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Data Export through the Web UI

The WEBKNOSSOS UI comes with a fully featured Download panel offering a wide variety of download export options:

  • Export cutouts of the data as OME-TIFF or TIFF stack (uses long-running jobs for export)
  • Download the complete annotation, including all metadata, skeletons (as NML files), and volume layers (as Zarr, by default). You can customize this to skip volume layers entirely, or download them as WKW files (not available for n-dimensional volume annotations).
  • Instructions for using the WEBKNOSSOS Python library for download

To access the download panel:

  1. Click on the overflow menu (dropdown), next to the Save button in the WEBKNOSSOS navbar
  2. Select Download entry
  3. Select the desired data for download or export

The "Download" dialog for exporting and downloading annotations and dataset layers. WEBKNOSSOS offers downloads as Tiff stacks, the native WEBKNOSSOS file formats, and through the Python library.

The "Download" dialog for exporting and downloading annotations and dataset layers. WEBKNOSSOS offers downloads as Tiff stacks, the native WEBKNOSSOS file formats, and through the Python library.

To export skeleton trees, nodes, and edges as CSV files, use the Skeleton (Trees) tab in the right-hand sidebar rather than the Download dialog.

Exporting TIFF / OME-TIFF cutouts

To export a cutout of your data as a TIFF stack or OME-TIFF:

  1. Open the Export as Tiff tab in the Download dialog.
  2. Pick the layer to export.
  3. Choose a bounding box, either one of your user-defined bounding boxes or the full layer.
  4. Choose the format (TIFF stack or OME-TIFF) and a magnification.
  5. Start the export.

TIFF exports run as a long-running job; you can track progress and download the result from the Jobs Overview page. Maximum volume and edge-length limits apply to the selected bounding box.