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Allen Goodman
Researcher at Broad Institute
Publications - 27
Citations - 3113
Allen Goodman is an academic researcher from Broad Institute. The author has contributed to research in topics: Deep learning & Convolutional neural network. The author has an hindex of 11, co-authored 25 publications receiving 1465 citations. Previous affiliations of Allen Goodman include McMaster University & San Jose State University.
Papers
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Journal ArticleDOI
CellProfiler 3.0: Next-generation image processing for biology.
Claire McQuin,Allen Goodman,Vasiliy S. Chernyshev,Vasiliy S. Chernyshev,Lee Kamentsky,Beth A. Cimini,Kyle W. Karhohs,Minh Doan,Liya Ding,Susanne M. Rafelski,Derek Thirstrup,Winfried Wiegraebe,Shantanu Singh,Tim Becker,Juan C. Caicedo,Anne E. Carpenter +15 more
TL;DR: CellProfiler 3.0 is described, a new version of the software supporting both whole-volume and plane-wise analysis of three-dimensional image stacks, increasingly common in biomedical research.
Journal ArticleDOI
Nucleus segmentation across imaging experiments: the 2018 Data Science Bowl.
Juan C. Caicedo,Allen Goodman,Kyle W. Karhohs,Beth A. Cimini,Jeanelle Ackerman,Marzieh Haghighi,CherKeng Heng,Tim Becker,Minh Doan,Claire McQuin,Mohammad Hossein Rohban,Shantanu Singh,Anne E. Carpenter +12 more
TL;DR: The 2018 Data Science Bowl attracted 3,891 teams worldwide to make the first attempt to build a segmentation method that could be applied to any two-dimensional light microscopy image of stained nuclei across experiments, with no human interaction.
Journal ArticleDOI
CellProfiler 4: improvements in speed, utility and usability.
David R. Stirling,Madison J. Swain-Bowden,Alice Lucas,Anne E. Carpenter,Beth A. Cimini,Allen Goodman +5 more
TL;DR: The CellProfiler 4 as discussed by the authors is a new version of this software with expanded functionality based on user feedback, and it has made several user interface refinements to improve the usability of the software.
Journal ArticleDOI
Evaluation of Deep Learning Strategies for Nucleus Segmentation in Fluorescence Images
Juan C. Caicedo,Jonathan R. Roth,Allen Goodman,Tim Becker,Kyle W. Karhohs,Matthieu Broisin,Matthieu Broisin,Csaba Molnar,Csaba Molnar,Claire McQuin,Shantanu Singh,Fabian J. Theis,Anne E. Carpenter +12 more
TL;DR: An evaluation framework is presented to measure accuracy, types of errors, and computational efficiency of deep learning strategies and classical approaches; and it is shown that deep learning improves accuracy and can reduce the number of biologically relevant errors by half.
Posted ContentDOI
CellProfiler 4: Improvements in Speed, Utility and Usability
David R. Stirling,Madison J. Swain-Bowden,Alice Lucas,Anne E. Carpenter,Beth A. Cimini,Allen Goodman +5 more
TL;DR: The CellProfiler 4 as mentioned in this paper is a new version of this software which has been ported to the Python 3 language based on user feedback, which has made several user interface refinements to improve the usability of the software.