Microscopic image segmentation is indispensable biomedical research. However, accurately segmenting using traditional automatic segmentation methods remains challenging due to fluorescence presenting high intra- and inter-image variability, hindering biomedical analysis. Deep learning (DL)-based methods show remarkable potential in microscopic image segmentation. However, DL models typically require GPU resources, specialized programming skills, and a non-trivial environment setup, making it difficult for medical researchers to use them currently. Therefore, we propose a turnkey solution for microscopic image segmentation by Look-up Table (LUT) which is a data structure used for storing input values and pre-calculated results. Our solution can inherit the segmentation accuracy of DL-based methods and eliminates the need for extensive computational resources, specialized programming, and a complex implementation environment. Specifically, (1) By transferring all potential inputs and their DL model-computed outputs into a LUT, segmentation is achieved through direct output look-up for given pixel values. (2) Additionally, we develop a dilated CNN with adaptive edge padding, enhancing feature learning while meeting LUT building requirements. (3) Moreover, we publicly release a confocal microscopic image dataset and develop a LUT-based plugin (SEG-LUT plugin) for Fiji ImageJ. The experimental results show our framework outperforms other automatic segmentation methods in the Fiji ImageJ. Our solution offers a pathway for easily utilizing DL-based methods for microscopic image segmentation. Our codes, plugin, and dataset are available at https://github.com/MoriLabNU/Microscopic_Image_Segment_LUT.

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A Deployable Microscopic Image Segmentation Look-Up Table Based on A Dilated CNN

  • Yunheng Wu,
  • Jiazhen Pan,
  • Shuntaro Kawamura,
  • Masahiro Oda,
  • Yuichiro Hayashi,
  • Takanori Takebe,
  • Daniel Rueckert,
  • Kensaku Mori

摘要

Microscopic image segmentation is indispensable biomedical research. However, accurately segmenting using traditional automatic segmentation methods remains challenging due to fluorescence presenting high intra- and inter-image variability, hindering biomedical analysis. Deep learning (DL)-based methods show remarkable potential in microscopic image segmentation. However, DL models typically require GPU resources, specialized programming skills, and a non-trivial environment setup, making it difficult for medical researchers to use them currently. Therefore, we propose a turnkey solution for microscopic image segmentation by Look-up Table (LUT) which is a data structure used for storing input values and pre-calculated results. Our solution can inherit the segmentation accuracy of DL-based methods and eliminates the need for extensive computational resources, specialized programming, and a complex implementation environment. Specifically, (1) By transferring all potential inputs and their DL model-computed outputs into a LUT, segmentation is achieved through direct output look-up for given pixel values. (2) Additionally, we develop a dilated CNN with adaptive edge padding, enhancing feature learning while meeting LUT building requirements. (3) Moreover, we publicly release a confocal microscopic image dataset and develop a LUT-based plugin (SEG-LUT plugin) for Fiji ImageJ. The experimental results show our framework outperforms other automatic segmentation methods in the Fiji ImageJ. Our solution offers a pathway for easily utilizing DL-based methods for microscopic image segmentation. Our codes, plugin, and dataset are available at https://github.com/MoriLabNU/Microscopic_Image_Segment_LUT.