Image Stack to Dataset¶

This example shows how to create a new WEBKNOSSOS dataset from a stack of images, e.g. Tiff, JPEG, etc files.

There are a few assumptions we made about the images used for this example:

all images have the same size
they have the same dtype (e.g. uint8 or float)
they are greyscale images from microscopy / MRI / CT scan, therefore the category is color
masks and segmentations are not included yet

from pathlib import Path

from webknossos import Dataset
from webknossos.dataset import COLOR_CATEGORY

INPUT_FILES = (
    Path(__file__).parent.parent / "testdata" / "tiff" / "test.0000.tiff",
    Path(__file__).parent.parent / "testdata" / "tiff" / "test.0001.tiff",
)
OUTPUT_FOLDER = Path("testoutput/tiff_dataset")


def main() -> None:
    """Convert a list of images into a WEBKNOSSOS dataset and directly add them as a new layer."""
    dataset = Dataset(
        dataset_path=OUTPUT_FOLDER,
        voxel_size=(11, 11, 11),
        name="My_new_dataset",
        exist_ok=False,
    )
    dataset.add_layer_from_images(
        images=INPUT_FILES,
        layer_name="test",
        category=COLOR_CATEGORY,
    )

    # dataset.upload()


if __name__ == "__main__":
    main()