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

• Main Authors: Kassis, Timothy (Author), Hernandez Gordillo, Victor (Author), Langer, Ronit (Author), Griffin, Linda G. (Author)
• Other Authors: Massachusetts Institute of Technology. Department of Biological Engineering (Contributor), Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science (Contributor)
• Format: Article
• Language: English
• Published: Springer Science and Business Media LLC, 2020-03-24T21:19:38Z.
• Subjects: Article
• Online Access: Get fulltext

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.
National Institutes of Health (U.S.) (5R01EB021908-03)
United States. Defense Advanced Research Projects Agency (W911NF-12-2-0039)