Napari-3D-Counter: A manual cell counter for napari

Area of Science:

• Biological imaging
• Quantitative image analysis
• Bioimage informatics

Background:

• Accurate object quantification in biological images is crucial for research.
• Manual counting by experts is common but can be time-consuming.
• Existing tools may lack user-friendliness or integration capabilities.

Purpose of the Study:

• Introduce Napari-3D-Counter, a novel widget for efficient object counting in 2D and 3D images.
• Provide a user-friendly interface for both novice and experienced users.
• Facilitate seamless integration into existing bioimage analysis workflows.

Main Methods:

• Development of the Count3D widget within the napari visualization environment.
• Implementation of auxiliary plugins for upstream and downstream analysis integration.
• Focus on intuitive design and continuous updates since its 2023 release.

Main Results:

• Napari-3D-Counter provides a streamlined interface for manual object counting.
• The tool supports both 2D and 3D image analysis.
• Auxiliary plugins enhance its utility within broader analytical pipelines.

Conclusions:

• Napari-3D-Counter simplifies and accelerates expert-driven object quantification in biological imaging.
• The package offers a valuable, user-friendly solution for researchers across biological fields.
• Availability on PyPI, conda-forge, and indexing on napari-hub ensures broad accessibility.