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OME-TIFF sample data

This section provides some sample data in OME-TIFF format. They include data produced from an acquisition system as well as artificial sample datasets (i.e. designed for developer testing that illustrate some possible data organizations, which should be useful if you are interested in implementing support for OME-TIFF within your software.

All the OME-TIFF sample data discussed below are available from our OME-TIFF sample images resource.

Single file OME-TIFF

This section lists various examples of single file OME-TIFF. For examples of OME-TIFF dataset distributed across multiple TIFF files, see Multi-file OME-TIFF filesets.

Artificial datasets

All datasets in the following table were artificially generated with each plane labeled according to its dimensional position for easy testing. Each one consists of a single OME-TIFF file (2016-06 schema version) containing every constituent image plane.

Sample Channels Focal planes Time points
single-channel.ome.tif 1 1 1
multi-channel.ome.tif 3 1 1
z-series.ome.tif 1 5 1
time-series.ome.tif 1 1 7
multi-channel-z-series.ome.tif 3 5 1
multi-channel-time-series.ome.tif 3 1 7
4D-series.ome.tif 1 5 7
multi-channel-4D-series.ome.tif 3 5 7

Modulo datasets

Sample files implementing the 6D, 7D and 8D storage are available from the Modulo folder of the image downloads resource.

SPIM

Big lambda

FLIM

  • FLIM-ModuloAlongT-TSCPC.ome.tiff - 2 channels and 8 histogram bins each recorded at 2 ‘real-time’ points T, with additional relative-time points (time relative to the excitation pulse) interleaved as ModuloAlongT.
  • FLIM-ModuloAlongC.ome.tiff - 2 real channels and 8 histogram bins each recorded at 2 timepoints, with additional relative-time points interleaved between channels as ModuloAlongC.

Multi-file OME-TIFF filesets

This section lists various examples of OME-TIFF datasets distributed across multiple TIFF files.

Sample biological dataset

The following OME-TIFF datasets consist of tubulin histone GFP coexpressing C. elegans embryos. Many thanks to Josh Bembenek for preparing and imaging this sample data.

The datasets were acquired on a multiphoton workstation (2.1 GHz Athlon XP 3200+ with 1GB of RAM) using WiscScan. All image planes were collected at 512x512 resolution in 8-bit grayscale, with an integration value of 2.

The files available for download have been updated to the current schema version since their initial creation.

Fileset Zipped fileset Channels Focal planes Time points Number of files
tubhiswt-2D tubhiswt-2D.zip 2 1 1 2
tubhiswt-3D tubhiswt-3D.zip 2 1 20 2
tubhiswt-4D tubhiswt-4D.zip 2 10 43 86

Partial OME-XML metadata filesets

The master OME-TIFF fileset and companion OME-XML fileset both contain a set of 18 by 24 pixel images with black and white text on each plane giving its time, z-depth and channel. Each of the five focal planes is saved as a separate OME-TIFF named multifile-Zxx.ome.tiff where xx is the index of the focal plane.

Master OME-TIFF fileset

For this sample, the full OME-XML metadata describing the whole fileset is embedded into a master OME-TIFF file. Partial OME-XML metadata blocks are embedded into the four other OME-TIFF files and refer to the master OME-TIFF file as described in the specification.

Companion OME-XML fileset

For this sample, the full OME-XML metadata describing the whole fileset is stored into a separate companion OME-XML file. Partial OME-XML metadata blocks are embedded into the five OME-TIFF files and refer to the companion OME-XML file as described in the specification.