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MedViz

MedViz is a Python package for medical image visualization. It provides a set of functions for visualizing medical images and masks. The package is built on top of the matplotlib and nibabel packages.

Installation

To install the package, use pip:

pip install medviz

Usage

To use the package, import it in your Python code:

import medviz

medviz.layered_plot(image_path="dataset/1-1.nii", mask_paths=["dataset/small_bowel.nii", "dataset/1-1-label.nii"], mask_colors=["red", "yellow"], title="Layered Plot")

The layered_plot function creates a layered plot of an image and one or more masks. The masks are overlaid on top of the image using the specified colors. The resulting plot can be used to visualize the location of structures or regions of interest in the image.

import medviz

medviz.gif(
    image_path="dataset/1-1.nii",
    mask_paths=[
        "dataset/small_bowel.nii",
        "dataset/1-1-label.nii",
        "dataset/vertebrae_L3.nii.gz",
        "dataset/vertebrae_L4.nii.gz",
        "dataset/vertebrae_L5.nii.gz",
    ],
    mask_colors=["red", "yellow", "green", "blue", "purple"],
    title="Expert Annotations",
    interval=70,
    start_slice=30,
    end_slice=130,
    save_path="animation.gif",
)

The gif function creates an animated GIF of an image and one or more masks. The masks are overlaid on top of the image using the specified colors. The resulting GIF can be used to visualize the location of structures or regions of interest in the image.

GitHub repository: [https://github.com/mohsenhariri/medviz](https://github.com/mohsenhariri/medviz)