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Benchmarking of deep learning algorithms for 3D instance segmentation of confocal image datasets.
Kar, Anuradha; Petit, Manuel; Refahi, Yassin; Cerutti, Guillaume; Godin, Christophe; Traas, Jan.
Afiliação
  • Kar A; Laboratoire RDP, Université de Lyon 1, ENS-Lyon INRAE, INRIA, CNRS, UCBL, Lyon, France.
  • Petit M; Institut du Cerveau-Paris Brain Institute, Paris, France.
  • Refahi Y; Laboratoire RDP, Université de Lyon 1, ENS-Lyon INRAE, INRIA, CNRS, UCBL, Lyon, France.
  • Cerutti G; Université de Reims Champagne Ardenne, INRAE, FARE, UMR A 614, Reims, France.
  • Godin C; Laboratoire RDP, Université de Lyon 1, ENS-Lyon INRAE, INRIA, CNRS, UCBL, Lyon, France.
  • Traas J; Laboratoire RDP, Université de Lyon 1, ENS-Lyon INRAE, INRIA, CNRS, UCBL, Lyon, France.
PLoS Comput Biol ; 18(4): e1009879, 2022 04.
Article em En | MEDLINE | ID: mdl-35421081
ABSTRACT
Segmenting three-dimensional (3D) microscopy images is essential for understanding phenomena like morphogenesis, cell division, cellular growth, and genetic expression patterns. Recently, deep learning (DL) pipelines have been developed, which claim to provide high accuracy segmentation of cellular images and are increasingly considered as the state of the art for image segmentation problems. However, it remains difficult to define their relative performances as the concurrent diversity and lack of uniform evaluation strategies makes it difficult to know how their results compare. In this paper, we first made an inventory of the available DL methods for 3D cell segmentation. We next implemented and quantitatively compared a number of representative DL pipelines, alongside a highly efficient non-DL method named MARS. The DL methods were trained on a common dataset of 3D cellular confocal microscopy images. Their segmentation accuracies were also tested in the presence of different image artifacts. A specific method for segmentation quality evaluation was adopted, which isolates segmentation errors due to under- or oversegmentation. This is complemented with a 3D visualization strategy for interactive exploration of segmentation quality. Our analysis shows that the DL pipelines have different levels of accuracy. Two of them, which are end-to-end 3D and were originally designed for cell boundary detection, show high performance and offer clear advantages in terms of adaptability to new data.
Assuntos

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Aprendizado Profundo Idioma: En Revista: PLoS Comput Biol Assunto da revista: BIOLOGIA / INFORMATICA MEDICA Ano de publicação: 2022 Tipo de documento: Article País de afiliação: França

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Aprendizado Profundo Idioma: En Revista: PLoS Comput Biol Assunto da revista: BIOLOGIA / INFORMATICA MEDICA Ano de publicação: 2022 Tipo de documento: Article País de afiliação: França