CytoDataFrame

CytoDataFrame extends Pandas functionality to help display single-cell profile data alongside related images.

CytoDataFrame is an advanced in-memory data analysis format designed for single-cell profiling, integrating not only the data profiles but also their corresponding microscopy images and segmentation masks. Traditional single-cell profiling often excludes the associated images from analysis, limiting the scope of research. CytoDataFrame bridges this gap, offering a purpose-built solution for comprehensive analysis that incorporates both the data and images, empowering more detailed and visual insights in single-cell research.

CytoDataFrame development began within coSMicQC - a single-cell profile quality control package.

Installation

Install CytoDataFrame from source using the following:

# install from pypi
pip install cytodataframe

# or install directly from source
pip install git+https://github.com/WayScience/CytoDataFrame.git

Contributing, Development, and Testing

Please see our contributing documentation for more details on contributions, development, and testing.

References

• coSMicQC
• pycytominer
• CellProfiler
• CytoTable