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Volumn 16, Issue 1, 2015, Pages

Survey statistics of automated segmentations applied to optical imaging of mammalian cells

Author keywords

Accelerated execution of segmentation for high throughput biological application; Cell segmentation; Cellular measurements; Segmentation evaluation; Segmented objects

Indexed keywords

AUTOMATION; C (PROGRAMMING LANGUAGE); CYTOLOGY; HTTP; MAMMALS; OPTICAL IMAGE STORAGE; OPTICAL MICROSCOPY; PAPER; SCAFFOLDS (BIOLOGY); STATISTICS; STEM CELLS; SURVEYS; WEBSITES;

EID: 84944402905     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/s12859-015-0762-2     Document Type: Article
Times cited : (40)

References (169)
  • 1
    • 65649084852 scopus 로고    scopus 로고
    • Live cell imaging for target and drug discovery
    • Watson P. Live cell imaging for target and drug discovery. Drug News Perspect. 2009;22(2):69-79.
    • (2009) Drug News Perspect , vol.22 , Issue.2 , pp. 69-79
    • Watson, P.1
  • 3
    • 34547564349 scopus 로고    scopus 로고
    • Preclinical medical student training in radiology: the effect of early exposure
    • Branstetter BF, Faix LE, Humphrey A, Schumann J. Preclinical medical student training in radiology: the effect of early exposure. Am J Roentgenol (AJR). 2007;188:W9-14.
    • (2007) Am J Roentgenol (AJR) , vol.188 , pp. W9-14
    • Branstetter, B.F.1    Faix, L.E.2    Humphrey, A.3    Schumann, J.4
  • 5
    • 84991837501 scopus 로고    scopus 로고
    • Cell Stains
    • Cell Stains [ http://www.lifetechnologies.com/order/catalog/en/US/adirect/lt?cmd=IVGNcatDisplayCategory&catKey=68901 )].
  • 6
    • 4243089813 scopus 로고    scopus 로고
    • A new classification scheme of science fields and subfields designed for scientometric evaluation purposes
    • Glanzel W, Schubert A. A new classification scheme of science fields and subfields designed for scientometric evaluation purposes. Scientometrics. 2003;56:357-67.
    • (2003) Scientometrics , vol.56 , pp. 357-367
    • Glanzel, W.1    Schubert, A.2
  • 7
    • 55349134773 scopus 로고    scopus 로고
    • Fraunhofer-Institut für Techno- undWirtschaftsmathematik, Kaiserslautern, Germany, Last time accessed: 10-12-2015.
    • Wirjadi O. Report: Survey of 3D Image Segmentation Methods. Fraunhofer-Institut für Techno- undWirtschaftsmathematik, Kaiserslautern, Germany, 2007: 1-29; ISSN 1434-9973; https://kluedo.ub.unikl.de/files/1978/bericht123.pdf ; Last time accessed: 10-12-2015.
    • (2007) Report: Survey of 3D Image Segmentation Methods. , pp. 1-29
    • Wirjadi, O.1
  • 8
    • 84929178756 scopus 로고    scopus 로고
    • University of Zagreb, Zagreb, Croatia; Last time accessed: 10-12-2015.
    • Kalinic H. Report: Atlas-Based Image Segmentation: A Survey. University of Zagreb, Zagreb, Croatia; 2008:1-7. http://bib.irb.hr/datoteka/435355.jnrl.pdf ; Last time accessed: 10-12-2015.
    • (2008) Report: Atlas-Based Image Segmentation: A Survey. , pp. 1-7
    • Kalinic, H.1
  • 9
    • 0030216623 scopus 로고    scopus 로고
    • A survey on evaluation methods for image segmentation
    • Zhang Y. A survey on evaluation methods for image segmentation. Pattern Recogn. 1996;29:1335-46.
    • (1996) Pattern Recogn , vol.29 , pp. 1335-1346
    • Zhang, Y.1
  • 11
    • 38649100599 scopus 로고    scopus 로고
    • Quantifying myosin light chain phosphorylation in single adherent cells with automated fluorescence microscopy
    • Bhadriraju K, Elliott JT, Nguyen M, Plant AL. Quantifying myosin light chain phosphorylation in single adherent cells with automated fluorescence microscopy. BMC Cell Biol. 2007;8:43.
    • (2007) BMC Cell Biol , vol.8 , pp. 43
    • Bhadriraju, K.1    Elliott, J.T.2    Nguyen, M.3    Plant, A.L.4
  • 12
    • 29944435174 scopus 로고    scopus 로고
    • Seeing is believing? A beginners' guide to practical pitfalls in image acquisition
    • North AJ. Seeing is believing? A beginners' guide to practical pitfalls in image acquisition. J Cell Biol. 2006;172:9-18.
    • (2006) J Cell Biol , vol.172 , pp. 9-18
    • North, A.J.1
  • 13
    • 84896381325 scopus 로고    scopus 로고
    • A review of reagents for fluorescence microscopy of cellular compartments and structures, part I: BacMam labeling and reagents for vesicular structures
    • Chapter 12, Unit 12.30
    • Dolman NJ, Kilgore JA, Davidson MW. A review of reagents for fluorescence microscopy of cellular compartments and structures, part I: BacMam labeling and reagents for vesicular structures. Current protocols in cytometry / editorial board, J Paul Robinson, managing editor [et al]. 2013;Chapter 12(July):Unit 12.30.
    • (2013) Current protocols in cytometry / editorial board, J Paul Robinson, managing editor [et al] , Issue.JULY
    • Dolman, N.J.1    Kilgore, J.A.2    Davidson, M.W.3
  • 15
    • 84905674463 scopus 로고    scopus 로고
    • A review of reagents for fluorescence microscopy of cellular compartments and structures, Part III: reagents for actin, tubulin, cellular membranes, and whole cell and cytoplasm
    • January, Unit 12.32
    • Kilgore JA, Dolman NJ, Davidson MW. A review of reagents for fluorescence microscopy of cellular compartments and structures, Part III: reagents for actin, tubulin, cellular membranes, and whole cell and cytoplasm. Current protocols in cytometry / editorial board, J Paul Robinson, managing editor [et al]. 2014;67(January):Unit 12.32.
    • (2014) Current protocols in cytometry / editorial board, J Paul Robinson, managing editor [et al] , vol.67
    • Kilgore, J.A.1    Dolman, N.J.2    Davidson, M.W.3
  • 16
    • 39049185794 scopus 로고    scopus 로고
    • Reagents to measure and manipulate cell functions.
    • Edited by D. L. Taylor, J. R. Haskins and KG.;
    • Giuliano K, Taylor D, Waggoner A. Reagents to measure and manipulate cell functions. In Methods in Molecular Biology. Volume 356. Edited by D. L. Taylor, J. R. Haskins and KG. Humana Press, Inc.; 2006:141-162.
    • (2006) In Methods in Molecular Biology. Humana Press, Inc. , vol.356 , pp. 141-162
    • Giuliano, K.1    Taylor, D.2    Waggoner, A.3
  • 17
    • 51849116864 scopus 로고    scopus 로고
    • Cyclic olefin polymers: innovative materials for high-density multiwell plates
    • Niles WD, Coassin PJ. Cyclic olefin polymers: innovative materials for high-density multiwell plates. Assay Drug Dev Technol. 2008;6:577-90.
    • (2008) Assay Drug Dev Technol , vol.6 , pp. 577-590
    • Niles, W.D.1    Coassin, P.J.2
  • 18
    • 84885385963 scopus 로고    scopus 로고
    • Assay Development Guidelines for Image-Based High Content Screening, High Content Analysis and High Content Imaging.
    • In: Sittampalam G, Coussens N, Nelson H, editors. Volume Intenet. Bethesda, MD: Eli Lilly & Company and the National Center for Advancing Translational Sciences;
    • Buchser W, Collins M, Garyantes T, Guha R, Haney S, Lemmon V, et al. Assay Development Guidelines for Image-Based High Content Screening, High Content Analysis and High Content Imaging. In: Sittampalam G, Coussens N, Nelson H, editors. Assay Guidance Manual. Volume Intenet. Bethesda, MD: Eli Lilly & Company and the National Center for Advancing Translational Sciences; 2014. p. 1-71.
    • (2014) Assay Guidance Manual. , pp. 1-71
    • Buchser, W.1    Collins, M.2    Garyantes, T.3    Guha, R.4    Haney, S.5    Lemmon, V.6
  • 23
    • 83755228921 scopus 로고    scopus 로고
    • New concepts for building vocabulary for cell image ontologies
    • Plant AL, Elliott JT, Bhat TN. New concepts for building vocabulary for cell image ontologies. BMC Bioinformatics. 2011;12:487.
    • (2011) BMC Bioinformatics , vol.12 , pp. 487
    • Plant, A.L.1    Elliott, J.T.2    Bhat, T.N.3
  • 24
    • 84930744382 scopus 로고    scopus 로고
    • ProtocolNavigator: emulation-based software for the design, documentation and reproduction biological experiments
    • Khan I, Fraser A, Bray M-A, Smith PJ, White NS, Carpenter AE, et al. ProtocolNavigator: emulation-based software for the design, documentation and reproduction biological experiments. Bioinformatics (Oxford, England). 2014;30:3440-2.
    • (2014) Bioinformatics (Oxford, England) , vol.30 , pp. 3440-3442
    • Khan, I.1    Fraser, A.2    Bray, M.-A.3    Smith, P.J.4    White, N.S.5    Carpenter, A.E.6
  • 25
    • 28544447780 scopus 로고    scopus 로고
    • The Open Microscopy Environment (OME) Data Model and XML file: open tools for informatics and quantitative analysis in biological imaging
    • Goldberg IG, Allan C, Burel J-M, Creager D, Falconi A, Hochheiser H, et al. The Open Microscopy Environment (OME) Data Model and XML file: open tools for informatics and quantitative analysis in biological imaging. Genome Biol. 2005;6:R47.
    • (2005) Genome Biol , vol.6 , pp. R47
    • Goldberg, I.G.1    Allan, C.2    Burel, J.-M.3    Creager, D.4    Falconi, A.5    Hochheiser, H.6
  • 27
    • 84859169880 scopus 로고    scopus 로고
    • Drug development: raise standards for preclinical cancer research
    • Begley CG, Ellis LM. Drug development: raise standards for preclinical cancer research. Nature. 2012;483:531-3.
    • (2012) Nature , vol.483 , pp. 531-533
    • Begley, C.G.1    Ellis, L.M.2
  • 28
    • 84877752060 scopus 로고    scopus 로고
    • A survey on data reproducibility in cancer research provides insights into our limited ability to translate findings from the laboratory to the clinic
    • Mobley A, Linder S, Braeuer R, Ellis L, Zwelling L. A survey on data reproducibility in cancer research provides insights into our limited ability to translate findings from the laboratory to the clinic. PLoS One. 2013;8:3-6.
    • (2013) PLoS One , vol.8 , pp. 3-6
    • Mobley, A.1    Linder, S.2    Braeuer, R.3    Ellis, L.4    Zwelling, L.5
  • 29
    • 44349162752 scopus 로고    scopus 로고
    • Transcriptome-wide noise controls lineage choice in mammalian progenitor cells
    • Chang HH, Hemberg M, Barahona M, Ingber DE, Huang S. Transcriptome-wide noise controls lineage choice in mammalian progenitor cells. Nature. 2008;453(May):4-8.
    • (2008) Nature , vol.453 , Issue.MAY , pp. 4-8
    • Chang, H.H.1    Hemberg, M.2    Barahona, M.3    Ingber, D.E.4    Huang, S.5
  • 31
    • 33745391854 scopus 로고    scopus 로고
    • Dynamic proteomics in individual human cells uncovers widespread cell-cycle dependence of nuclear proteins
    • Sigal A, Milo R, Cohen A, Geva-Zatorsky N, Klein Y, Alaluf I, et al. Dynamic proteomics in individual human cells uncovers widespread cell-cycle dependence of nuclear proteins. Nat Methods. 2006;3:525.
    • (2006) Nat Methods , vol.3 , pp. 525
    • Sigal, A.1    Milo, R.2    Cohen, A.3    Geva-Zatorsky, N.4    Klein, Y.5    Alaluf, I.6
  • 36
    • 0032877311 scopus 로고    scopus 로고
    • Cell volume measurements by fluorescence confocal microscopy: theoretical and practical aspects
    • Blatter LA. Cell volume measurements by fluorescence confocal microscopy: theoretical and practical aspects. Methods Enzymology. 1999;307:274-95.
    • (1999) Methods Enzymology , vol.307 , pp. 274-295
    • Blatter, L.A.1
  • 37
    • 84871051963 scopus 로고    scopus 로고
    • Three-dimensional cell morphometry for the quantification of cell-substrate interactions
    • Shaw M, Faruqui N, Gurdak E, Tomlins P. Three-dimensional cell morphometry for the quantification of cell-substrate interactions. Tissue engineering Part C, Methods. 2013;19:48-56.
    • (2013) Tissue engineering Part C, Methods , vol.19 , pp. 48-56
    • Shaw, M.1    Faruqui, N.2    Gurdak, E.3    Tomlins, P.4
  • 38
    • 33846487897 scopus 로고    scopus 로고
    • Determining refractive index of single living cell using an integrated microchip
    • Liang XJ, Liu AQ, Lim CS, Ayi TC, Yap PH. Determining refractive index of single living cell using an integrated microchip. Sensors Actuators A Phys. 2007;133:349-54.
    • (2007) Sensors Actuators A Phys , vol.133 , pp. 349-354
    • Liang, X.J.1    Liu, A.Q.2    Lim, C.S.3    Ayi, T.C.4    Yap, P.H.5
  • 39
    • 84876708809 scopus 로고    scopus 로고
    • Highly sensitive refractive index measurement with a sandwiched single-flow-channel microfluidic chip
    • Chaitavon K, Sumriddetchkajorn S, Nukeaw J. Highly sensitive refractive index measurement with a sandwiched single-flow-channel microfluidic chip. RSC Advances. 2013;3:6981.
    • (2013) RSC Advances , vol.3 , pp. 6981
    • Chaitavon, K.1    Sumriddetchkajorn, S.2    Nukeaw, J.3
  • 41
    • 84879983002 scopus 로고    scopus 로고
    • Survey of contemporary trends in color image segmentation
    • Vantaram SR, Saber E. Survey of contemporary trends in color image segmentation. J Electronic Imaging. 2012;21:040901-1.
    • (2012) J Electronic Imaging , vol.21
    • Vantaram, S.R.1    Saber, E.2
  • 42
    • 32244445804 scopus 로고    scopus 로고
    • Automated cell lineage construction: a rapid method to analyze clonal development established with murine neural progenitor cells
    • Al-Kofahi O, Radke RJ, Goderie SK, Shen Q, Temple S, Roysam B. Automated cell lineage construction: a rapid method to analyze clonal development established with murine neural progenitor cells. Cell cycle (Georgetown, Tex). 2006;5:327-35.
    • (2006) Cell cycle (Georgetown, Tex) , vol.5 , pp. 327-335
    • Al-Kofahi, O.1    Radke, R.J.2    Goderie, S.K.3    Shen, Q.4    Temple, S.5    Roysam, B.6
  • 45
    • 84991873297 scopus 로고    scopus 로고
    • Principles and applications of differential interference contrast light microscopy
    • Way D. Principles and applications of differential interference contrast light microscopy. Microscopy and Analysis; Light Microscopy Supplement. 2006;20:9-11.
    • (2006) Microscopy and Analysis; Light Microscopy Supplement , vol.20 , pp. 9-11
    • Way, D.1
  • 47
    • 33947355325 scopus 로고    scopus 로고
    • Single-cell quantification of molecules and rates using open-source microscope-based cytometry.
    • Gordon A, Colman-Lerner A, Chin TE, Benjamin KR, Yu RC, Brent R. Single-cell quantification of molecules and rates using open-source microscope-based cytometry. Nat Methods. 2007;175-181.
    • (2007) Nat Methods. , pp. 175-181
    • Gordon, A.1    Colman-Lerner, A.2    Chin, T.E.3    Benjamin, K.R.4    Yu, R.C.5    Brent, R.6
  • 50
    • 10744223479 scopus 로고    scopus 로고
    • Computer-assisted enhanced volumetric segmentation magnetic resonance imaging data using a mixture of artificial neural networks
    • Pérez De Alejo R, Ruiz-Cabello J, Cortijo M, Rodriguez I, Echave I, Regadera J, et al. Computer-assisted enhanced volumetric segmentation magnetic resonance imaging data using a mixture of artificial neural networks. Magn Reson Imaging. 2003;21:901-12.
    • (2003) Magn Reson Imaging , vol.21 , pp. 901-912
    • Pérez De Alejo, R.1    Ruiz-Cabello, J.2    Cortijo, M.3    Rodriguez, I.4    Echave, I.5    Regadera, J.6
  • 52
    • 0035063579 scopus 로고    scopus 로고
    • An automated segmentation method for three-dimensional carotid ultrasound images
    • Zahalka A, Fenster A. An automated segmentation method for three-dimensional carotid ultrasound images. Phys Med Biol. 2001;46:1321-42.
    • (2001) Phys Med Biol , vol.46 , pp. 1321-1342
    • Zahalka, A.1    Fenster, A.2
  • 53
    • 41949100170 scopus 로고    scopus 로고
    • Image segmentation evaluation: a survey of unsupervised methods
    • Zhang H, Fritts JE, Goldman SA. Image segmentation evaluation: a survey of unsupervised methods. Comput Vis Image Underst. 2008;110:260-80.
    • (2008) Comput Vis Image Underst , vol.110 , pp. 260-280
    • Zhang, H.1    Fritts, J.E.2    Goldman, S.A.3
  • 54
    • 34548299771 scopus 로고    scopus 로고
    • A multi-model approach to simultaneous segmentation and classification of heterogeneous populations of cell nuclei in 3D confocal microscope images
    • Lin G, Chawla MK, Olson K, Barnes CA, Guzowski JF, Bjornsson C, et al. A multi-model approach to simultaneous segmentation and classification of heterogeneous populations of cell nuclei in 3D confocal microscope images. Cytometry Part A. 2007;71:724-36.
    • (2007) Cytometry Part A , vol.71 , pp. 724-736
    • Lin, G.1    Chawla, M.K.2    Olson, K.3    Barnes, C.A.4    Guzowski, J.F.5    Bjornsson, C.6
  • 59
    • 40649095676 scopus 로고    scopus 로고
    • The cell centered database project: an update on building community resources for managing and sharing 3D imaging data
    • Martone ME, Tran J, Wong WW, Sargis J, Fong L, Larson S, et al. The cell centered database project: an update on building community resources for managing and sharing 3D imaging data. J Struct Biol. 2008;161:220-31.
    • (2008) J Struct Biol , vol.161 , pp. 220-231
    • Martone, M.E.1    Tran, J.2    Wong, W.W.3    Sargis, J.4    Fong, L.5    Larson, S.6
  • 62
    • 84888159747 scopus 로고    scopus 로고
    • Estimating the Number of Manually Segmented Cellular Objects Required to Evaluate the Accuracy of a Segmentation Algorithm.
    • New York, NY, USA: ACM;
    • Peskin A, Chalfoun J, Kafadar K, Elliott J. Estimating the Number of Manually Segmented Cellular Objects Required to Evaluate the Accuracy of a Segmentation Algorithm. In: Proceedings of ACM BCB. New York, NY, USA: ACM; 2013. p. 2 doi: 10.1145/2506583.2512384.
    • (2013) In: Proceedings of ACM BCB. , pp. 2
    • Peskin, A.1    Chalfoun, J.2    Kafadar, K.3    Elliott, J.4
  • 63
    • 3042547731 scopus 로고    scopus 로고
    • Combining intensity, edge and shape information for 2D and 3D segmentation of cell nuclei in tissue sections
    • Wählby C, Sintorn I-M, Erlandsson F, Borgefors G, Bengtsson E. Combining intensity, edge and shape information for 2D and 3D segmentation of cell nuclei in tissue sections. J Microsc. 2004;215:67-76.
    • (2004) J Microsc , vol.215 , pp. 67-76
    • Wählby, C.1    Sintorn, I.-M.2    Erlandsson, F.3    Borgefors, G.4    Bengtsson, E.5
  • 64
    • 84884937865 scopus 로고    scopus 로고
    • 3D time series analysis of cell shape using Laplacian approaches
    • Du C, Hawkins P. 3D time series analysis of cell shape using Laplacian approaches. BMC Bioinformatics. 2013;14:296.
    • (2013) BMC Bioinformatics , vol.14 , pp. 296
    • Du, C.1    Hawkins, P.2
  • 65
    • 84883818286 scopus 로고    scopus 로고
    • Spline-based deforming ellipsoids for interactive 3D bioimage segmentation
    • Delgado-Gonzalo R, Chenouard N, Unser M. Spline-based deforming ellipsoids for interactive 3D bioimage segmentation. IEEE Trans Image Process. 2013;22:3926-40.
    • (2013) IEEE Trans Image Process , vol.22 , pp. 3926-3940
    • Delgado-Gonzalo, R.1    Chenouard, N.2    Unser, M.3
  • 67
    • 65549116620 scopus 로고    scopus 로고
    • A unified framework for automated 3-d segmentation of surface-stained living cells and a comprehensive segmentation evaluation
    • Hodneland E, Bukoreshtliev NV, Eichler TW, Tai X-C, Gurke S, Lundervold A, et al. A unified framework for automated 3-d segmentation of surface-stained living cells and a comprehensive segmentation evaluation. IEEE Trans Med Imaging. 2009;28:720-38.
    • (2009) IEEE Trans Med Imaging , vol.28 , pp. 720-738
    • Hodneland, E.1    Bukoreshtliev, N.V.2    Eichler, T.W.3    Tai, X.-C.4    Gurke, S.5    Lundervold, A.6
  • 70
    • 79958279665 scopus 로고    scopus 로고
    • Gebiss: an ImageJ plugin for the specification of ground truth and the performance evaluation of 3D segmentation algorithms
    • Kriston-Vizi J, Thong NW, Poh CL, Yee KC, Ling JSP, Kraut R, et al. Gebiss: an ImageJ plugin for the specification of ground truth and the performance evaluation of 3D segmentation algorithms. BMC Bioinformatics. 2011;12:232.
    • (2011) BMC Bioinformatics , vol.12 , pp. 232
    • Kriston-Vizi, J.1    Thong, N.W.2    Poh, C.L.3    Yee, K.C.4    Ling, J.S.P.5    Kraut, R.6
  • 72
    • 84897907928 scopus 로고    scopus 로고
    • Fast segmentation of stained nuclei in terabyte-scale, time resolved 3D microscopy image stacks
    • Stegmaier J, Otte JC, Kobitski A, Bartschat A, Garcia A, Nienhaus GU, et al. Fast segmentation of stained nuclei in terabyte-scale, time resolved 3D microscopy image stacks. PLoS One. 2014;9, e90036.
    • (2014) PLoS One , vol.9
    • Stegmaier, J.1    Otte, J.C.2    Kobitski, A.3    Bartschat, A.4    Garcia, A.5    Nienhaus, G.U.6
  • 73
    • 84864626365 scopus 로고    scopus 로고
    • Algorithm selection based on a region similarity metric for intracellular image segmentation.
    • Edited by Dr Ho P-G. InTech;
    • Takemoto S, Yokota H. Algorithm selection based on a region similarity metric for intracellular image segmentation. In Image Segmentation. Edited by Dr Ho P-G. InTech; 2011:419-434.
    • (2011) In Image Segmentation. , pp. 419-434
    • Takemoto, S.1    Yokota, H.2
  • 76
    • 84894631471 scopus 로고    scopus 로고
    • Automated nucleus and cytoplasm segmentation of overlapping cervical cells.
    • Berlin Heidelberg: Lecture Notes in Computer Science; Springer-Verlag;
    • Lu Z, Carneiro G, Bradley A. Automated nucleus and cytoplasm segmentation of overlapping cervical cells. In: Medical Image Computing and Computer-Assisted Intervention (MICCAI). Volume 8149. Berlin Heidelberg: Lecture Notes in Computer Science; Springer-Verlag; 2013. p. 452-60.
    • (2013) In: Medical Image Computing and Computer-Assisted Intervention (MICCAI). , vol.8149 , pp. 452-460
    • Lu, Z.1    Carneiro, G.2    Bradley, A.3
  • 77
    • 84867839682 scopus 로고    scopus 로고
    • Overlapping cell nuclei segmentation using a spatially adaptive active physical model
    • Plissiti ME, Nikou C. Overlapping cell nuclei segmentation using a spatially adaptive active physical model. IEEE Trans Image Process. 2012;21:4568-80.
    • (2012) IEEE Trans Image Process , vol.21 , pp. 4568-4580
    • Plissiti, M.E.1    Nikou, C.2
  • 81
  • 84
    • 84896073709 scopus 로고    scopus 로고
    • A rapid and efficient 2D/3D nuclear segmentation method for analysis of early mouse embryo and stem cell image data
    • Lou X, Kang M, Xenopoulos P, Muñoz-Descalzo S, Hadjantonakis A-K. A rapid and efficient 2D/3D nuclear segmentation method for analysis of early mouse embryo and stem cell image data. Stem Cell Reports. 2014;2:382-97.
    • (2014) Stem Cell Reports , vol.2 , pp. 382-397
    • Lou, X.1    Kang, M.2    Xenopoulos, P.3    Muñoz-Descalzo, S.4    Hadjantonakis, A.-K.5
  • 86
    • 78549240782 scopus 로고    scopus 로고
    • Quantitative imaging reveals heterogeneous growth dynamics and treatment-dependent residual tumor distributions in a three-dimensional ovarian cancer model
    • Celli JP, Rizvi I, Evans CL, Abu-Yousif AO, Hasan T. Quantitative imaging reveals heterogeneous growth dynamics and treatment-dependent residual tumor distributions in a three-dimensional ovarian cancer model. J Biomed Opt. 2010;15:051603.
    • (2010) J Biomed Opt , vol.15
    • Celli, J.P.1    Rizvi, I.2    Evans, C.L.3    Abu-Yousif, A.O.4    Hasan, T.5
  • 87
    • 84859016779 scopus 로고    scopus 로고
    • Vertebrate neural stem cell segmentation, tracking and lineaging with validation and editing
    • Winter M, Wait E, Roysam B, Goderie SK, Ali RAN, Kokovay E, et al. Vertebrate neural stem cell segmentation, tracking and lineaging with validation and editing. Nat Protoc. 2011;6:1942-52.
    • (2011) Nat Protoc , vol.6 , pp. 1942-1952
    • Winter, M.1    Wait, E.2    Roysam, B.3    Goderie, S.K.4    Ali, R.A.N.5    Kokovay, E.6
  • 90
    • 27844470693 scopus 로고    scopus 로고
    • Survey over image thresholding techniques and
    • Sezgin M, Sankur B. Survey over image thresholding techniques and. J Electronic Imaging. 2004;13:220.
    • (2004) J Electronic Imaging , vol.13 , pp. 220
    • Sezgin, M.1    Sankur, B.2
  • 92
    • 84991904822 scopus 로고    scopus 로고
    • MATLAB Multicore [ http://www.mathworks.com/discovery/matlab-multicore.html ].
  • 93
    • 84991885087 scopus 로고    scopus 로고
    • Methods research on future research needs: defining an optimal format for presenting research needs.
    • Trikalinos T, Dahabreh I, Lee J. Methods research on future research needs: defining an optimal format for presenting research needs. Methods Future Res Needs Report. 2011;1-43.
    • (2011) Methods Future Res Needs Report. , pp. 1-43
    • Trikalinos, T.1    Dahabreh, I.2    Lee, J.3
  • 94
    • 84991837678 scopus 로고    scopus 로고
    • Guide for Using Fluorescence Microscopy to Quantify the Spread Area of Fixed Cells 1.
    • ASTM International, 100 Barr Harbor Drive, PO Box C700, West Conshohocken, PA 19428-2959. United States: Designation; F2998-14
    • ASTM. Guide for Using Fluorescence Microscopy to Quantify the Spread Area of Fixed Cells 1. ASTM International, 100 Barr Harbor Drive, PO Box C700, West Conshohocken, PA 19428-2959. United States: Designation; 2014. p. F2998-14.
    • (2014)
  • 95
    • 0029057619 scopus 로고
    • Photobleaching kinetics of fluorescein in quantitative fluorescent microscopy
    • Song L, Hennink E, Young I, Tanke H. Photobleaching kinetics of fluorescein in quantitative fluorescent microscopy. Biophys J. 1995;68:2588-600.
    • (1995) Biophys J , vol.68 , pp. 2588-2600
    • Song, L.1    Hennink, E.2    Young, I.3    Tanke, H.4
  • 96
    • 84991867571 scopus 로고    scopus 로고
    • Antibody Validation Criteria [ http://www.antibodypedia.com/text/validation_criteria ].
  • 98
    • 84881304772 scopus 로고    scopus 로고
    • Six red flags for suspect work
    • Begley CG. Six red flags for suspect work. Nature. 2013;497:433-4.
    • (2013) Nature , vol.497 , pp. 433-434
    • Begley, C.G.1
  • 99
    • 0036178781 scopus 로고    scopus 로고
    • Simple method for reduction of autofluorescence in fluorescence microscopy
    • Neumann M, Gabel D. Simple method for reduction of autofluorescence in fluorescence microscopy. J Histochemistry Cytochemistry. 2002;50:437-9.
    • (2002) J Histochemistry Cytochemistry , vol.50 , pp. 437-439
    • Neumann, M.1    Gabel, D.2
  • 102
    • 33646365074 scopus 로고    scopus 로고
    • Combinatorial screen of the effect of surface energy on fibronectin-mediated osteoblast adhesion, spreading and proliferation
    • Kennedy SB, Washburn NR, Simon CG, Amis EJ. Combinatorial screen of the effect of surface energy on fibronectin-mediated osteoblast adhesion, spreading and proliferation. Biomaterials. 2006;27:3817-24.
    • (2006) Biomaterials , vol.27 , pp. 3817-3824
    • Kennedy, S.B.1    Washburn, N.R.2    Simon, C.G.3    Amis, E.J.4
  • 103
    • 84892383382 scopus 로고    scopus 로고
    • ConfocalCheck--a software tool for the automated monitoring of confocal microscope performance
    • Hng KI, Dormann D. ConfocalCheck--a software tool for the automated monitoring of confocal microscope performance. PLoS One. 2013;8, e79879.
    • (2013) PLoS One , vol.8
    • Hng, K.I.1    Dormann, D.2
  • 106
    • 80955152014 scopus 로고    scopus 로고
    • Measuring and interpreting point spread functions to determine confocal microscope resolution and ensure quality control
    • Cole RW, Jinadasa T, Brown CM. Measuring and interpreting point spread functions to determine confocal microscope resolution and ensure quality control. Nat Protoc. 2011;6:1929-41.
    • (2011) Nat Protoc , vol.6 , pp. 1929-1941
    • Cole, R.W.1    Jinadasa, T.2    Brown, C.M.3
  • 108
    • 84874030940 scopus 로고    scopus 로고
    • Note: a three-dimensional calibration device for the confocal microscope
    • Jensen KE, Weitz DA, Spaepen F. Note: a three-dimensional calibration device for the confocal microscope. Rev Sci Instrum. 2013;84:016108.
    • (2013) Rev Sci Instrum , vol.84
    • Jensen, K.E.1    Weitz, D.A.2    Spaepen, F.3
  • 109
    • 0021956248 scopus 로고
    • Digital imaging fluorescence microscopy: spatial heterogeneity of photobleaching rate constants in individual cells
    • Benson DM, Bryan J, Plant AL, Gotto AM, Smith LC. Digital imaging fluorescence microscopy: spatial heterogeneity of photobleaching rate constants in individual cells. J Cell Biol. 1985;100(April):1309-23.
    • (1985) J Cell Biol , vol.100 , Issue.APRIL , pp. 1309-1323
    • Benson, D.M.1    Bryan, J.2    Plant, A.L.3    Gotto, A.M.4    Smith, L.C.5
  • 110
    • 0035421135 scopus 로고    scopus 로고
    • A standard for calibration and shading correction of a fluorescence microscope
    • Model MA, Burkhardt JK. A standard for calibration and shading correction of a fluorescence microscope. Cytometry. 2001;44:309-16.
    • (2001) Cytometry , vol.44 , pp. 309-316
    • Model, M.A.1    Burkhardt, J.K.2
  • 111
    • 26244468212 scopus 로고    scopus 로고
    • Shading correction: compensation for illumination and sensor inhomogeneities.
    • Wiley On-line.
    • Young IT. Shading correction: compensation for illumination and sensor inhomogeneities. In: Current Protocols in Cytometry. 2000. p. 1-14. Wiley On-line.
    • (2000) In: Current Protocols in Cytometry. , pp. 1-14
    • Young, I.T.1
  • 114
    • 84886314384 scopus 로고    scopus 로고
    • To be or not to be assembled: progressing into nuclear actin filaments
    • Grosse R, Vartiainen MK. To be or not to be assembled: progressing into nuclear actin filaments. Nat Rev Mol Cell Biol. 2013;14:693-7.
    • (2013) Nat Rev Mol Cell Biol , vol.14 , pp. 693-697
    • Grosse, R.1    Vartiainen, M.K.2
  • 115
    • 23044515069 scopus 로고    scopus 로고
    • Feature point tracking and trajectory analysis for video imaging in cell biology
    • Sbalzarini IF, Koumoutsakos P. Feature point tracking and trajectory analysis for video imaging in cell biology. J Struct Biol. 2005;151:182-95.
    • (2005) J Struct Biol , vol.151 , pp. 182-195
    • Sbalzarini, I.F.1    Koumoutsakos, P.2
  • 116
    • 33644770578 scopus 로고    scopus 로고
    • Three-dimensional volume reconstruction of extracellular matrix proteins in uveal melanoma from fluorescent confocal laser scanning microscope images
    • Bajcsy P, Lee S-C, Lin A, Folberg R. Three-dimensional volume reconstruction of extracellular matrix proteins in uveal melanoma from fluorescent confocal laser scanning microscope images. J Microsc. 2006;221(Pt 1):30-45.
    • (2006) J Microsc , vol.221 , pp. 30-45
    • Bajcsy, P.1    Lee, S.-C.2    Lin, A.3    Folberg, R.4
  • 120
  • 122
    • 84924084001 scopus 로고    scopus 로고
    • FogBank: a single cell segmentation across multiple cell lines and image modalities
    • Chalfoun J, Majurski M, Dima A, Stuelten C, Peskin A. FogBank: a single cell segmentation across multiple cell lines and image modalities. BMC Bioinformatics. 2014;15:431.
    • (2014) BMC Bioinformatics , vol.15 , pp. 431
    • Chalfoun, J.1    Majurski, M.2    Dima, A.3    Stuelten, C.4    Peskin, A.5
  • 123
    • 79958844030 scopus 로고    scopus 로고
    • An automatic segmentation algorithm for 3D cell cluster splitting using volumetric confocal images
    • Indhumathi C, Cai YY, Guan YQ, Opas M. An automatic segmentation algorithm for 3D cell cluster splitting using volumetric confocal images. J Microsc. 2011;243:60-76.
    • (2011) J Microsc , vol.243 , pp. 60-76
    • Indhumathi, C.1    Cai, Y.Y.2    Guan, Y.Q.3    Opas, M.4
  • 126
  • 129
    • 84921538445 scopus 로고    scopus 로고
    • Empirical gradient threshold technique for automated segmentation across image modalities and cell lines.
    • Chalfoun J, Majurski M, Peskin A, Breen C, Bajcsy P. Empirical gradient threshold technique for automated segmentation across image modalities and cell lines. J Microsc. 2014;1-18.
    • (2014) J Microsc. , pp. 1-18
    • Chalfoun, J.1    Majurski, M.2    Peskin, A.3    Breen, C.4    Bajcsy, P.5
  • 131
    • 42149087604 scopus 로고    scopus 로고
    • Active Contour-Based Multiresolution Transforms for the Segmentation of Fluorescence Microscope Images.
    • In: Van De Ville D, Goyal VK, Papadakis M, editors.
    • Srinivasa G, Fickus M, Kovăević J. Active Contour-Based Multiresolution Transforms for the Segmentation of Fluorescence Microscope Images. In: Van De Ville D, Goyal VK, Papadakis M, editors. Proceedings of the SPIE. 2007. p. 6701.
    • (2007) Proceedings of the SPIE. , pp. 6701
    • Srinivasa, G.1    Fickus, M.2    Kovăević, J.3
  • 136
  • 138
    • 44649148372 scopus 로고    scopus 로고
    • Reconstruction of cellular biological structures from optical microscopy data
    • Mosaliganti K, Cooper L. Reconstruction of cellular biological structures from optical microscopy data. IEEE Trans Vis Comput Graph. 2008;14:863-76.
    • (2008) IEEE Trans Vis Comput Graph , vol.14 , pp. 863-876
    • Mosaliganti, K.1    Cooper, L.2
  • 139
    • 35948953980 scopus 로고    scopus 로고
    • 3D cell nuclei segmentation based on gradient flow tracking
    • Li G, Liu T, Tarokh A, Nie J, Guo L, Mara A, et al. 3D cell nuclei segmentation based on gradient flow tracking. BMC Cell Biol. 2007;8:40.
    • (2007) BMC Cell Biol , vol.8 , pp. 40
    • Li, G.1    Liu, T.2    Tarokh, A.3    Nie, J.4    Guo, L.5    Mara, A.6
  • 140
    • 77950679704 scopus 로고    scopus 로고
    • V3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets
    • Peng H, Ruan Z, Long F, Simpson JH, Myers EW. V3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets. Nat Biotechnol. 2010;28:348-53.
    • (2010) Nat Biotechnol , vol.28 , pp. 348-353
    • Peng, H.1    Ruan, Z.2    Long, F.3    Simpson, J.H.4    Myers, E.W.5
  • 142
    • 19544372619 scopus 로고    scopus 로고
    • Free-D: an integrated environment for three-dimensional reconstruction from serial sections
    • Andrey P, Maurin Y. Free-D: an integrated environment for three-dimensional reconstruction from serial sections. J Neurosci Methods. 2005;145:233-44.
    • (2005) J Neurosci Methods , vol.145 , pp. 233-244
    • Andrey, P.1    Maurin, Y.2
  • 143
    • 69549097485 scopus 로고    scopus 로고
    • A 3D digital atlas of C. elegans and its application to single-cell analyses
    • Long F, Peng H, Liu X, Kim SK, Myers E. A 3D digital atlas of C. elegans and its application to single-cell analyses. Nat Methods. 2009;6:667-72.
    • (2009) Nat Methods , vol.6 , pp. 667-672
    • Long, F.1    Peng, H.2    Liu, X.3    Kim, S.K.4    Myers, E.5
  • 144
    • 33845792555 scopus 로고    scopus 로고
    • Cell Profiler: image analysis software for identifying and quantifying cell phenotypes.
    • Carpenter AE, Jones TR. Cell Profiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biol. 2006;7.
    • (2006) Genome Biol. , pp. 7
    • Carpenter, A.E.1    Jones, T.R.2
  • 145
    • 77953689289 scopus 로고    scopus 로고
    • Fully automatic stitching and distortion correction of transmission electron microscope images
    • Kaynig V, Fischer B, Müller E, Buhmann JM. Fully automatic stitching and distortion correction of transmission electron microscope images. J Struct Biol. 2010;171:163-73.
    • (2010) J Struct Biol , vol.171 , pp. 163-173
    • Kaynig, V.1    Fischer, B.2    Müller, E.3    Buhmann, J.M.4
  • 147
    • 84907959940 scopus 로고    scopus 로고
    • Visualization and correction of automated segmentation, tracking and lineaging from 5-D stem cell image sequences
    • Wait E, Winter M, Bjornsson C, Kokovay E, Wang Y, Goderie S, et al. Visualization and correction of automated segmentation, tracking and lineaging from 5-D stem cell image sequences. BMC Bioinformatics. 2014;15:328.
    • (2014) BMC Bioinformatics , vol.15 , pp. 328
    • Wait, E.1    Winter, M.2    Bjornsson, C.3    Kokovay, E.4    Wang, Y.5    Goderie, S.6
  • 149
    • 77957714521 scopus 로고    scopus 로고
    • Computer control of microscopes using μManager.
    • In: Ausubel FM, editor., Chapter 14:Unit14.20. San Diego, CA, USA: Academic Press; Jun 25, 2014 - Science.
    • Edelstein A, Amodaj N, Hoover K, Vale R, Stuurman N. Computer control of microscopes using μManager. In: Ausubel FM, editor. Current protocols in molecular biology, Chapter 14:Unit14.20. San Diego, CA, USA: Academic Press; 2010. p. 588. Jun 25, 2014 - Science.
    • (2010) Current protocols in molecular biology , pp. 588
    • Edelstein, A.1    Amodaj, N.2    Hoover, K.3    Vale, R.4    Stuurman, N.5
  • 150
    • 84855858086 scopus 로고    scopus 로고
    • Structural differences in the osteocyte network between the calvaria and long bone revealed by three-dimensional fluorescence morphometry, possibly reflecting distinct mechano-adaptations and sensitivities
    • Himeno-Ando A, Izumi Y, Yamaguchi A, Iimura T. Structural differences in the osteocyte network between the calvaria and long bone revealed by three-dimensional fluorescence morphometry, possibly reflecting distinct mechano-adaptations and sensitivities. Biochem Biophys Res Commun. 2012;417:765-70.
    • (2012) Biochem Biophys Res Commun , vol.417 , pp. 765-770
    • Himeno-Ando, A.1    Izumi, Y.2    Yamaguchi, A.3    Iimura, T.4
  • 151
    • 84891541235 scopus 로고    scopus 로고
    • A framework for automated cell tracking in phase contrast microscopic videos based on normal velocities
    • Moeller M, Burger M, Dieterich P, Schwab A. A framework for automated cell tracking in phase contrast microscopic videos based on normal velocities. J Vis Commun Image Represent. 2014;25:396-409.
    • (2014) J Vis Commun Image Represent , vol.25 , pp. 396-409
    • Moeller, M.1    Burger, M.2    Dieterich, P.3    Schwab, A.4
  • 152
    • 77956339402 scopus 로고    scopus 로고
    • Cell Cognition: time-resolved phenotype annotation in high-throughput live cell imaging
    • Held M, Schmitz MHA, Fischer B, Walter T, Neumann B, Olma MH, et al. Cell Cognition: time-resolved phenotype annotation in high-throughput live cell imaging. Nat Methods. 2010;7:747-54.
    • (2010) Nat Methods , vol.7 , pp. 747-754
    • Held, M.1    Schmitz, M.H.A.2    Fischer, B.3    Walter, T.4    Neumann, B.5    Olma, M.H.6
  • 153
    • 84991910536 scopus 로고    scopus 로고
    • Systems Science of Biological Dynamics (SSBD) database [ http://ssbd.qbic.riken.jp/ ].
  • 156
    • 67649409345 scopus 로고    scopus 로고
    • Segmentation of fluorescence microscopy images for quantitative analysis of cell nuclear architecture
    • Russell RA, Adams NM, Stephens DA, Batty E, Jensen K, Freemont PS. Segmentation of fluorescence microscopy images for quantitative analysis of cell nuclear architecture. Biophys J. 2009;96:3379-89.
    • (2009) Biophys J , vol.96 , pp. 3379-3389
    • Russell, R.A.1    Adams, N.M.2    Stephens, D.A.3    Batty, E.4    Jensen, K.5    Freemont, P.S.6
  • 158
    • 84862788900 scopus 로고    scopus 로고
    • Understanding the phase contrast optics to restore artifact-free microscopy images for segmentation
    • Yin Z, Kanade T, Chen M. Understanding the phase contrast optics to restore artifact-free microscopy images for segmentation. Med Image Anal. 2012;16:1047-62.
    • (2012) Med Image Anal , vol.16 , pp. 1047-1062
    • Yin, Z.1    Kanade, T.2    Chen, M.3
  • 160
    • 3042547731 scopus 로고    scopus 로고
    • Combining intensity, edge and shape information for 2D and 3D segmentation of cell nuclei in tissue sections
    • Bengtsson E. Combining intensity, edge and shape information for 2D and 3D segmentation of cell nuclei in tissue sections. J Microsc. 2004;215(January):67-76.
    • (2004) J Microsc , vol.215 , Issue.JANUARY , pp. 67-76
    • Bengtsson, E.1
  • 162
    • 84864147928 scopus 로고    scopus 로고
    • Tracking transcriptional activities with high-content epifluorescent imaging
    • Hua J, Sima C, Cypert M, Gooden GC, Shack S, Alla L, et al. Tracking transcriptional activities with high-content epifluorescent imaging. J Biomed Opt. 2012;17:046008.
    • (2012) J Biomed Opt , vol.17
    • Hua, J.1    Sima, C.2    Cypert, M.3    Gooden, G.C.4    Shack, S.5    Alla, L.6
  • 163
    • 62849127621 scopus 로고    scopus 로고
    • Automated tracking of migrating cells in phase-contrast video microscopy sequences using image registration
    • Hand AJ, Sun T, Barber DC, Hose DR, MacNeil S. Automated tracking of migrating cells in phase-contrast video microscopy sequences using image registration. J Microsc. 2009;234:62-79.
    • (2009) J Microsc , vol.234 , pp. 62-79
    • Hand, A.J.1    Sun, T.2    Barber, D.C.3    Hose, D.R.4    MacNeil, S.5
  • 164
    • 37549026179 scopus 로고    scopus 로고
    • Novel cell segmentation and online SVM for cell cycle phase identification in automated microscopy
    • Wang M, Zhou X, Li F, Huckins J, King RW, Wong STC. Novel cell segmentation and online SVM for cell cycle phase identification in automated microscopy. Bioinformatics. 2008;24:94-101.
    • (2008) Bioinformatics , vol.24 , pp. 94-101
    • Wang, M.1    Zhou, X.2    Li, F.3    Huckins, J.4    King, R.W.5    Wong, S.T.C.6
  • 165
    • 77950648883 scopus 로고    scopus 로고
    • Significantly improved precision of cell migration analysis in time-lapse video microscopy through use of a fully automated tracking system
    • Huth J, Buchholz M, Kraus JM, Schmucker M, von Wichert G, Krndija D, et al. Significantly improved precision of cell migration analysis in time-lapse video microscopy through use of a fully automated tracking system. BMC Cell Biol. 2010;11:24.
    • (2010) BMC Cell Biol , vol.11 , pp. 24
    • Huth, J.1    Buchholz, M.2    Kraus, J.M.3    Schmucker, M.4    Wichert, G.5    Krndija, D.6
  • 167
    • 43749106246 scopus 로고    scopus 로고
    • Neuronal nuclei localization in 3D using level set and watershed segmentation from laser scanning microscopy images.
    • In: Reinhardt JM, Pluim JPW, editors. 691441-691441-8
    • Zhu Y, Olson E, Subramanian A, Feiglin D, Varshney PK, Krol A. Neuronal nuclei localization in 3D using level set and watershed segmentation from laser scanning microscopy images. In: Reinhardt JM, Pluim JPW, editors. Proc. SPIE. Volume 6914. 2008. p. 691441-691441-8.
    • (2008) Proc. SPIE. , vol.6914
    • Zhu, Y.1    Olson, E.2    Subramanian, A.3    Feiglin, D.4    Varshney, P.K.5    Krol, A.6
  • 169
    • 0025388712 scopus 로고
    • A survey of parallel computer architecture.
    • Duncan R. A survey of parallel computer architecture. Computer. 1990;5-16.
    • (1990) Computer. , pp. 5-16
    • Duncan, R.1


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