High Throughput Automated Detection of Axial Malformations in Medaka Embryo
From LRDE
- Authors
- Diane Genest, Élodie Puybareau, Marc Léonard, Jean Cousty, Noémie De Crozé, Hugues Talbot
- Journal
- Computers in Biology and Medicine
- Type
- article
- Projects
- Olena
- Keywords
- Image
- Date
- 2019-01-22
Abstract
Fish embryo models are widely used as screening tools to assess the efficacy and/or toxicity of chemicals. This assessment involves the analysis of embryo morphological abnormalities. In this article, we propose a multi-scale pipeline to allow automated classification of fish embryos (Medaka: Oryzias latipes) based on the presence or absence of spine malformations. The proposed pipeline relies on the acquisition of fish embryo 2D images, on feature extraction based on mathematical morphology operators and on machine learning classification. After image acquisitionsegmentation tools are used to detect the embryo before analysing several morphological features. An approach based on machine learning is then applied to these features to automatically classify embryos according to the presence of axial malformations. We built and validated our learning model on 1459 images with a 10-fold cross-validation by comparison with the gold standard of 3D observations performed under a microscope by a trained operator. Our pipeline results in correct classification in 85% of the cases included in the database. This percentage is similar to the percentage of success of a trained human operator working on 2D images. The key benefit of our approach is the low computational cost of our image analysis pipelinewhich guarantees optimal throughput analysis..
Bibtex (lrde.bib)
@Article{ puybareau.19.cbm, author = {Diane Genest and \'Elodie Puybareau and Marc L\'eonard and Jean Cousty and No\'emie De Croz\'e and Hugues Talbot}, title = {High Throughput Automated Detection of Axial Malformations in {M}edaka Embryo}, journal = {Computers in Biology and Medicine}, year = 2019, month = feb, pages = {157--168}, volume = {105}, abstract = {Fish embryo models are widely used as screening tools to assess the efficacy and/or toxicity of chemicals. This assessment involves the analysis of embryo morphological abnormalities. In this article, we propose a multi-scale pipeline to allow automated classification of fish embryos (Medaka: Oryzias latipes) based on the presence or absence of spine malformations. The proposed pipeline relies on the acquisition of fish embryo 2D images, on feature extraction based on mathematical morphology operators and on machine learning classification. After image acquisition, segmentation tools are used to detect the embryo before analysing several morphological features. An approach based on machine learning is then applied to these features to automatically classify embryos according to the presence of axial malformations. We built and validated our learning model on 1459 images with a 10-fold cross-validation by comparison with the gold standard of 3D observations performed under a microscope by a trained operator. Our pipeline results in correct classification in 85\% of the cases included in the database. This percentage is similar to the percentage of success of a trained human operator working on 2D images. The key benefit of our approach is the low computational cost of our image analysis pipeline, which guarantees optimal throughput analysis..}, doi = {10.1016/j.compbiomed.2018.12.016} }