An ImageJ-based tool for three-dimensional registration between different types of microscopic images

Area of Science:

• Microscopy
• Bioimage Analysis
• Developmental Biology

Background:

• Accurate alignment of 3D microscopic images is crucial for studying delicate biological samples such as mouse embryos and organoids.
• Existing 3D registration tools are often not readily accessible to experimental biologists, hindering research progress.

Purpose of the Study:

• To develop an accessible, ImageJ-based tool for 3D image registration and reconstruction.
• To provide quantitative evaluation of registration accuracy for microscopic image datasets.

Main Methods:

• Manual landmark identification in two microscopic images to compute 3D rotation.
• Utilizing multiple corresponding points (e.g., nuclei) for quantitative correspondence exploration.
• Applying computed 3D rotation to reconstruct aligned image volumes.

Main Results:

• Successful 3D registration and reconstruction of microscopic images from mouse embryos (pre- and post-implantation).
• Demonstrated accuracy in aligning live and fixed embryo images.
• Validated the tool's utility for diverse biological tissues and species.

Conclusions:

• The developed ImageJ-based tool offers a versatile solution for 3D image registration and reconstruction.
• Facilitates the study of 3D rotated biological samples, including embryos and organoids.
• Enhances quantitative analysis capabilities in bioimage processing for experimental biologists.