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

5D datasets

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

Plate

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.

ROI

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.

Sub-resolutions

A set of OME-TIFF datasets representative of the Sub-resolutions section of the OME-TIFF specification were derived from a few large X Y images.

Dataset

Image dimensions (XYZCT)

Notes

Provenance

Copyright

Leica-1.ome.tiff

36832 × 38432 × 1 × 3 × 1

WSI, 2 RGB images

OpenSlide

Public Domain

Leica-2.ome.tiff

39168 × 26048 × 1 × 3 × 1

WSI, 5 RGB images

OpenSlide

Public Domain

LuCa-7color_Scan1.ome.tiff

24960 × 34560 × 1 × 5 × 1

WSI, multi-channel, fluorescence

PerkinElmer

CC-BY 4.0

BGal_000438_frames.ome.tiff

7676 × 7420 × 38 × 1 × 1

EM, Floating-point

EMPIAR

Public Domain

retina_large.ome.tiff

2048 × 1567 × 64 × 2 × 1

Multi-Z stack

Bitplane

CC-BY 4.0

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.

The first two 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.

The third dataset contains a plate with 4 wells at position A2, B1, B3 and C2. The first three wells contain one field of view and the fourth well contains 2 fields of view. Each well sample is saved as a separate OME-TIFF.

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-TIFF fileset

18 × 24 × 5 × 1 × 1

multifile.companion.ome

multifile-Z[1-5].ome.tiff

Companion OME-TIFF plate

96 × 96 × 1 × 1 × 1

hcs.companion.ome

well-*.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.