Skip to content

Download segment masks

This example accesses a volume annotation on webKnososs and creates segment masks from selected segments. The segment masks are stored as tiff sequences. The segments have been selected from the "Segments" tab in webKnossos. The BufferedSliceReader is used to efficiently request sections from the remote segmentation data.

import numpy as np
from tifffile import imwrite

import webknossos as wk

ANNOTATION_ID = "634e8fe1010000b4006f3cf4"
SEGMENT_IDS = [32, 667325]
MAG = wk.Mag("4-4-1")


def main() -> None:
    dataset = wk.Annotation.open_as_remote_dataset(
        ANNOTATION_ID, webknossos_url="https://webknossos.org"
    )
    mag_view = dataset.get_segmentation_layers()[0].get_mag(MAG)

    z = mag_view.layer.bounding_box.topleft.z
    with mag_view.get_buffered_slice_reader() as reader:
        for slice_data in reader:
            slice_data = slice_data[0]  # First channel only
            for segment_id in SEGMENT_IDS:
                segment_mask = (slice_data == segment_id).astype(
                    np.uint8
                ) * 255  # Make a binary mask 0=empty, 255=segment
                segment_mask = segment_mask.T  # Tiff likes the data transposed
                imwrite(
                    f"l4_sample_segments/seg{segment_id:04d}_mag{MAG}_z{z:04d}.tiff",
                    segment_mask,
                )

            print(f"Downloaded z={z:04d}")
            z += MAG.z


if __name__ == "__main__":
    main()
Back to top