The OME Blog Because metadata is worth a thousand pictures

Public OME-Zarr data (Nov. 2020)

The OME team is leading a community effort to design a new cloud-friendly “Next Generation” file format (NGFF). See the announcement and other image.sc posts tagged with ome-ngff.

The ome-zarr spec is currently under development and includes a changelog with version numbers. A number of tools are being developed to work with ome-zarr data. The vizarr viewer is used below to view OME-Zarr images.

As part of this work, we are converting sample datasets from Image Data Resource (IDR) into OME-Zarr, to correspond to each version of the spec. These are publicly available and hosted on S3 storage in the Embassy Cloud at the European Bioinformatics Institute (EBI). Below are listed Images converted into version 0.1 of the OME-Zarr spec. This list is also available in JSON format.

We are currently working on a spec for representing HCS data in OME-Zarr. When this spec is finalised, we will also provide links to sample HCS data in this format.

Image Study X Y Z C T Viewer S3-endpoint
IDR thumbnail for image:1884807 idr0021 256 256 1 3 1 view copy
IDR thumbnail for image:4007801 idr0044 2169 2048 988 2 532 view copy
IDR thumbnail for image:4495402 idr0053 921600 380928 1 1 1 view copy
IDR thumbnail for image:6001237 idr0062 1024 1024 39 4 1 view copy
IDR thumbnail for image:6001238 idr0062 1024 1024 27 4 1 view copy
IDR thumbnail for image:6001239 idr0062 1024 1024 36 4 1 view copy
IDR thumbnail for image:6001240 idr0062 271 275 236 2 1 view copy
IDR thumbnail for image:6001241 idr0062 278 263 236 2 1 view copy
IDR thumbnail for image:6001242 idr0062 481 275 237 2 1 view copy
IDR thumbnail for image:6001243 idr0062 212 218 237 2 1 view copy
IDR thumbnail for image:6001244 idr0062 325 281 239 2 1 view copy
IDR thumbnail for image:6001245 idr0062 220 226 257 2 1 view copy
IDR thumbnail for image:6001246 idr0062 281 284 257 2 1 view copy
IDR thumbnail for image:6001247 idr0062 253 210 257 2 1 view copy
(with labels)
IDR thumbnail for image:6001248 idr0062 234 269 195 2 1 view copy
IDR thumbnail for image:6001249 idr0062 246 241 195 2 1 view copy
IDR thumbnail for image:6001250 idr0062 246 241 195 2 1 view copy
IDR thumbnail for image:6001251 idr0062 170 163 140 2 1 view copy
IDR thumbnail for image:6001252 idr0062 170 163 297 2 1 view copy
IDR thumbnail for image:6001253 idr0062 803 1024 297 2 1 view copy
IDR thumbnail for image:6001254 idr0062 393 354 51 4 1 view copy
IDR thumbnail for image:6001255 idr0062 551 416 32 4 1 view copy
IDR thumbnail for image:6001256 idr0062 350 372 61 4 1 view copy
IDR thumbnail for image:6001257 idr0062 3763 2860 145 4 1 view copy
IDR thumbnail for image:6001258 idr0062 1282 838 36 3 1 view copy
IDR thumbnail for image:9798462 idr0073 21115 16433 1 3 1 view copy
IDR thumbnail for image:9822151 idr0083 79360 167424 1 1 1 view copy
IDR thumbnail for image:9822152 idr0083 144384 93184 1 1 1 view copy
IDR thumbnail for image:9836831 idr0077 1920 1920 259 4 259 view copy
IDR thumbnail for image:9836832 idr0077 1920 1920 259 4 259 view copy
IDR thumbnail for image:9836833 idr0077 1920 1920 259 4 259 view copy
IDR thumbnail for image:9836834 idr0077 1920 1920 259 4 259 view copy
IDR thumbnail for image:9836835 idr0077 1920 1920 259 4 259 view copy
IDR thumbnail for image:9836836 idr0077 1920 1920 259 4 259 view copy
IDR thumbnail for image:9836837 idr0077 1920 1920 259 4 259 view copy
IDR thumbnail for image:9836838 idr0077 1920 1920 259 4 259 view copy
IDR thumbnail for image:9836839 idr0077 1920 1920 259 4 259 view copy
IDR thumbnail for image:9836840 idr0077 1920 1920 259 4 259 view copy
IDR thumbnail for image:9836841 idr0077 1920 1920 259 4 259 view copy
IDR thumbnail for image:9836842 idr0077 1920 1920 259 4 259 view copy
IDR thumbnail for image:9836843 idr0077 1920 1920 259 4 259 view copy
IDR thumbnail for image:9836844 idr0077 1920 1920 259 4 259 view copy
IDR thumbnail for image:9836845 idr0077 1920 1920 259 4 259 view copy
IDR thumbnail for image:9836846 idr0077 1920 1920 259 4 259 view copy
IDR thumbnail for image:9836950 idr0079 1636 816 156 1 1 view copy