Analyzing microtomography data with Python']Python and the scikit-image library

被引:25
作者
Gouillart, Emmanuelle [1 ]
Nunez-Iglesias, Juan [2 ]
van der Walt, Stefan [3 ]
机构
[1] St Gobain, CNRS, UMR 125, Surface Verre & Interfaces, F-93303 Aubervilliers, France
[2] Univ Melbourne, Victorian Life Sci Computat Initiat, Carlton, Vic, Australia
[3] Stellenbosch Univ, Div Appl Math, Stellenbosch, South Africa
关键词
Scikit-image; !text type='Python']Python[!/text; Image processing library; 3D image;
D O I
10.1186/s40679-016-0031-0
中图分类号
TH742 [显微镜];
学科分类号
摘要
The exploration and processing of images is a vital aspect of the scientific workflows of many X-ray imaging modalities. Users require tools that combine interactivity, versatility, and performance. scikit-image is an open-source image processing toolkit for the Python language that supports a large variety of file formats and is compatible with 2D and 3D images. The toolkit exposes a simple programming interface, with thematic modules grouping functions according to their purpose, such as image restoration, segmentation, and measurements. scikit-image users benefit from a rich scientific Python ecosystem that contains many powerful libraries for tasks such as visualization or machine learning. scikit-image combines a gentle learning curve, versatile image processing capabilities, and the scalable performance required for the high-throughput analysis of X-ray imaging data.
引用
收藏
页数:11
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[21]   SNAKES - ACTIVE CONTOUR MODELS [J].
KASS, M ;
WITKIN, A ;
TERZOPOULOS, D .
INTERNATIONAL JOURNAL OF COMPUTER VISION, 1987, 1 (04) :321-331
[22]   Jupyter Notebooks-a publishing format for reproducible computational workflows [J].
Kluyver, Thomas ;
Ragan-Kelley, Benjamin ;
Perez, Fernando ;
Granger, Brian ;
Bussonnier, Matthias ;
Frederic, Jonathan ;
Kelley, Kyle ;
Hamrick, Jessica ;
Grout, Jason ;
Corlay, Sylvain ;
Ivanov, Paul ;
Avila, Damin ;
Abdalla, Safia ;
Willing, Carol .
POSITIONING AND POWER IN ACADEMIC PUBLISHING: PLAYERS, AGENTS AND AGENDAS, 2016, :87-90
[23]   FabIO: easy access to two-dimensional X-ray detector images in Python']Python [J].
Knudsen, Erik B. ;
Sorensen, Henning O. ;
Wright, Jonathan P. ;
Goret, Gael ;
Kieffer, Jerome .
JOURNAL OF APPLIED CRYSTALLOGRAPHY, 2013, 46 :537-539
[24]   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
[25]   Quantitative X-ray tomography [J].
Maire, E. ;
Withers, P. J. .
INTERNATIONAL MATERIALS REVIEWS, 2014, 59 (01) :1-43
[26]   A fluoroscopy-based planning and guidance software tool for minimally invasive hip refixation by cement injection [J].
Malan, Daniel F. ;
van der Walt, Stefan J. ;
Raidou, Renata G. ;
van den Berg, Bas ;
Stoel, Berend C. ;
Botha, Charl P. ;
Nelissen, Rob G. H. H. ;
Valstar, Edward R. .
INTERNATIONAL JOURNAL OF COMPUTER ASSISTED RADIOLOGY AND SURGERY, 2016, 11 (02) :281-296
[27]   Fast reconstruction algorithm dealing with tomography artifacts [J].
Marone, Federica ;
Muench, Beat ;
Stampanoni, Marco .
DEVELOPMENTS IN X-RAY TOMOGRAPHY VII, 2010, 7804
[28]   The PyHST2 hybrid distributed code for high speed tomographic reconstruction with iterative reconstruction and a priori knowledge capabilities [J].
Mirone, Alessandro ;
Brun, Emmanuel ;
Gouillart, Emmanuelle ;
Tafforeau, Paul ;
Kieffer, Jerome .
NUCLEAR INSTRUMENTS & METHODS IN PHYSICS RESEARCH SECTION B-BEAM INTERACTIONS WITH MATERIALS AND ATOMS, 2014, 324 :41-48
[29]  
Nunez-Iglesias J., 2016, COUNTING PROGRAMMING, DOI [10. 5281/ zenodo. 163863, DOI 10.5281/ZEN0D0.163863]
[30]   Python']Python for scientific computing [J].
Oliphant, Travis E. .
COMPUTING IN SCIENCE & ENGINEERING, 2007, 9 (03) :10-20