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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 and licensed under Creative Commons Attribution 4.0 International License unless specified otherwise.

Biological datasets

Tubhiswt

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 512 × 512 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.

Dataset (zip bundle) Image dimensions (XYZCT) Number of files
Tubhiswt 2D (tubhiswt-2D.zip) 512 × 512 × 1 × 2 × 1 2
Tubhiswt 3D (tubhiswt-3D.zip) 512 × 512 × 1 × 2 × 20 2
Tubhiswt 4D (tubhiswt-4D.zip) 512 × 512 × 10 × 2 × 43 86

BBBC

An OME-TIFF dataset representative of the High Content Screening section of the OME Data Model, derived from the public Broad Bioimage Benchmark Collection.

Dataset Image dimensions (XYZCT) Provenance Copyright
NIRHTa-001.ome.tiff 512 × 512 × 1 × 3 × 1 BBBC017 CC-BY-NC-SA 3.0

See Ljosa V, Sokolnicki KL, Carpenter AE (2012). Annotated high-throughput microscopy image sets for validation. Nature Methods 9(7):637.

MitoCheck

An OME-TIFF dataset representative of the ROI section of the OME Data Model, derived from the public MitoCheck project.

Dataset Image dimensions (XYZCT) Provenance Copyright
00001_01.ome.tiff 1344 × 1024 × 1 × 1 × 93 IDR Public Domain

See Neumann B et al. (2010). Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes. Nature 464(7289):721.

Artificial datasets

5D datasets

All datasets in the following table are single OME-TIFF files generated using Bio-Formats loci.formats.tools.MakeTestOmeTiff. Each plane is labeled according to its dimensional position for easy testing.

Name Image dimensions (XYZCT) Available extensions
Single channel 439 × 167 × 1 × 1 × 1 ome.tif, ome.tiff, ome.tf8, ome.btf, ome.tf2
Multi channel 439 × 167 × 1 × 3 × 1 ome.tif, ome.tiff, ome.tf8, ome.btf, ome.tf2
Z series 439 × 167 × 5 × 1 × 1 ome.tif, ome.tiff, ome.tf8, ome.btf, ome.tf2
Time series 439 × 167 × 1 × 1 × 7 ome.tif, ome.tiff, ome.tf8, ome.btf, ome.tf2
Multi channel Z series 439 × 167 × 5 × 3 × 1 ome.tif, ome.tiff, ome.tf8, ome.btf, ome.tf2
Multi channel time series 439 × 167 × 1 × 3 × 7 ome.tif, ome.tiff, ome.tf8, ome.btf, ome.tf2
4D series 439 × 167 × 5 × 1 × 7 ome.tif, ome.tiff, ome.tf8, ome.btf, ome.tf2
Multi channel 4D series 439 × 167 × 5 × 3 × 7 ome.tif, ome.tiff, ome.tf8, ome.btf, ome.tf2

Modulo datasets

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

Name Image dimensions (XYZCT) Modulo description
SPIM-ModuloAlongZ.ome.tiff 160 × 220 × 8 × 2 × 12 4 tiles interleaved as ModuloAlongT each recorded at 4 angles interleaved as ModuloAlongZ
LAMBDA-ModuloAlongZ-ModuloAlongT.ome.tiff 200 × 200 × 5 × 1 × 10 excitation of 5 wavelength [Λ, big-lambda] interleaved as ModuloAlongZ, each recorded at 10 emission wavelength ranges [λ, lambda] interleaved as ModuloAlongT
FLIM-ModuloAlongT-TSCPC.ome.tiff 180 × 220 × 1 × 2 × 16 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 180 × 150 × 1 × 16 × 1 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. Both datasets contain a set of 18 × 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.

Dataset Image dimensions (XYZCT) Full metadata file* Partial metadata files†
Master OME-TIFF fileset 18 × 24 × 5 × 1 × 1 multifile-Z1.ome.tiff multifile-Z[2-5].ome.tiff
Companion OME-XML fileset 18 × 24 × 5 × 1 × 1 multifile.companion.ome multifile-Z[1-5].ome.tiff
*
The full OME-XML metadata describing the whole fileset is either embedded into an OME-TIFF or stored in a companion OME-XML file
Partial OME-XML metadata blocks are embedded into the OME-TIFF files and refer to the file containing the full OME-XML metadata as described in the specification.