BOrg: A Brain Organoid-Based Mitosis Dataset for Automatic Analysis of Brain Diseases

TL;DR

This paper introduces BOrg, a specialized dataset with an annotation pipeline for analyzing mitosis in brain organoids, enabling improved automated detection and analysis of cell division stages relevant to neurodevelopmental research.

Contribution

The paper presents BOrg, a novel brain organoid mitosis dataset with an efficient annotation method and benchmarks adapted models for mitosis detection, advancing automated analysis in neurodevelopmental studies.

Findings

State-of-the-art models significantly improve mitosis detection accuracy.

Automated tools developed from BOrg facilitate neurodevelopmental research.

Benchmark results demonstrate enhanced efficiency over existing methods.

Abstract

Recent advances have enabled the study of human brain development using brain organoids derived from stem cells. Quantifying cellular processes like mitosis in these organoids offers insights into neurodevelopmental disorders, but the manual analysis is time-consuming, and existing datasets lack specific details for brain organoid studies. We introduce BOrg, a dataset designed to study mitotic events in the embryonic development of the brain using confocal microscopy images of brain organoids. BOrg utilizes an efficient annotation pipeline with sparse point annotations and techniques that minimize expert effort, overcoming limitations of standard deep learning approaches on sparse data. We adapt and benchmark state-of-the-art object detection and cell counting models on BOrg for detecting and analyzing mitotic cells across prophase, metaphase, anaphase, and telophase stages. Our results demonstrate these adapted models significantly improve mitosis analysis efficiency and accuracy for brain organoid research compared to existing methods. BOrg facilitates the development of automated tools to quantify statistics like mitosis rates, aiding mechanistic studies of neurodevelopmental processes and disorders. Data and code are available at https://github.com/awaisrauf/borg.