skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Cellular structure image classification with small targeted training samples

Abstract

Cell shapes provide crucial biological information on complex tissues. Different cell types often have distinct cell shapes, and collective shape changes usually indicate morphogenetic events and mechanisms. The identification and detection of collective cell shape changes in an extensive collection of 3D time-lapse images of complex tissues is an important step in assaying such mechanisms but is a tedious and time-consuming task. Machine learning provides new opportunities to automatically detect cell shape changes. However, it is challenging to generate sufficient training samples for pattern identification through deep learning because of a limited amount of images and annotations. We present a deep learning approach with minimal well-annotated training samples and apply it to identify multicellular rosettes from 3D live images of the Caenorhabditis elegans embryo with fluorescently labeled cell membranes. Our strategy is to combine two approaches, namely, feature transfer and generative adversarial networks (GANs), to boost image classification with small training samples. Specifically, we use a GAN framework and conduct an unsupervised training to capture the general characteristics of cell membrane images with 11,250 unlabelled images. We then transfer the structure of the GAN discriminator into a new Alex-style neural network for further learning with several dozen labeled samples. Ourmore » experiments showed that with 10–15 well-labeled rosette images and 30–40 randomly selected nonrosette images our approach can identify rosettes with more than 80% accuracy and capture more than 90% of the model accuracy achieved with a training data et that is five times larger. We also established a public benchmark dataset for rosette detection. This GAN-based transfer approach can be applied to the study of other cellular structures with minimal training samples.« less

Authors:
ORCiD logo [1];  [2];  [3];  [2];  [3];  [3]
  1. Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  2. Univ. of Tennessee, Knoxville, TN (United States)
  3. Sloan Kettering Inst., New York, NY (United States)
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1561625
Grant/Contract Number:  
AC05-00OR22725
Resource Type:
Accepted Manuscript
Journal Name:
IEEE Access
Additional Journal Information:
Journal Name: IEEE Access; Journal ID: ISSN 2169-3536
Publisher:
IEEE
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Cell structure identification; embryogenesis; small dataset; generative adversarial network

Citation Formats

Wang, Dali, Lu, Zheng, Xu, Yichi, Wang, Zi, Santella, Anthony, and Bao, Zhirong. Cellular structure image classification with small targeted training samples. United States: N. p., 2019. Web. doi:10.1109/ACCESS.2019.2940161.
Wang, Dali, Lu, Zheng, Xu, Yichi, Wang, Zi, Santella, Anthony, & Bao, Zhirong. Cellular structure image classification with small targeted training samples. United States. doi:10.1109/ACCESS.2019.2940161.
Wang, Dali, Lu, Zheng, Xu, Yichi, Wang, Zi, Santella, Anthony, and Bao, Zhirong. Mon . "Cellular structure image classification with small targeted training samples". United States. doi:10.1109/ACCESS.2019.2940161. https://www.osti.gov/servlets/purl/1561625.
@article{osti_1561625,
title = {Cellular structure image classification with small targeted training samples},
author = {Wang, Dali and Lu, Zheng and Xu, Yichi and Wang, Zi and Santella, Anthony and Bao, Zhirong},
abstractNote = {Cell shapes provide crucial biological information on complex tissues. Different cell types often have distinct cell shapes, and collective shape changes usually indicate morphogenetic events and mechanisms. The identification and detection of collective cell shape changes in an extensive collection of 3D time-lapse images of complex tissues is an important step in assaying such mechanisms but is a tedious and time-consuming task. Machine learning provides new opportunities to automatically detect cell shape changes. However, it is challenging to generate sufficient training samples for pattern identification through deep learning because of a limited amount of images and annotations. We present a deep learning approach with minimal well-annotated training samples and apply it to identify multicellular rosettes from 3D live images of the Caenorhabditis elegans embryo with fluorescently labeled cell membranes. Our strategy is to combine two approaches, namely, feature transfer and generative adversarial networks (GANs), to boost image classification with small training samples. Specifically, we use a GAN framework and conduct an unsupervised training to capture the general characteristics of cell membrane images with 11,250 unlabelled images. We then transfer the structure of the GAN discriminator into a new Alex-style neural network for further learning with several dozen labeled samples. Our experiments showed that with 10–15 well-labeled rosette images and 30–40 randomly selected nonrosette images our approach can identify rosettes with more than 80% accuracy and capture more than 90% of the model accuracy achieved with a training data et that is five times larger. We also established a public benchmark dataset for rosette detection. This GAN-based transfer approach can be applied to the study of other cellular structures with minimal training samples.},
doi = {10.1109/ACCESS.2019.2940161},
journal = {IEEE Access},
number = ,
volume = ,
place = {United States},
year = {2019},
month = {9}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Save / Share: