OME-NGFF-Prototypes

Prototypes for ome.zarr / ome.ngff. Example data with the goal to collect diverse applications.

Examples

Single Image

The examples in single_image contain data that is described with a single multiscales metadata for all relevant tczyx axes combinations:

• yx.ome.zarr: 2d image, nucleus channel of an image from [1]
• zyx.ome.zarr: 3d volume, EM volume from [2]
• cyx.ome.zarr: 2d image with channels, image with nucleus, virus marker and serum channels from [1]
• tyx.ome.zarr: timeseries of 2d images, timeseries of central slice of membrane channel from [3]
• tzyx.ome.zarr: timeseries of 3d images, timeseries of membrane channel volume from [3]
• tcyx.ome.zarr: timeseries of images with channel, timeseries of central slice of membrane + nucleus channel from [3]
• czyx.ome.zarr: 3d volume with channel, single timepoint of membrane and nucleus channel from [3]
• tczyx.ome.zarr: timeseries of 3d volumes with channel, full data from [3]
• multi-image.ome.zarr: a simple example for multiple images in one ome.zarr, stores all four channels from cyx.ome.zarr as separate 2d images.

Publications:

• [1] https://onlinelibrary.wiley.com/doi/full/10.1002/bies.202000257
• [2] https://www.sciencedirect.com/science/article/pii/S193131282030620X
• [3] https://elifesciences.org/articles/57613

Data availability

• The initial data in h5 format is available at https://oc.embl.de/index.php/s/4bDrWVnuDHIKmRF.
• The data in ome.zarr format version 0.1 is available at
  • https://s3.embl.de/i2k-2020/ngff-example-data/v0.1 (via s3)
• The data in ome.zarr format version 0.2 is available at
  • https://s3.embl.de/i2k-2020/ngff-example-data/v0.2 (via s3)
• The data in ome.zarr format version 0.3 is available at
  • https://s3.embl.de/i2k-2020/ngff-example-data/v0.3 (via s3)
• The data in ome.zarr format version 0.4 is available at:
  • https://s3.embl.de/i2k-2020/ngff-example-data/v0.4 (via s3)
  • https://oc.embl.de/index.php/s/0TPPw4CUt0G6nng (as single zip with all the data for v0.4)

Workflows

The workflows folder contains example workflows for creating and using more complex projects with ome.ngff data. Currently, it creates an example for creating an ngff data based MoBIE project and converting spatial transcriptomics data to ngff.