메뉴 건너뛰기




Volumn 9, Issue 7, 2012, Pages 697-710

Biological imaging software tools

(14)  Eliceiri, Kevin W a   Berthold, Michael R b   Goldberg, Ilya G c   Ibáñez, Luis d   Manjunath, B S e   Martone, Maryann E f   Murphy, Robert F g   Peng, Hanchuan h   Plant, Anne L i   Roysam, Badrinath j   Stuurmann, Nico k   Swedlow, Jason R l   Tomancak, Pavel m   Carpenter, Anne E n  


Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; COMPUTER PROGRAM; CONFOCAL MICROSCOPY; DIGITAL IMAGING; HUMAN; ILLUMINATION; IMAGE ANALYSIS; IMAGE PROCESSING; IMAGE RETRIEVAL; IMAGING SYSTEM; MACHINE LEARNING; MULTIPHOTON MICROSCOPY; NONHUMAN; PHOTON; PRIORITY JOURNAL; REVIEW; THREE DIMENSIONAL IMAGING; WORKFLOW;

EID: 84863208608     PISSN: 15487091     EISSN: 15487105     Source Type: Journal    
DOI: 10.1038/nmeth.2084     Document Type: Review
Times cited : (433)

References (60)
  • 1
    • 50549104043 scopus 로고    scopus 로고
    • Bioimage informatics: A new area of engineering biology
    • Peng, H. Bioimage informatics: a new area of engineering biology. Bioinformatics 24, 1827-1836 (2008).
    • (2008) Bioinformatics , vol.24 , pp. 1827-1836
    • Peng, H.1
  • 2
    • 24944539530 scopus 로고    scopus 로고
    • Nonlinear structured-illumination microscopy: Wide-field fluorescence imaging with theoretically unlimited resolution
    • DOI 10.1073/pnas.0406877102
    • Gustafsson, M.G. Nonlinear structured-illumination microscopy: wide-field fluorescence imaging with theoretically unlimited resolution. Proc. Natl. Acad. Sci. USA 102, 13081-13086 (2005). (Pubitemid 41324982)
    • (2005) Proceedings of the National Academy of Sciences of the United States of America , vol.102 , Issue.37 , pp. 13081-13086
    • Gustafsson, M.G.L.1
  • 3
    • 38949216802 scopus 로고    scopus 로고
    • Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy
    • DOI 10.1126/science.1153529
    • Huang, B., Wang, W., Bates, M. & Zhuang, X. Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy. Science 319, 810-813 (2008). (Pubitemid 351225870)
    • (2008) Science , vol.319 , Issue.5864 , pp. 810-813
    • Huang, B.1    Wang, W.2    Bates, M.3    Zhuang, X.4
  • 4
    • 33845360042 scopus 로고    scopus 로고
    • Ultra-high resolution imaging by fluorescence photoactivation localization microscopy
    • DOI 10.1529/biophysj.106.091116
    • Hess, S.T., Girirajan, T.P. & Mason, M.D. Ultra-high resolution imaging by fluorescence photoactivation localization microscopy. Biophys. J. 91, 4258-4272 (2006). (Pubitemid 44887284)
    • (2006) Biophysical Journal , vol.91 , Issue.11 , pp. 4258-4272
    • Hess, S.T.1    Girirajan, T.P.K.2    Mason, M.D.3
  • 5
    • 79957823841 scopus 로고    scopus 로고
    • Fast, three-dimensional super-resolution imaging of live cells
    • Jones, S.A., Shim, S.H., He, J. & Zhuang, X. Fast, three-dimensional super-resolution imaging of live cells. Nat. Methods 8, 499-508 (2011).
    • (2011) Nat. Methods , vol.8 , pp. 499-508
    • Jones, S.A.1    Shim, S.H.2    He, J.3    Zhuang, X.4
  • 6
    • 79955586247 scopus 로고    scopus 로고
    • Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination
    • Planchon, T.A. et al. Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination. Nat. Methods 8, 417-423 (2011).
    • (2011) Nat. Methods , vol.8 , pp. 417-423
    • Planchon, T.A.1
  • 8
    • 77956857860 scopus 로고    scopus 로고
    • Bimolecular fluorescence complementation analysis of eukaryotic fusion products
    • Lin, H.P., Vincenz, C., Eliceiri, K.W., Kerppola, T.K. & Ogle, B.M. Bimolecular fluorescence complementation analysis of eukaryotic fusion products. Biol. Cell 102, 525-537 (2010).
    • (2010) Biol. Cell , vol.102 , pp. 525-537
    • Lin, H.P.1    Vincenz, C.2    Eliceiri, K.W.3    Kerppola, T.K.4    Ogle, B.M.5
  • 9
    • 0041458603 scopus 로고    scopus 로고
    • ScanImage: Flexible software for operating laser scanning microscopes
    • Pologruto, T.A., Sabatini, B.L. & Svoboda, K. ScanImage: flexible software for operating laser scanning microscopes. Biomed. Eng. Online 2, 13 (2003).
    • (2003) Biomed. Eng. Online , vol.2 , pp. 13
    • Pologruto, T.A.1    Sabatini, B.L.2    Svoboda, K.3
  • 10
    • 79952189489 scopus 로고    scopus 로고
    • Micropilot: Automation of fluorescence microscopy-based imaging for systems biology
    • Conrad, C. et al. Micropilot: automation of fluorescence microscopy-based imaging for systems biology. Nat. Methods 8, 246-249 (2011).
    • (2011) Nat. Methods , vol.8 , pp. 246-249
    • Conrad, C.1
  • 11
    • 84863393849 scopus 로고    scopus 로고
    • OMERO: Flexible, model-driven data management for experimental biology
    • Allan, C. et al. OMERO: flexible, model-driven data management for experimental biology. Nat. Methods 9, 245-253 (2012).
    • (2012) Nat. Methods , vol.9 , pp. 245-253
    • Allan, C.1
  • 14
    • 84858593012 scopus 로고    scopus 로고
    • The iPlant Collaborative: Cyberinfrastructure for plant biology
    • Goff, S.A. et al. The iPlant Collaborative: cyberinfrastructure for plant biology. Frontiers in Plant Science 2, 34 (2011).
    • (2011) Frontiers in Plant Science , vol.2 , pp. 34
    • Goff, S.A.1
  • 15
    • 33845760114 scopus 로고    scopus 로고
    • Automated subcellular location determination and high-throughput microscopy
    • DOI 10.1016/j.devcel.2006.12.007, PII S1534580706005703
    • Glory, E. & Murphy, R.F. Automated subcellular location determination and high-throughput microscopy. Dev. Cell 12, 7-16 (2007). (Pubitemid 46002604)
    • (2007) Developmental Cell , vol.12 , Issue.1 , pp. 7-16
    • Glory, E.1    Murphy, R.F.2
  • 16
    • 74549174645 scopus 로고    scopus 로고
    • Introduction to the quantitative analysis of two-dimensional fluorescence microscopy images for cell-based screening
    • Ljosa, V. & Carpenter, A.E. Introduction to the quantitative analysis of two-dimensional fluorescence microscopy images for cell-based screening. PLoS Comput. Biol. 5, e1000603 (2009).
    • (2009) PLoS Comput. Biol. , vol.5
    • Ljosa, V.1    Carpenter, A.E.2
  • 18
    • 84863204506 scopus 로고    scopus 로고
    • BioImageXD: An open, general-purpose and high-throughput image-processing platform
    • Kankaanpää, P. et al. BioImageXD: an open, general-purpose and high-throughput image-processing platform. Nat. Methods 9, 683-689 (2012).
    • (2012) Nat. Methods , vol.9 , pp. 683-689
    • Kankaanpää, P.1
  • 19
    • 84863191618 scopus 로고    scopus 로고
    • Icy: An open bioimage informatics platform for extended reproducible research
    • de Chaumont, F. et al. Icy: an open bioimage informatics platform for extended reproducible research. Nat. Methods 9, 690-696 (2012).
    • (2012) Nat. Methods , vol.9 , pp. 690-696
    • De Chaumont, F.1
  • 20
    • 84862520770 scopus 로고    scopus 로고
    • Fiji: An open-source platform for biological-image analysis
    • Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676-682 (2012).
    • (2012) Nat. Methods , vol.9 , pp. 676-682
    • Schindelin, J.1
  • 21
    • 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, J.H. & Myers, E.W. V3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets. Nat. Biotechnol. 28, 348-353 (2010).
    • (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
  • 22
    • 33845792555 scopus 로고    scopus 로고
    • CellProfiler: Image analysis software for identifying and quantifying cell phenotypes
    • Carpenter, A.E. et al. CellProfiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biol. 7, R100 (2006).
    • (2006) Genome Biol. , vol.7
    • Carpenter, A.E.1
  • 23
    • 17144363197 scopus 로고    scopus 로고
    • Reconstruct: A free editor for serial section microscopy
    • DOI 10.1111/j.1365-2818.2005.01466.x
    • Fiala, J.C. Reconstruct: a free editor for serial section microscopy. J. Microsc. 218, 52-61 (2005). (Pubitemid 40524168)
    • (2005) Journal of Microscopy , vol.218 , Issue.1 , pp. 52-61
    • Fiala, J.C.1
  • 25
    • 15044352366 scopus 로고    scopus 로고
    • OsiriX: An open-source software for navigating in multidimensional DICOM images
    • DOI 10.1007/s10278-004-1014-6
    • Rosset, A., Spadola, L., Ratib, O. & Osiri, X. An open-source software for navigating in multidimensional DICOM images. J. Digit. Imaging 17, 205-216 (2004). (Pubitemid 40378992)
    • (2004) Journal of Digital Imaging , vol.17 , Issue.3 , pp. 205-216
    • Rosset, A.1    Spadola, L.2    Ratib, O.3
  • 26
    • 0029879295 scopus 로고    scopus 로고
    • Computer visualization of three-dimensional image data using IMOD
    • DOI 10.1006/jsbi.1996.0013
    • Kremer, J.R., Mastronarde, D.N. & McIntosh, J.R. Computer visualization of three-dimensional image data using IMOD. J. Struct. Biol. 116, 71-76 (1996). (Pubitemid 26093126)
    • (1996) Journal of Structural Biology , vol.116 , Issue.1 , pp. 71-76
    • Kremer, J.R.1    Mastronarde, D.N.2    McIntosh, J.R.3
  • 27
    • 36048945922 scopus 로고    scopus 로고
    • ImageJ for microscopy
    • Collins, T.J. ImageJ for microscopy. Biotechniques 43, 25-30 (2007).
    • (2007) Biotechniques , vol.43 , pp. 25-30
    • Collins, T.J.1
  • 29
    • 84863205849 scopus 로고    scopus 로고
    • NIH Image to ImageJ: 25 years of image analysis
    • Schneider, C.A., Rasband, W.S. & Eliceiri, K.W. NIH Image to ImageJ: 25 years of image analysis. Nat. Methods 9, 671-675 (2012).
    • (2012) Nat. Methods , vol.9 , pp. 671-675
    • Schneider, C.A.1    Rasband, W.S.2    Eliceiri, K.W.3
  • 30
    • 79954500285 scopus 로고    scopus 로고
    • Improved structure, function and compatibility for CellProfiler: Modular high-throughput image analysis software
    • Kamentsky, L. et al. Improved structure, function and compatibility for CellProfiler: modular high-throughput image analysis software. Bioinformatics 27, 1179-1180 (2011).
    • (2011) Bioinformatics , vol.27 , pp. 1179-1180
    • Kamentsky, L.1
  • 31
    • 77952987028 scopus 로고    scopus 로고
    • Software for bead-based registration of selective plane illumination microscopy data
    • Preibisch, S., Saalfeld, S., Schindelin, J. & Tomancak, P. Software for bead-based registration of selective plane illumination microscopy data. Nat. Methods 7, 418-419 (2010).
    • (2010) Nat. Methods , vol.7 , pp. 418-419
    • Preibisch, S.1    Saalfeld, S.2    Schindelin, J.3    Tomancak, P.4
  • 32
    • 79960413901 scopus 로고    scopus 로고
    • Robust, globally consistent and fully automatic multi-image registration and montage synthesis for 3-D multi-channel images
    • Tsai, C.L. et al. Robust, globally consistent and fully automatic multi-image registration and montage synthesis for 3-D multi-channel images. J. Microsc. 243, 154-171 (2011).
    • (2011) J. Microsc. , vol.243 , pp. 154-171
    • Tsai, C.L.1
  • 33
    • 65649134709 scopus 로고    scopus 로고
    • Globally optimal stitching of tiled 3D microscopic image acquisitions
    • Preibisch, S., Saalfeld, S. & Tomancák, P. Globally optimal stitching of tiled 3D microscopic image acquisitions. Bioinformatics 25, 1463-1465 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 1463-1465
    • Preibisch, S.1    Saalfeld, S.2    Tomancák, P.3
  • 34
    • 84863192622 scopus 로고    scopus 로고
    • Elastic volume reconstruction from series of ultrathin microscopy sections
    • Saalfeld, S., Fetter, R., Cardona, R. & Tomancak, P. Elastic volume reconstruction from series of ultrathin microscopy sections. Nat. Methods 9, 717-720 (2012).
    • (2012) Nat. Methods , vol.9 , pp. 717-720
    • Saalfeld, S.1    Fetter, R.2    Cardona, R.3    Tomancak, P.4
  • 35
    • 77649266028 scopus 로고    scopus 로고
    • Visualization of image data from cells to organisms
    • Walter, T. et al. Visualization of image data from cells to organisms. Nat. Methods 7, S26-S41 (2010).
    • (2010) Nat. Methods , vol.7
    • Walter, T.1
  • 36
    • 67650770056 scopus 로고    scopus 로고
    • CATMAID: Collaborative annotation toolkit for massive amounts of image data
    • Saalfeld, S., Cardona, A., Hartenstein, V. & Tomancák, P. CATMAID: collaborative annotation toolkit for massive amounts of image data. Bioinformatics 25, 1984-1986 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 1984-1986
    • Saalfeld, S.1    Cardona, A.2    Hartenstein, V.3    Tomancák, P.4
  • 37
    • 80053993379 scopus 로고    scopus 로고
    • Simultaneous recognition and segmentation of cells: Application in C. elegans
    • Qu, L. et al. Simultaneous recognition and segmentation of cells: application in C. elegans. Bioinformatics 27, 2895-2902 (2011).
    • (2011) Bioinformatics , vol.27 , pp. 2895-2902
    • Qu, L.1
  • 38
    • 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, S.K. & Myers, E. A 3D digital atlas of C. elegans and its application to single-cell analyses. Nat. Methods 6, 667-672 (2009).
    • (2009) Nat. Methods , vol.6 , pp. 667-672
    • Long, F.1    Peng, H.2    Liu, X.3    Kim, S.K.4    Myers, E.5
  • 39
    • 77951959633 scopus 로고    scopus 로고
    • EBImage-an R package for image processing with applications to cellular phenotypes
    • Pau, G., Fuchs, F., Sklyar, O., Boutros, M. & Huber, W. EBImage-an R package for image processing with applications to cellular phenotypes. Bioinformatics 26, 979-981 (2010).
    • (2010) Bioinformatics , vol.26 , pp. 979-981
    • Pau, G.1    Fuchs, F.2    Sklyar, O.3    Boutros, M.4    Huber, W.5
  • 41
    • 79956124247 scopus 로고    scopus 로고
    • An active role for machine learning in drug development
    • Murphy, R.F. An active role for machine learning in drug development. Nat. Chem. Biol. 7, 327-330 (2011).
    • (2011) Nat. Chem. Biol. , vol.7 , pp. 327-330
    • Murphy, R.F.1
  • 42
    • 0141921564 scopus 로고    scopus 로고
    • Robust numerical features for description and classification of subcellular location patterns in fluorescence microscope images
    • Murphy, R.F., Velliste, M. & Porreca, G. Robust numerical features for description and classification of subcellular location patterns in fluorescence microscope images. J. VLSI Signal Process. 35, 311-321 (2003).
    • (2003) J. VLSI Signal Process. , vol.35 , pp. 311-321
    • Murphy, R.F.1    Velliste, M.2    Porreca, G.3
  • 43
    • 0037212267 scopus 로고    scopus 로고
    • Human vs. machine: Evaluation of fluorescence micrographs
    • DOI 10.1016/S0010-4825(02)00060-4, PII S0010482502000604
    • Nattkemper, T.W., Twellmann, T., Ritter, H. & Schubert, W. Human vs machine: evaluation of fluorescence micrographs. Comput. Biol. Med. 33, 31-43 (2003). (Pubitemid 35461950)
    • (2003) Computers in Biology and Medicine , vol.33 , Issue.1 , pp. 31-43
    • Nattkemper, T.W.1    Twellmann, T.2    Ritter, H.3    Schubert, W.4
  • 44
    • 51349152402 scopus 로고    scopus 로고
    • Quantitative image analysis reveals distinct structural transitions during aging in Caenorhabditis elegans tissues
    • Johnston, J., Iser, W.B., Chow, D.K., Goldberg, I.G. & Wolkow, C.A. Quantitative image analysis reveals distinct structural transitions during aging in Caenorhabditis elegans tissues. PLoS ONE 3, e2821 (2008).
    • (2008) PLoS ONE , vol.3
    • Johnston, J.1    Iser, W.B.2    Chow, D.K.3    Goldberg, I.G.4    Wolkow, C.A.5
  • 45
    • 13844300843 scopus 로고    scopus 로고
    • From quantitative microscopy to automated image understanding
    • DOI 10.1117/1.1779233
    • Huang, K. & Murphy, R.F. From quantitative microscopy to automated image understanding. J. Biomed. Opt. 9, 893-912 (2004). (Pubitemid 41268671)
    • (2004) Journal of Biomedical Optics , vol.9 , Issue.5 , pp. 893-912
    • Huang, K.1    Murphy, R.F.2
  • 46
    • 48349111792 scopus 로고    scopus 로고
    • Wndchrm-an open source utility for biological image analysis
    • Shamir, L. et al. Wndchrm-an open source utility for biological image analysis. Source Code Biol. Med. 3, 13 (2008).
    • (2008) Source Code Biol. Med. , vol.3 , pp. 13
    • Shamir, L.1
  • 47
    • 34250216344 scopus 로고    scopus 로고
    • Image-based multivariate profiling of drug responses from single cells
    • DOI 10.1038/nmeth1032, PII NMETH1032
    • Loo, L.H., Wu, L.F. & Altschuler, S.J. Image-based multivariate profiling of drug responses from single cells. Nat. Methods 4, 445-453 (2007). (Pubitemid 46901279)
    • (2007) Nature Methods , vol.4 , Issue.5 , pp. 445-453
    • Loo, L.-H.1    Wu, L.F.2    Altschuler, S.J.3
  • 49
    • 15844414198 scopus 로고    scopus 로고
    • Objective clustering of proteins based on subcellular location patterns
    • DOI 10.1155/JBB.2005.87
    • Chen, X. & Murphy, R.F. Objective clustering of proteins based on subcellular location patterns. J. Biomed. Biotechnol. 2005, 87-95 (2005). (Pubitemid 41627864)
    • (2005) Journal of Biomedicine and Biotechnology , vol.2005 , Issue.2 , pp. 87-95
    • Chen, X.1    Murphy, R.F.2
  • 50
    • 60549104030 scopus 로고    scopus 로고
    • Scoring diverse cellular morphologies in image-based screens with iterative feedback and machine learning
    • Jones, T.R. et al. Scoring diverse cellular morphologies in image-based screens with iterative feedback and machine learning. Proc. Natl. Acad. Sci. USA 106, 1826-1831 (2009).
    • (2009) Proc. Natl. Acad. Sci. USA , vol.106 , pp. 1826-1831
    • Jones, T.R.1
  • 51
    • 79959390442 scopus 로고    scopus 로고
    • Model building and intelligent acquisition with application to protein subcellular location classification
    • Jackson, C., Glory-Afshar, E., Murphy, R.F. & Kovacevic, J. Model building and intelligent acquisition with application to protein subcellular location classification. Bioinformatics 27, 1854-1859 (2011).
    • (2011) Bioinformatics , vol.27 , pp. 1854-1859
    • Jackson, C.1    Glory-Afshar, E.2    Murphy, R.F.3    Kovacevic, J.4
  • 52
    • 77649263885 scopus 로고    scopus 로고
    • Determining the distribution of probes between different subcellular locations through automated unmixing of subcellular patterns
    • Peng, T. et al. Determining the distribution of probes between different subcellular locations through automated unmixing of subcellular patterns. Proc. Natl. Acad. Sci. USA 107, 2944-2949 (2010).
    • (2010) Proc. Natl. Acad. Sci. USA , vol.107 , pp. 2944-2949
    • Peng, T.1
  • 53
    • 77954179297 scopus 로고    scopus 로고
    • Quantifying the distribution of probes between subcellular locations using unsupervised pattern unmixing
    • Coelho, L.P., Peng, T. & Murphy, R.F. Quantifying the distribution of probes between subcellular locations using unsupervised pattern unmixing. Bioinformatics 26, i7-i12 (2010).
    • (2010) Bioinformatics , vol.26
    • Coelho, L.P.1    Peng, T.2    Murphy, R.F.3
  • 55
    • 84863225010 scopus 로고    scopus 로고
    • Current challenges in open-source bioimage informatics
    • Cardona, A. & Tomancak, P. Current challenges in open-source bioimage informatics. Nat. Methods 9, 661-665 (2012).
    • (2012) Nat. Methods , vol.9 , pp. 661-665
    • Cardona, A.1    Tomancak, P.2
  • 57
    • 77953153778 scopus 로고    scopus 로고
    • Metadata matters: Access to image data in the real world
    • Linkert, M. et al. Metadata matters: access to image data in the real world. J. Cell Biol. 189, 777-782 (2010).
    • (2010) J. Cell Biol. , vol.189 , pp. 777-782
    • Linkert, M.1
  • 58
    • 84892535082 scopus 로고    scopus 로고
    • Ontologies for neuroscience: What are they and what are they good for?
    • Larson, S.D. & Martone, M.E. Ontologies for neuroscience: what are they and what are they good for? Front. Neurosci. 3, 60-67 (2009).
    • (2009) Front. Neurosci. , vol.3 , pp. 60-67
    • Larson, S.D.1    Martone, M.E.2
  • 59
    • 83755228921 scopus 로고    scopus 로고
    • New concepts for building vocabulary for cell image ontologies
    • Plant, A.L., Elliott, J.T. & Bhat, T.N. New concepts for building vocabulary for cell image ontologies. BMC Bioinformatics 12, 487 (2011).
    • (2011) BMC Bioinformatics , vol.12 , pp. 487
    • Plant, A.L.1    Elliott, J.T.2    Bhat, T.N.3
  • 60
    • 79952272336 scopus 로고    scopus 로고
    • Finding an image in a haystack: The case for public image repositories
    • Swedlow, J.R. Finding an image in a haystack: the case for public image repositories. Nat. Cell Biol. 13, 183 (2011).
    • (2011) Nat. Cell Biol. , vol.13 , pp. 183
    • Swedlow, J.R.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.