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Exercise 5: Validate the Converted OME-Zarr Files

In this exercise, you will validate and explore the converted OME-Zarr using different tools .

The ome_zarr Command

The ome_zarr tool is preinstalled and available for all BAND desktops. You can use it to validate the converted zarr files.

NOTE: Due to the network restrictions on BAND, ome_zarr view will not work

  1. Open a terminal, or use the same terminal from the previous steps

  2. Run the following command:

    bash ome_zarr info ~/nf-conversion-results/ftsz3.zarr

  3. You should see the output as shown in the screenshot below.

  4. Try to validate other zarr files by replacing the path.

queue

The Neuroglancer

Neuroglancer is a WebGL-based viewer for volumetric data. It is capable of displaying arbitrary (non axis-aligned) cross-sectional views of volumetric data, as well as 3-D meshes and line-segment based models (skeletons).

It is preinstalled on BAND. A convenient wrapper command ome_zarr_neuroglancer is available for you to use.

To open OME-Zarr in Neuroglancer:

  1. Open a terminal, or use the same terminal from the previous steps

  2. Run ome_zarr_neuroglancer with the pat to a Zarr file, e.g. ome_zarr_neuroglancer ~/

    bash nf-conversion-results/filament.zarr

  3. A browser will open with Neuroglance displaying the Zarr.

validate