Publication: Keras R-CNN: library for cell detection in biological images using deep neural networks
Issued Date
2020-07-11
Resource Type
ISSN
14712105
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2-s2.0-85087872385
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Mahidol University
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SCOPUS
Bibliographic Citation
BMC bioinformatics. Vol.21, No.1 (2020), 300
Suggested Citation
Jane Hung, Allen Goodman, Deepali Ravel, Stefanie C.P. Lopes, Gabriel W. Rangel, Odailton A. Nery, Benoit Malleret, Francois Nosten, Marcus V.G. Lacerda, Marcelo U. Ferreira, Laurent Rénia, Manoj T. Duraisingh, Fabio T.M. Costa, Matthias Marti, Anne E. Carpenter Keras R-CNN: library for cell detection in biological images using deep neural networks. BMC bioinformatics. Vol.21, No.1 (2020), 300. doi:10.1186/s12859-020-03635-x Retrieved from: https://repository.li.mahidol.ac.th/handle/20.500.14594/57697
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Title
Keras R-CNN: library for cell detection in biological images using deep neural networks
Other Contributor(s)
A-Star, Singapore Immunology Network
Fundacao de Medicina Tropical do Amazonas
Shoklo Malaria Research Unit
Harvard T.H. Chan School of Public Health
Universidade Estadual de Campinas
Yong Loo Lin School of Medicine
Fundacao Oswaldo Cruz
Massachusetts Institute of Technology
Nuffield Department of Medicine
Universidade de Sao Paulo - USP
College of Medical, Veterinary & Life Sciences
Broad Institute
Fundacao de Medicina Tropical do Amazonas
Shoklo Malaria Research Unit
Harvard T.H. Chan School of Public Health
Universidade Estadual de Campinas
Yong Loo Lin School of Medicine
Fundacao Oswaldo Cruz
Massachusetts Institute of Technology
Nuffield Department of Medicine
Universidade de Sao Paulo - USP
College of Medical, Veterinary & Life Sciences
Broad Institute
Abstract
BACKGROUND: A common yet still manual task in basic biology research, high-throughput drug screening and digital pathology is identifying the number, location, and type of individual cells in images. Object detection methods can be useful for identifying individual cells as well as their phenotype in one step. State-of-the-art deep learning for object detection is poised to improve the accuracy and efficiency of biological image analysis. RESULTS: We created Keras R-CNN to bring leading computational research to the everyday practice of bioimage analysts. Keras R-CNN implements deep learning object detection techniques using Keras and Tensorflow ( https://github.com/broadinstitute/keras-rcnn ). We demonstrate the command line tool's simplified Application Programming Interface on two important biological problems, nucleus detection and malaria stage classification, and show its potential for identifying and classifying a large number of cells. For malaria stage classification, we compare results with expert human annotators and find comparable performance. CONCLUSIONS: Keras R-CNN is a Python package that performs automated cell identification for both brightfield and fluorescence images and can process large image sets. Both the package and image datasets are freely available on GitHub and the Broad Bioimage Benchmark Collection.