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Upload Image Data

Loads the cell dataset, writes it into a wkw Dataset and uploads it to a local webknossos instance using webknossos_context.

from time import gmtime, strftime

from skimage import data

import webknossos as wk

with wk.webknossos_context(url="http://localhost:9000", token="secretScmBoyToken"):
    img = data.cell()
    time_str = strftime("%Y-%m-%d_%H-%M-%S", gmtime())
    name = f"cell_{time_str}"
    ds = wk.Dataset.create(name, scale=(107, 107, 107))
    layer = ds.add_layer(
        "color",
        "color",
        dtype_per_layer=img.dtype,
    )
    # add channel and z dimensions and put X before Y,
    # resulting dimensions are C, X, Y, Z.
    layer.add_mag(1, compress=True).write(img.T[None, :, :, None])
    url = ds.upload()
    print(f"Successfully uploaded {url}")

Skin Dataset

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