J. AU - Cochennec, J. AU - Loll, F. AU - Escudé, C. AU - Boudier, T. PY - 2013 DA - 2013// TI - TANGO: A generic tool for high-throughput 3D image analysis for studying nuclear organization JO - Bioinformatics VL - 29 UR - https://doi.org/10.1093/bioinformatics/btt276 DO - 10.1093/bioinformatics/btt276 ID - Ollion2013 ER - TY - STD TI - ilastik. [http://ilastik.org/] UR - http://ilastik.org/ ID - ref43 ER - TY - JOUR AU - Song, Y. AU - Cai, W. AU - Huang, H. AU - Wang, Y. AU - Feng, D. D. AU - Chen, M. PY - 2013 DA - 2013// TI - Region-based progressive localization of cell nuclei in microscopic images with data adaptive modeling JO - BMC Bioinformatics VL - 14 UR - https://doi.org/10.1186/1471-2105-14-173 DO - 10.1186/1471-2105-14-173 ID - Song2013 ER - TY - JOUR AU - Meijering, E. AU - Dzyubachyk, O. AU - Smal, I. PY - 2012 DA - 2012// TI - Methods for cell and particle tracking JO - Methods Enzymol VL - 504 UR - https://doi.org/10.1016/B978-0-12-391857-4.00009-4 DO - 10.1016/B978-0-12-391857-4.00009-4 ID - Meijering2012 ER - TY - JOUR AU - Bai, X. AU - Sun, C. AU - Zhou, F. PY - 2009 DA - 2009// TI - Splitting touching cells based on concave points and ellipse fitting JO - Pattern Recognit VL - 42 UR - https://doi.org/10.1016/j.patcog.2009.04.003 DO - 10.1016/j.patcog.2009.04.003 ID - Bai2009 ER - TY - JOUR AU - Latorre, A. AU - Alonso-Nanclares, L. AU - Muelas, S. AU - Peña, J. -. M. AU - Defelipe, J. PY - 2013 DA - 2013// TI - 3D segmentations of neuronal nuclei from confocal microscope image stacks JO - Front Neuroanat VL - 7 UR - https://doi.org/10.3389/fnana.2013.00049 DO - 10.3389/fnana.2013.00049 ID - Latorre2013 ER - TY - JOUR AU - Pampaloni, F. AU - Reynaud, E. G. AU - Stelzer, E. H. K. PY - 2007 DA - 2007// TI - The third dimension bridges the gap between cell culture and live tissue JO - Nat Rev Mol Cell Biol VL - 8 UR - https://doi.org/10.1038/nrm2236 DO - 10.1038/nrm2236 ID - Pampaloni2007 ER - TY - JOUR AU - Schrode, N. AU - Xenopoulos, P. AU - Piliszek, A. AU - Frankenberg, S. AU - Plusa, B. AU - Hadjantonakis, A. -. K. PY - 2013 DA - 2013// TI - Anatomy of a blastocyst: cell behaviors driving cell fate choice and morphogenesis in the early mouse embryo JO - Genesis VL - 51 UR - https://doi.org/10.1002/dvg.22368 DO - 10.1002/dvg.22368 ID - Schrode2013 ER -