SegmentAnything helps microscopy images based automatic and quantitative organoid detection and analysis

by   Xiaodan Xing, et al.
Imperial College London

Organoids are self-organized 3D cell clusters that closely mimic the architecture and function of in vivo tissues and organs. Quantification of organoid morphology helps in studying organ development, drug discovery, and toxicity assessment. Recent microscopy techniques provide a potent tool to acquire organoid morphology features, but manual image analysis remains a labor and time-intensive process. Thus, this paper proposes a comprehensive pipeline for microscopy analysis that leverages the SegmentAnything to precisely demarcate individual organoids. Additionally, we introduce a set of morphological properties, including perimeter, area, radius, non-smoothness, and non-circularity, allowing researchers to analyze the organoid structures quantitatively and automatically. To validate the effectiveness of our approach, we conducted tests on bright-field images of human induced pluripotent stem cells (iPSCs) derived neural-epithelial (NE) organoids. The results obtained from our automatic pipeline closely align with manual organoid detection and measurement, showcasing the capability of our proposed method in accelerating organoids morphology analysis.


page 2

page 3


Towards a Digital Diatom: image processing and deep learning analysis of Bacillaria paradoxa dynamic morphology

Recent years have witnessed a convergence of data and methods that allow...

Automatic Multi-Stain Registration of Whole Slide Images in Histopathology

Joint analysis of multiple biomarker images and tissue morphology is imp...

Generative Modeling with Conditional Autoencoders: Building an Integrated Cell

We present a conditional generative model to learn variation in cell and...

Spherical Harmonics for Shape-Constrained 3D Cell Segmentation

Recent microscopy imaging techniques allow to precisely analyze cell mor...

Automatic Quantitative Analysis of Brain Organoids via Deep Learning

Recent advances in brain organoid technology are exciting new ways, whic...

Please sign up or login with your details

Forgot password? Click here to reset