Hostname: page-component-586b7cd67f-rcrh6 Total loading time: 0 Render date: 2024-11-27T11:16:36.652Z Has data issue: false hasContentIssue false
  • English
  • Français

Scientific Python: A Mature Computational Ecosystem for Microscopy

Published online by Cambridge University Press:  05 August 2019

Stéfan van der Walt
Stéfan van der Walt*
Affiliation:
Berkeley Institute for Data Science, University of California, BerkeleyUSA.
*
*Corresponding author: [email protected]

Abstract

An abstract is not available for this content so a preview has been provided. As you have access to this content, a full PDF is available via the ‘Save PDF’ action button.
Image of the first page of this content. For PDF version, please use the ‘Save PDF’ preceeding this image.'
Type
Data Acquisition Schemes, Machine Learning Algorithms, and Open Source Software Development for Electron Microscopy
Information
Microscopy and Microanalysis , Volume 25 , Supplement S2 , August 2019 , pp. 132 - 133
Copyright
Copyright © Microscopy Society of America 2019 

References

[1]Robinson, D., “Why is python growing so quickly?” Stack Overflow blog. https://stackoverflow.blog/2017/09/14/python-growing-quickly, 2017.Google Scholar
[2]Elliott, T., “The state of the octoverse: Machine learning.” https://github.blog/2019-01-24-the-state-of-the-octoverse-machine-learning/, 2019.Google Scholar
[3]van der Walt, S. J., Colbert, S. C., and Varoquaux, G., “The NumPy array: a structure for efficient numerical computation,” Computing in Science & Engineering, vol. 13, no. 2, p. 22, 2011.Google Scholar
[4]Hoyer, S. and Hamman, J., “Xarray: N-D labeled arrays and datasets in Python,” Journal of Open Research Software, vol. 5, no. 1, 2017 [Online]. Available: http://doi.org/10.5334/jors.148Google Scholar
[5]Ramachandran, P. and Varoquaux, G., “Mayavi: 3D Visualization of Scientific Data,” Computing in Science & Engineering, vol. 13, no. 2, pp. 40–51, 2011.Google Scholar
[6]Carpenter, A. E. et al. , “CellProfiler: Image analysis software for identifying and quantifying cell phenotypes,” Genome Biology, vol. 7, no. 10, p. R100, Oct. 2006 [Online]. Available: https://doi.org/10.1186/gb-2006-7-10-r100Google Scholar
[7]Nunez-Iglesias, J., Blanch, A. J., Looker, O., Dixon, M. W., and Tilley, L., “A new python library to analyse skeleton images confirms malaria parasite remodelling of the red blood cell membrane skeleton,” in PeerJ, 2018.Google Scholar
[8]Allan, D. B., Caswell, T., Keim, N. C., and van der Wel, C. M., “Trackpy,” Apr. 2018 [Online]. Available: https://doi.org/10.5281/zenodo.1213240Google Scholar
[9]Somnath, S., Smith, C. R., Laanait, Nouamane, and Jesse, S., “Pycroscopy. Computer software. Oak ridge national laboratory” [Online]. Available: https://pycroscopy.github.io/pycroscopy/about.htmlGoogle Scholar
[10]Sommer, C., Straehle, C., Koethe, U., and Hamprecht, F. A., “Ilastik: Interactive learning and segmentation toolkit,” in Biomedical imaging: From nano to macro, 2011 ieee international symposium on, 2011, pp. 230–233.Google Scholar
[11]Rueden, C. T. et al. , “ImageJ2: ImageJ for the next generation of scientific image data,” BMC bioinformatics, vol. 18, no. 1, p. 529, 2017.Google Scholar
[12]Bradski, G., “The OpenCV Library,” Dr. Dobb's Journal of Software Tools, 2000.Google Scholar
[13]van der Walt, S. et al. , “Scikit-image: Image processing in Python,” PeerJ, vol. 2, p. e453, Jun. 2014 [Online]. Available: https://doi.org/10.7717/peerj.453Google Scholar
[14]Abernathey, R. et al. , “Pangeo NSF Earthcube Proposal,” Aug. 2017 [Online]. Available: https://figshare. com/articles/Pangeo_NSF_Earthcube_Proposal/5361094Google Scholar