Cellfinder
Automated 3D cell detection and classification in large-scale volumetric brain images using deep learning.
What is Cellfinder?
cellfinder is an open-source software tool for automated 3D cell detection and classification in large-scale volumetric brain images, such as those from serial two-photon or lightsheet microscopy. It uses deep learning algorithms to identify cells in whole-brain datasets, enabling high-throughput neuroanatomical analysis. The tool addresses the challenge of manually analyzing vast 3D image volumes by providing automated, scalable detection.
Neuroscientists, bioimage analysts, and researchers working with large-scale 3D brain imaging data who need automated cell detection and classification. It is particularly useful for labs using lightsheet or serial two-photon microscopy to study whole-brain cellular distributions.
Developers choose cellfinder for its deep learning-based accuracy, integration with the BrainGlobe ecosystem, and multiple interface options (CLI, GUI, API) that cater to different workflows. Its ability to handle very large 3D images and classify cells makes it a specialized tool for neuroimaging analysis.
Overview
Automated 3D cell detection in very large images
Use Cases
Best For
- Automating cell detection in whole-brain lightsheet microscopy datasets
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