Improved structure, function and compatibility for CellProfiler: modular high-throughput image analysis software

被引:756
作者
Kamentsky, Lee [1 ]
Jones, Thouis R. [1 ]
Fraser, Adam [1 ]
Bray, Mark-Anthony [1 ]
Logan, David J. [1 ]
Madden, Katherine L. [1 ]
Ljosa, Vebjorn [1 ]
Rueden, Curtis [2 ]
Eliceiri, Kevin W. [2 ]
Carpenter, Anne E. [1 ]
机构
[1] Harvard & MIT, Broad Inst, Cambridge, MA 02142 USA
[2] Univ Wisconsin, Lab Opt & Computat Instrumentat, Madison, WI 53706 USA
基金
美国国家卫生研究院;
关键词
D O I
10.1093/bioinformatics/btr095
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
There is a strong and growing need in the biology research community for accurate, automated image analysis. Here, we describe CellProfiler 2.0, which has been engineered to meet the needs of its growing user base. It is more robust and user friendly, with new algorithms and features to facilitate high-throughput work. ImageJ plugins can now be run within a CellProfiler pipeline.
引用
收藏
页码:1179 / 1180
页数:2
相关论文
共 11 条
[1]   CellProfiler: image analysis software for identifying and quantifying cell phenotypes [J].
Carpenter, Anne E. ;
Jones, Thouis Ray ;
Lamprecht, Michael R. ;
Clarke, Colin ;
Kang, In Han ;
Friman, Ola ;
Guertin, David A. ;
Chang, Joo Han ;
Lindquist, Robert A. ;
Moffat, Jason ;
Golland, Polina ;
Sabatini, David M. .
GENOME BIOLOGY, 2006, 7 (10)
[2]   Robust single-particle tracking in live-cell time-lapse sequences [J].
Jaqaman, Khuloud ;
Loerke, Dinah ;
Mettlen, Marcel ;
Kuwata, Hirotaka ;
Grinstein, Sergio ;
Schmid, Sandra L. ;
Danuser, Gaudenz .
NATURE METHODS, 2008, 5 (08) :695-702
[3]   Scoring diverse cellular morphologies in image-based screens with iterative feedback and machine learning [J].
Jones, Thouis R. ;
Carpenter, Anne E. ;
Lamprecht, Michael R. ;
Moffat, Jason ;
Silver, Serena J. ;
Grenier, Jennifer K. ;
Castoreno, Adam B. ;
Eggert, Ulrike S. ;
Root, David E. ;
Golland, Polina ;
Sabatini, David M. .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2009, 106 (06) :1826-1831
[4]  
Knutsson H., 1993, Proceedings. 1993 IEEE Computer Society Conference on Computer Vision and Pattern Recognition (Cat. No.93CH3309-2), P515, DOI 10.1109/CVPR.1993.341081
[5]   CellProfilerTM:: free, versatile software for automated biological image analysis [J].
Lamprecht, Michael R. ;
Sabatini, David M. ;
Carpenter, Anne E. .
BIOTECHNIQUES, 2007, 42 (01) :71-75
[6]  
Lindblad J., 2001, Proceedings of 12th Scandinavian Conference on Image Analysis, P264
[7]   Enhanced CellClassifier: a multi-class classification tool for microscopy images [J].
Misselwitz, Benjamin ;
Strittmatter, Gerhard ;
Periaswamy, Balamurugan ;
Schlumberger, Markus C. ;
Rout, Samuel ;
Horvath, Peter ;
Kozak, Karol ;
Hardt, Wolf-Dietrich .
BMC BIOINFORMATICS, 2010, 11
[8]   Python']Python for scientific computing [J].
Oliphant, Travis E. .
COMPUTING IN SCIENCE & ENGINEERING, 2007, 9 (03) :10-20
[9]   CellClassifier: supervised learning of cellular phenotypes [J].
Raemoe, Pauli ;
Sacher, Raphael ;
Snijder, Berend ;
Begemann, Boris ;
Pelkmans, Lucas .
BIOINFORMATICS, 2009, 25 (22) :3028-3030
[10]  
RIKLINRAVIV T, 2010, C MED IM COMP COMP A