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Enforcing Morphological Information in Fully Convolutional Networks to Improve Cell Instance Segmentation in Fluorescence Microscopy Images

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Advances in Computational Intelligence (IWANN 2021)

Abstract

Cell instance segmentation in fluorescence microscopy images is becoming essential for cancer dynamics and prognosis. Data extracted from cancer dynamics allows to understand and accurately model different metabolic processes such as proliferation. This enables customized and more precise cancer treatments. However, accurate cell instance segmentation, necessary for further cell tracking and behavior analysis, is still challenging in scenarios with high cell concentration and overlapping edges. Within this framework, we propose a novel cell instance segmentation approach based on the well-known U-Net architecture. To enforce the learning of morphological information per pixel, a deep distance transformer (DDT) acts as a back-bone model. The DDT output is subsequently used to train a top-model. The following top-models are considered: a three-class (e.g., foreground, background and cell border) U-net, and a watershed transform. The obtained results suggest a performance boost over traditional U-Net architectures. This opens an interesting research line around the idea of injecting morphological information into a fully convolutional model.

This work is partially supported by the following Spanish grants: TIN2016-75097-P, RTI2018-094645-B-I00 and UMA18-FEDERJA-084. All of them include funds from the European Regional Development Fund (ERDF). The authors acknowledge the funding from the Universidad de Málaga and the Instituto de Investigación Biomédica de Málaga - IBIMA.

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Notes

  1. 1.

    https://github.com/wizaca23/BBBC006-Instance-Segmentation.

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Correspondence to Miguel A. Molina-Cabello .

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Zamora-Cárdenas, W. et al. (2021). Enforcing Morphological Information in Fully Convolutional Networks to Improve Cell Instance Segmentation in Fluorescence Microscopy Images. In: Rojas, I., Joya, G., Català, A. (eds) Advances in Computational Intelligence. IWANN 2021. Lecture Notes in Computer Science(), vol 12861. Springer, Cham. https://doi.org/10.1007/978-3-030-85030-2_4

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  • DOI: https://doi.org/10.1007/978-3-030-85030-2_4

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