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paper.bib
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@ARTICLE{behnel:2010,
author={Behnel, S. and Bradshaw, R. and Citro, C. and Dalcin, L. and Seljebotn, D.S. and Smith, K.},
journal={Computing in Science Engineering},
title={Cython: The Best of Both Worlds},
year={2011},
month={march-april},
volume={13},
number={2},
pages={31 -39},
keywords={Cython language;Fortran code;Python language extension;numerical loops;programming language;C language;numerical analysis;},
doi={10.1109/MCSE.2010.118},
ISSN={1521-9615},
}
@software{Clark:2016,
author={Alex Clark, Andrew Murray, Alexander Karpinsky, Christoph Gohlke, Brian Crowell, David Schmidt, Alastair Houghton, Steve Johnson, Sandro Mani, Josh Ware, David Caro, Steve Kossouho, Eric W. Brown, Antony Lee, Mikhail Korobov, Michał Górny, Esteban Santana Santana, Nicolas Pieuchot, Oliver Tonnhofer, Michael Brown, Benoit Pierre, Joaquín Cuenca Abela, Lars Jørgen Solberg, Felipe Reyes, Alexey Buzanov, Yifu Yu, Fredrik Tolf, wiredfool, Hugo, eliempje, ThoughtSynth},
title={Pillow},
year={2016},
doi={10.5281/zenodo.44297}
}
@software{Costa-Luis:2019,
author={{da Costa-Luis}, Casper},
title={tqdm: A Fast, Extensible Progress Meter for Python and CLI},
journal={Journal of Open Source Software},
year={2019},
doi={10.21105/joss.01277}
}
@article{Durden:2019,
author={Andrew Durden},
title={Modelling Diffuse Subcellular Protein Structures as Dynamic Social Networks},
year={2019},
eprint={1904.12960},
archivePrefix={arXiv},
primaryClass={q-bio.SC}
}
@InProceedings{ Andrew_Durden-proc-scipy-2018,
author = { {A}ndrew {D}urden and {A}llyson {T} {L}oy and {B}arbara {R}eaves and {M}ojtaba {F}azli and {A}bigail {C}ourtney and {F}rederick {D} {Q}uinn and {S} {C}hakra {C}hennubhotla and {S}hannon {P} {Q}uinn },
title = { {D}ynamic {S}ocial {N}etwork {M}odeling of {D}iffuse {S}ubcellular {M}orphologies },
booktitle = { {P}roceedings of the 17th {P}ython in {S}cience {C}onference },
pages = { 1 - 7 },
year = { 2018 },
editor = { {F}atih {A}kici and {D}avid {L}ippa and {D}illon {N}iederhut and {M} {P}acer },
doi = { 10.25080/Majora-4af1f417-000 }
}
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author={Eric A. Hagberg, Daniel A. Schult and Pieter J. Swart},
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journal={Proceedings of the 7th Python in Science Conference (SciPy2008)},
pages={11--15},
month={Aug},
year={2008}
}
@Article{Hunter:2007,
Author = {Hunter, J. D.},
Title = {Matplotlib: A 2D graphics environment},
Journal = {Computing in Science \& Engineering},
Volume = {9},
Number = {3},
Pages = {90--95},
abstract = {Matplotlib is a 2D graphics package used for Python for
application development, interactive scripting, and publication-quality
image generation across user interfaces and operating systems.},
publisher = {IEEE COMPUTER SOC},
doi = {10.1109/MCSE.2007.55},
year = {2007}
}
@misc{kiwisolver2018,
month = {5},
title = {kiwisolver},
version = {rev 5dtKQ1Z3cpsFKT8nfQEpQhw3PNcqim},
year = {2018}
}
@software{Klein:2019,
author={Almar Klein, Steven Silvester, Anthony Tanbakuchi, Paul Müller, Juan Nunez-Iglesias, Mark Harfouche, Matt McCormick, Ariel Ladegaard, Arash Rai, OrganicIrradiation, Tim D. Smith, Marcin Konowalczyk, rreilink, Joel Nises, jackwalker64, Ghislain Antony Vaillant, Chris Barnes, Zulko, Po-Chuan Hsieh, NiklasRosenstein, Michael Hirsch, Ph.D., Maximilian Schambach, Joe Singleton, Hugo van Kemenade, Graham Inggs, Ge Yang, Felix Kohlgrüber, Chris Dusold, Anselm Levskaya, Addison Elliott},
title={Imageio},
year={2019},
doi={10.5281/zenodo.3475011}
}
@software{Lee:2019,
author={Gregory R. Lee, Ralf Gommers, Filip Wasilewski, Kai Wohlfahrt, Aaron O’Leary},
title={PyWavelets: A Python package for wavelet analysis},
journal={Journal of Open Source Software},
year={2019},
doi={10.21105/joss.01237}
}
@book{Mcguire:2007,
author = {McGuire, Paul},
title = {Getting Started with Pyparsing},
year = {2007},
isbn = {9780596514235},
publisher = {O’Reilly},
edition = {First}
}
@Misc{Numpy:2006,
author = {Travis Oliphant},
title = {{NumPy}: A guide to {NumPy}},
year = {2006--},
howpublished = {USA: Trelgol Publishing},
url = {http://www.numpy.org/},
note = {[Online; accessed <today>]}
}
@article{opencv_library,
author = {Bradski, G.},
journal = {Dr. Dobb's Journal of Software Tools},
keywords = {bibtex-import},
title = {{The OpenCV Library}},
year = {2000}
}
@techreport{Python:1995,
title={Python tutorial, Technical Report CS-R9526},
publisher={Centrum voor Wiskunde en Informatica (CWI)},
author={G. van Rossum},
year={1995},
month={May}
}
@article{Ruan:2019,
Archiveprefix = {bioRxiv},
Author = {{Ruan}, X. and {Johnson}, G.~R. and {Johnson}, I.~B. and {Nitschke}, R. and {Boerries}, M. and {Busch}, H. and {Murphy}, R.~F.},
DOI = {10.1101/522763},
Journal = {BioRXiv},
Keywords = {Cell Biology},
Month = {jan},
Title = {{Image-derived Models of Cell Organization Changes During Differentiation of PC12 Cells}},
Year = {2019}
}
@software{scikit-image:2014,
author={Stéfan van der Walt, Johannes L. Schönberger, Juan Nunez-Iglesias, François Boulogne, Joshua D. Warner, Neil Yager, Emmanuelle Gouillart, Tony Yu, and the scikit-image contributors},
title={scikit-image: Image processing in Python},
eprint={PeerJ 2:e453},
year={2014},
doi={10.7717/peerj.453}
}
@article{scikit-learn:2011,
title={Scikit-learn: Machine Learning in {P}ython},
author={Pedregosa, F. and Varoquaux, G. and Gramfort, A. and Michel, V.
and Thirion, B. and Grisel, O. and Blondel, M. and Prettenhofer, P.
and Weiss, R. and Dubourg, V. and Vanderplas, J. and Passos, A. and
Cournapeau, D. and Brucher, M. and Perrot, M. and Duchesnay, E.},
journal={Journal of Machine Learning Research},
volume={12},
pages={2825--2830},
year={2011}
}
@ARTICLE{2019arXiv190710121V,
author = {{Virtanen}, Pauli and {Gommers}, Ralf and {Oliphant},
Travis E. and {Haberland}, Matt and {Reddy}, Tyler and
{Cournapeau}, David and {Burovski}, Evgeni and {Peterson}, Pearu
and {Weckesser}, Warren and {Bright}, Jonathan and {van der Walt},
St{\'e}fan J. and {Brett}, Matthew and {Wilson}, Joshua and
{Jarrod Millman}, K. and {Mayorov}, Nikolay and {Nelson}, Andrew
R.~J. and {Jones}, Eric and {Kern}, Robert and {Larson}, Eric and
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Eric W. and {Vand erPlas}, Jake and {Laxalde}, Denis and
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{Quintero}, E.~A. and {Harris}, Charles R and {Archibald}, Anne M.
and {Ribeiro}, Ant{\^o}nio H. and {Pedregosa}, Fabian and
{van Mulbregt}, Paul and {Contributors}, SciPy 1. 0},
title = "{SciPy 1.0--Fundamental Algorithms for Scientific
Computing in Python}",
journal = {arXiv e-prints},
year = "2019",
month = "Jul",
eid = {arXiv:1907.10121},
pages = {arXiv:1907.10121},
archivePrefix = {arXiv},
eprint = {1907.10121},
primaryClass = {cs.MS},
}
@techreport{Yoo:2002,
title={Engineering and Algorithm Design for an Image Processing API: A Technical Report on ITK - The Insight Toolkit},
author={T.S. Yoo, M. J. Ackerman, W. E. Lorensen, W. Schroeder, V. Chalana, S. Aylward, D. Metaxas, R. Whitaker},
journal={Proc. of Medicine Meets Virtual Reality, J. Westwood, ed.},
pages={586--592},
year={2002},
publisher={IOS Press Amsterdam}
}
@article {Chen:2016,
author = {Chen, Jianxu and Ding, Liya and Viana, Matheus P. and Hendershott, Melissa C. and Yang, Ruian and Mueller, Irina A. and Rafelski, Susanne M.},
title = {The Allen Cell Structure Segmenter: a new open source toolkit for segmenting 3D intracellular structures in fluorescence microscopy images},
elocation-id = {491035},
year = {2018},
doi = {10.1101/491035},
publisher = {Cold Spring Harbor Laboratory},
URL = {https://www.biorxiv.org/content/early/2018/12/08/491035},
eprint = {https://www.biorxiv.org/content/early/2018/12/08/491035.full.pdf},
journal = {bioRxiv}
}
@article {Stavru:2011,
author = {Stavru, Fabrizia and Cossart, Pascale},
year = {2011},
month = {05},
pages = {364-6},
title = {Listeria infection modulates mitochondrial dynamics},
volume = {4},
journal = {Communicative & integrative biology},
doi = {10.4161/cib.4.3.15506}
}
@article{Murphy:2015,
author = {Murphy, Robert},
year = {2015},
month = {10},
pages = {},
title = {Building Cell Models and Simulations from Microscope Images},
volume = {96},
journal = {Methods (San Diego, Calif.)},
doi = {10.1016/j.ymeth.2015.10.011}
}
@article{Eliceiri:2012,
author={Eliceiri KW, Berthold MR, Goldberg IG, Ibáñez L, Manjunath BS, Martone ME, Murphy RF, Peng H, Plant AL, Roysam B, Stuurman N, Swedlow JR, Tomanack P, Carpenter AE},
title={Biological imaging software tools},
journal={Nature Methods},
year={2012}
}