radiantkit

Radial Image Analysis Toolkit (RadIAnTkit)j is a Python3.7+ package containing tools for full-stack image analysis - from proprietary format conversion to tiff to cellular nuclei segmentation, from the selection of G1 nuclei to the measurement of radial patterns.

• Features (in short)
• Contributing
• License

Features (in short)

• Convert proprietary microscope formats CZI (Zeiss) and ND2 (Nikon) to open-source TIFF format.
• Segment cellular nuclei or other objects, in 2D or 3D, in an unsupervised manner. Then use the automatic segmentation to estimate background and foreground intensity.
• Select cellular nuclei, in G1-phase of the cell cycle, based on DNA staining and nuclear volume.
• Extract segmented objects and measure their features (e.g., volume, integral of intensity, shape descriptors).
• • Measure radial patterns as radial profiles (with different center definitions), and characterize them (e.g., peaks, inflection points, contrast).
• Generate snakemake-based workflows for seamless integration into fully reproducible streamlined analysis pipelines.

Contributing

We welcome any contributions to radiantkit. In short, we use black to standardize code format. Any code change also needs to pass mypy checks. For more details, please refer to our contribution guidelines if this is your first time contributing! Also, check out our code of conduct.

License

MIT License - Copyright (c) 2020 Gabriele Girelli