Napari-3D-Counter: A manual cell counter for napari
Abstract
A common task across biological fields is to quantify the number of objects in an image. Often, the most efficient solution to this problem is to have an expert manually count those objects. This package, Napari-3D-Counter, includes the Count3D widget, a user-friendly interface to allow an expert to quickly count objects in 2D or 3D images visualized using napari, as well as auxiliary plugins that help to integrate Count3D into upstream and downstream analyses. Napari-3D-Counter focuses on being user-friendly for beginners and experienced users, and has been continually updated since its 2023 release. The package is available on both PyPI and conda-forge, and is indexed on napari-hub.
Fields of Study & Subjects
Cell Image Analysis Techniques
Digital Image Processing Techniques
Single-cell and spatial transcriptomics
Publication details
- Journal / source
- The Journal of Open Source Software
- Volume
- 11
- Issue
- 119
- Pages
- 9091–9091
- Publication date
- 15 March 2026
- Language
- EN