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Image Stacks

WEBKNOSSOS works with a wide range of modern bio-imaging formats and image stacks:

Image stacks need to be converted to WKW for WEBKNOSSOS. This happens automatically when using the web upload on webknossos.org or can be done manually (see below).

Single-Layer Image File Sequence

When uploading multiple image files, these files are sorted numerically, and each one is interpreted as single section/slice within a 3D dataset. Alternatively, the same files can also be uploaded bundled in a single folder (or zip archive).

As an example, the following file structure would create a dataset with one layer which has a z-depth of 3:

dataset_name/
├── image_1.tif
├── image_2.tif
├── image_3.tif
└── ...

Multi-Layer Image File Sequence

The image file sequences explained above can be composed to build multiple layers. For example, the following file structure (note the additional hierarchy level) would create a dataset with two layers (named color and segmentation):

dataset_name/
├── color
│ ├── image_1.tif
│ ├── image_2.tif
│ └── ...
└── segmentation
  └── ...

Single-file images

WEBKNOSSOS understands most modern bio-imaging file formats and uses the BioFormats library upon import/conversion. It works particularly well with:

  • OME-Tiff
  • Tiff
  • PNG
  • JPEG
  • czi
  • nifti
  • raw
  • DM3
  • DM4

Manual Conversion

You can manually convert image stacks through:

Conversion with CLI

You can easily convert image stacks manually with the WEBKNOSSOS CLI. The CLI tool expects all image files in a single folder with numbered file names. After installing, you can convert image stacks to WKW datasets with the following command:

pip install webknossos

webknossos convert \
  --voxel-size 11.24,11.24,25 \
  --name my_dataset \
  data/source data/target

This snippet converts an image stack that is located in directory called data/source into a WKW dataset which will be located at data/target. It will create a so called color layer containing your raw greyscale/color image. The supplied --voxel-size is specified in nanometers.

Read the full documentation at WEBKNOSSOS CLI.

Conversion with Python

You can use the free WEBKNOSSSO Python library to convert image stacks to WKW or integrate the conversion as part of an existing workflow. 

import webknossos as wk

def main() -> None:
    """Convert a folder of image files to a WEBKNOSSOS dataset."""
    dataset = wk.Dataset.from_images(
        input_path=INPUT_DIR,
        output_path=OUTPUT_DIR,
        voxel_size=(11, 11, 11),
        layer_category=wk.COLOR_CATEGORY,
        compress=True,
    )

    print(f"Saved {dataset.name} at {dataset.path}.")

    with wk.webknossos_context(token="..."):
        dataset.upload()


if __name__ == "__main__":
    main()

Read the full example in the WEBKNOSSOS Python library documentation.

Please contact us or write a post in our support forum, if you have any issues with converting your datasets.