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 |
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 |
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. 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.
