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Scientific Python: A Mature Computational Ecosystem for Microscopy

Published online by Cambridge University Press:  05 August 2019

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

Abstract

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Type
Data Acquisition Schemes, Machine Learning Algorithms, and Open Source Software Development for Electron Microscopy
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. 4051, 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. 230233.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