OrgaQuant: Human Intestinal Organoid Localization and Quantification Using Deep Convolutional Neural Networks

Organoid cultures are proving to be powerful in vitro models that closely mimic the cellular constituents of their native tissue. Organoids are typically expanded and cultured in a 3D environment using either naturally derived or synthetic extracellular matrices. Assessing the morphology and growth...

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Bibliographic Details
Published in:Scientific reports 2019-08, Vol.9 (1), p.12479-7, Article 12479
Main Authors: Kassis, Timothy, Hernandez-Gordillo, Victor, Langer, Ronit, Griffith, Linda G.
Format: Article
Language:English
Subjects:
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Automation
Cell culture
Cell Culture Techniques
Databases, Factual
Humanities and Social Sciences
Humans
Image processing
Image Processing, Computer-Assisted
Intestine
Intestines - cytology
Localization
multidisciplinary
Neural networks
Neural Networks, Computer
Organoids
Organoids - cytology
Organoids - metabolism
Physical characteristics
Science
Science (multidisciplinary)
Segmentation
Size distribution
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Summary:Organoid cultures are proving to be powerful in vitro models that closely mimic the cellular constituents of their native tissue. Organoids are typically expanded and cultured in a 3D environment using either naturally derived or synthetic extracellular matrices. Assessing the morphology and growth characteristics of these cultures has been difficult due to the many imaging artifacts that accompany the corresponding images. Unlike single cell cultures, there are no reliable automated segmentation techniques that allow for the localization and quantification of organoids in their 3D culture environment. Here we describe OrgaQuant, a deep convolutional neural network implementation that can locate and quantify the size distribution of human intestinal organoids in brightfield images. OrgaQuant is an end-to-end trained neural network that requires no parameter tweaking; thus, it can be fully automated to analyze thousands of images with no user intervention. To develop OrgaQuant, we created a unique dataset of manually annotated human intestinal organoid images with bounding boxes and trained an object detection pipeline using TensorFlow. We have made the dataset, trained model and inference scripts publicly available along with detailed usage instructions.
ISSN:2045-2322
2045-2322
DOI:10.1038/s41598-019-48874-y