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ZEDprofiler [![Documentation](https://img.shields.io/badge/documentation-available-brightgreen)](https://zedprofiler.readthedocs.io/en/latest/) ![License](https://img.shields.io/badge/license-BSD%203--Clause-blue)[![Coverage](https://img.shields.io/badge/coverage-92%25-brightgreen)](#quality-gates)\n\n[![ZEDprofiler](https://github.com/WayScience/ZEDprofiler/raw/main/logo/with-text-for-dark-bg.png)](https://github.com/WayScience/ZEDprofiler)\n\nCPU-first 3D image feature extraction toolkit for high-content and high-throughput image-based profiling.\n\nThis repository is used for image-based feature extraction of objects in 3D microscopy images.\nIn this use case we extract features from single cells in 3D volumetric microscopy images.\nWe developed ZEDprofiler to be used on high-content and high-throughput microscopy images, which are often large in size and require efficient processing.\nZEDprofiler is extensible to any fluorescence microscopy image modality, and is designed to be modular.\n\n## Install environment\n\n```bash\njust env\n```\n\n## Data Contract\n\nWhere:\n\n- `x` is the width of the image in pixels\n- `y` is the height of the image in pixels\n- `z` is the depth of the image in pixels\n\nThough I have reservations about width, height, and depth being used to describe the dimensions of an image.\nDifferent fields use different dimensions for different meanings.\nWe use `x` and `y` to refer to the same dimensions captured in a 2D image, and `z` to refer to the \"depth\" dimension in a 3D image if looking down into the image stack.\nThe `x`, `y`, and `z` dimensions are less description and more absolute while `depth` is relative to angle of observation.\n\nAccepted image formats (order matters):\n\n- Single channel: `(z, y, x)`\n\n## Quality Gates\n\nWe lint and format code with our pre-commit configuration.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fwayscience%2Fzedprofiler","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fwayscience%2Fzedprofiler","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fwayscience%2Fzedprofiler/lists"}