Construction of a system using a deep learning algorithm to count cell numbers in nanoliter wells for viable single-cell experiments

Takashi Kamatani, Koichi Fukunaga, Kaede Miyata, Yoshitaka Shirasaki, Junji Tanaka, Rie Baba, Masako Matsusaka, Naoyuki Kamatani, Kazuyo Moro, Tomoko Betsuyaku, Sotaro Uemura

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Abstract

For single-cell experiments, it is important to accurately count the number of viable cells in a nanoliter well. We used a deep learning-based convolutional neural network (CNN) on a large amount of digital data obtained as microscopic images. The training set consisted of 103 019 samples, each representing a microscopic grayscale image. After extensive training, the CNN was able to classify the samples into four categories, i.e., 0, 1, 2, and more than 2 cells per well, with an accuracy of 98.3% when compared to determination by two trained technicians. By analyzing the samples for which judgments were discordant, we found that the judgment by technicians was relatively correct although cell counting was often difficult by the images of discordant samples. Based on the results, the system was further enhanced by introducing a new algorithm in which the highest outputs from CNN were used, increasing the accuracy to higher than 99%. Our system was able to classify the data even from wells with a different shape. No other tested machine learning algorithm showed a performance higher than that of our system. The presented CNN system is expected to be useful for various single-cell experiments, and for high-Throughput and high-content screening.

Original languageEnglish
Article number16831
JournalScientific Reports
Volume7
Issue number1
DOIs
Publication statusPublished - 2017 Dec 1

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Cite this

Kamatani, T., Fukunaga, K., Miyata, K., Shirasaki, Y., Tanaka, J., Baba, R., Matsusaka, M., Kamatani, N., Moro, K., Betsuyaku, T., & Uemura, S. (2017). Construction of a system using a deep learning algorithm to count cell numbers in nanoliter wells for viable single-cell experiments. Scientific Reports, 7(1), [16831]. https://doi.org/10.1038/s41598-017-17012-x