Scape Utils

scape_utils is a Python module designed for handling .3DU16 files, providing tools for reading and manipulating volumetric data. The module includes two main classes: ScapeVirtualStack and ScapeImageDecoder.

Installation

To install scape_utils, use pip:

pip install git+https://github.com/lycantrope/scape_util

Usage

To read a .3DU16 file, use the ScapeVirtualStack class. Below are examples of how to get volumes and ImageJ formatted volumes.

from pathlib import Path

import numpy as np
from scape_utils import ScapeVirtualStack

file_path = Path("path/to/your/file.3DU16")

with ScapeVirtualStack(file_path) as stack:
    # show information
    print(stack)

    # Get the 1st volume in format (TCZYX)
    volume_0 = stack.get_volume(0)
    
    # Get the 3rd volume in ImageJ format (TZCYX)
    volume_ij = stack.get_volume(2, imagej=True)

    # Get multiple stacks at once (from t0 to t10)
    volume_multi = stack.get_multi_volumes(0, 10)

    # save all volumes into ImageJ compatible tiff
    stack.save_all_volumes_to_tiff(file_path.with_suffix(".tif"))

License

This project is licensed under the MIT License.