CellProfiler is an image analysis application for researchers working with microscopy data.
It lets users build reproducible workflows that turn collections of biological images into quantitative data without needing to write image processing code. The software is aimed at biological assays ranging from small image sets to high-throughput experiments, with a strong focus on objective, repeatable phenotyping.
This is free and open source software.
Key Features
- Point-and-click graphical interface for constructing image analysis pipelines.
- Modular workflow system covering image loading, preprocessing, segmentation, object processing, and measurement.
- Measures properties such as cell or object size, shape, intensity, texture, colocalization, and image quality.
- Supports batch processing for large image collections, including use on clusters and cloud computing resources.
- Exports results to spreadsheets and databases for downstream statistical analysis.
- Includes modules for fluorescence microscopy workflows, high-content screening, and complex morphological assays.
- Supports plugins, OMERO access, pipeline examples, tutorials, and extensive documentation.
Website: github.com/CellProfiler/CellProfiler
Support:
Developer: CellProfiler
License: BSD 3-Clause License
CellProfiler is written in Python. Learn Python with our recommended free books and free tutorials.
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Read our verdict in the software roundup.
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