MiCellAnnGELo: Annotate microscopy time series of complex cell surfaces with 3D Virtual Reality

TL;DR

MiCellAnnGELo is a virtual reality tool that enables immersive viewing and annotation of 4D microscopy data, facilitating the analysis of complex cell surface processes in high-resolution live cell imaging.

Contribution

It introduces a novel VR-based software platform for efficient annotation of 3D microscopy data, addressing challenges in manual labeling for machine learning applications.

Findings

Supports annotation of cell motility, endocytosis, and signaling

Compatible with multiple operating systems and VR headsets

Available as open-source software with sample data

Abstract

Summary: Advances in 3D live cell microscopy are enabling high-resolution capture of previously unobserved processes. Unleashing the power of modern machine learning methods to fully benefit from these technologies is, however, frustrated by the difficulty of manually annotating 3D training data. MiCellAnnGELo virtual reality software offers an immersive environment for viewing and interacting with 4D microscopy data, including efficient tools for annotation. We present tools for labelling cell surfaces with a wide range of applications, including cell motility, endocytosis, and transmembrane signalling. Availability and implementation: MiCellAnnGELo employs the cross platform (Mac/Unix/Windows) Unity game engine and is available under the MIT licence at https://github.com/CellDynamics/MiCellAnnGELo.git, together with sample data and demonstration movies. MiCellAnnGELo can be run in desktop mode on a 2D screen or in 3D using a standard VR headset with compatible GPU.