Biology:Microscopy file formats

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Microscopy file formats are variations of image file formats used to encode results of microscopy acquision events along with metadata. There are hundreds of different file formats used in microscopy, including open formats like OME-TIFF and OME-Zarr and proprietary formats such as .lif and .czi.[1][2][3]

Conversions and data sharing

While microscope manufactures tailor formats to particular needs, data reuse and reproducibility are increased if image analysis pipelines are able to work with multiple file formats. For that reason, software tools like BioFormats and bioio provide utilities that convert different proprietary formats into a common representation, so the metadata and the pixel data can be processed by shared workflows.[4][5][6] This kind of tooling enables seamless use of multiple file formats in popular tools, like ImageJ.[7][8]

Community-driven formats

File:Tiff hdf zarr – microscopy file formats.png
Three formats that can be used to store microscopy data, TIFF, HDF and Zarr.[9]

OME-XML is a schema-centered metadata language representing imaging provenance (e.g., microscope, lens, detector), acquisition modality, coordinate mapping, and experiment details. Attributes such as channel wavelengths, Z index, timepoint, and objective are standardized for interoperability.[10][11]

File:Monolithic vs chunked microscopy file formats.png
A comparison of monolithic (e.g. TIFF) to chunked (e.g. Zarr) file formats for microscopy

The community-driven format OME-TIFF is an open, extensible format developed by the Open Microscopy Environment [12] that extends the classic TIFF structure-with its widespread library and tool support-by embedding structured OME-XML metadata within TIFF tags, particularly within the ImageDescription field of the first Image File Directory (IFD). The file specification is made available by the OME consortium.[13] OME-TIFF is adopted in research and academic pathology where comprehensive metadata and analysis pipeline integration are prioritized. The Bio-Formats Java library and OMERO server provide read/write and management capabilities, with desktop analysis supported by QuPath and Fiji/ImageJ.[14]

The OME-TIFF standard has also been adopted for use in digital pathology.[15] The growth in microscopy data size and the need for cloud-ready formats prompted the development of the Next Generation File Format (OME-NGFF) endeavour,[16] which selected Zarr, a standard storing large multidimensional array data.[17][18] as the base for the OME-Zarr next-generation format, encoding, for example multidimensional image pyramids.[19] The OME-Zarr specification enables representation of outputs of complex experiments, such as high content screening assays and parallel access to data chunks served over object storage.[19]

Multimodal endeavours such as spatial transcriptomics, which adds challenges from the transcriptomics to those of bioimaging also benefit from modern file formats, such as SpatialData, which builds upon the OME-Zarr standard.[20]

The open DICOM standard. commonly used in the medical domain, has also been used as a microscopy file format.[21]

List of microscopy file formats

The BioFormats library lists at least 164 different file formats used in microscopy,[22] though the total number of formats and variants may be considerably more.[23] A list of microscopy file formats includes:

name extension developer/owner example usage documentation
OME-TIFF .tiff, .ome.tiff Open Microscopy Environment WSI [15] official website
OME-Zarr .zarr, .ome.zarr, .ozx Open Microscopy Environment spatial transcriptomics [20], volume EM, light sheet fluorescence microscopy, FIB-SEM, STED [19] official website
CZI .czi [24] Zeiss CLSM,[21] WSI [15] official website
Leica Image File Format .lif [25] Leica Microsystems CLSM [21] BioFormats
Zeiss AxioVision ZVI (Zeiss Vision Image) .zvi [26] Zeiss WSI [21] BioFormats
Olympus FluoView FV1000 .oib, .oif[27] Olympus CLSM [21] BioFormats
Zeiss LSM 510/710 .lsm Zeiss CLSM [21] BioFormats
NDPI .ndpi, ndpis Hamamatsu WSI [21][15] OpenSlide
Aperio SVS .svs Aperio (now Leica) WSI [21] OpenSlide
Leica SCN .scn Leica WSI [21] BioFormats
Ventana BIF/TIF .bif, .tif Ventana (Roche Digital Diagnostics) WSI [21] OpenSlide
DICOM [21] .dcm National Electrical Manufacturers Association WSI, CLSM, FIB-SEM [21] OpenSlide
Nikon NIS-Elements ND2[28] .nd2 Nikon BioFormats
Image Cytometry Standard ICS/IDS[29] .ics/.ids -
Image Cytometry Standard ICS2[29] .ics -
Aperio AFI .afi Aperio (now Leica) WSI [15] BioFormats
Hamamatsu VMS .vms Hamamatsu WSI [15] OpenSlide
MIRAX .mrxs Mirax WSI [15] OpenSlide
PerkinElmer Vectra QPTIFF .qptiff PerkinElmer WSI [15] BioFormats
Philips TIFF .tiff Philips WSI [15] OpenSlide
Sakura format .svslide Sakura WSI [15] OpenSlide
Trestle TIF .tif Trestle WSI [15] OpenSlide
Olympus OIR .oir[30] Olympus BioFormats, FileInfo.com
Olympus packed OIR (POIR) .poir Olympus

See also

References

  1. ↑ "File Format | Cell Sciences Imaging Facility (CSIF)" (in en). https://microscopy.stanford.edu/guides/image-analysis-imagejfiji/file-format. 
  2. ↑ Moore, Josh (2023). "OME-Zarr: a cloud-optimized bioimaging file format with international community support". Histochemistry and Cell Biology (Springer Science and Business Media LLC) 160 (3): 223–251. doi:10.1007/s00418-023-02209-1. ISSN 1432-119X. PMID 37428210. 
  3. ↑ "Supported Formats — Bio-Formats 8.3.0 documentation". https://docs.openmicroscopy.org/bio-formats/8.3.0/supported-formats.html. 
  4. ↑ "Images to reveal all?" (in en). Nature Cell Biology 6 (10): 909. 2004-10-01. doi:10.1038/ncb1004-909. ISSN 1465-7392. PMID 15459713. https://www.nature.com/articles/ncb1004-909. 
  5. ↑ Linkert, Melissa; Rueden, Curtis T.; Allan, Chris; Burel, Jean-Marie; Moore, Will; Patterson, Andrew; Loranger, Brian; Moore, Josh et al. (2010-05-31). "Metadata matters: access to image data in the real world" (in en). Journal of Cell Biology 189 (5): 777–782. doi:10.1083/jcb.201004104. ISSN 1540-8140. PMID 20513764. PMC 2878938. https://rupress.org/jcb/article/189/5/777/35828/Metadata-matters-access-to-image-data-in-the-real. 
  6. ↑ Hohlbein, Johannes; Diederich, Benedict; Marsikova, Barbora; Reynaud, Emmanuel G.; Holden, Séamus; Jahr, Wiebke; Haase, Robert; Prakash, Kirti (September 2022). "Open microscopy in the life sciences: quo vadis?" (in en). Nature Methods 19 (9): 1020–1025. doi:10.1038/s41592-022-01602-3. ISSN 1548-7091. PMID 36008630. 
  7. ↑ Collins, Tony J. (July 2007). "ImageJ for Microscopy" (in en). BioTechniques 43 (sup1): 25–30. doi:10.2144/000112517. ISSN 0736-6205. PMID 17936939. https://www.tandfonline.com/doi/full/10.2144/000112517. 
  8. ↑ Schindelin, Johannes; Rueden, Curtis T.; Hiner, Mark C.; Eliceiri, Kevin W. (2015). "The ImageJ ecosystem: An open platform for biomedical image analysis" (in en). Molecular Reproduction and Development 82 (7–8): 518–529. doi:10.1002/mrd.22489. ISSN 1098-2795. PMID 26153368. 
  9. ↑ "The Open Microscopy Environment" (in en). https://www.openmicroscopy.org/2019/06/25/formats.html. 
  10. ↑ Goldberg, Ilya G.; Allan, Chris; Burel, Jean-Marie; Creager, Doug; Falconi, Andrea; Hochheiser, Harry; Johnston, Josiah; Mellen, Jeff et al. (2005-05-03). "The Open Microscopy Environment (OME) Data Model and XML file: open tools for informatics and quantitative analysis in biological imaging" (in en). Genome Biology 6 (5): R47. doi:10.1186/gb-2005-6-5-r47. ISSN 1474-760X. PMID 15892875. 
  11. ↑ Gupta, Yubraj; Costa, Carlos; Pinho, Eduardo; Bastião Silva, Luís (2022-03-17). "DICOMization of Proprietary Files Obtained from Confocal, Whole-Slide, and FIB-SEM Microscope Scanners" (in en). Sensors 22 (6): 2322. doi:10.3390/s22062322. ISSN 1424-8220. PMID 35336492. Bibcode: 2022Senso..22.2322G. 
  12. ↑ (Eva Maxfield Brown Dan Toloudis)
  13. ↑ "OME-TIFF specification — OME Data Model and File Formats 5.6.3 documentation". https://docs.openmicroscopy.org/ome-model/5.6.3/ome-tiff/specification.html. 
  14. ↑ Leigh, Roger; Gault, David; Linkert, Melissa; Burel, Jean-Marie; Moore, Josh; Besson, Sébastien; Swedlow, Jason R. (2017). "OME Files - an open source reference library for the OME-XML metadata model and the OME-TIFF file format". bioRxiv 10.1101/088740.
  15. ↑ 15.00 15.01 15.02 15.03 15.04 15.05 15.06 15.07 15.08 15.09 15.10 Besson, Sébastien; Leigh, Roger; Linkert, Melissa; Allan, Chris; Burel, Jean-Marie; Carroll, Mark; Gault, David; Gozim, Riad et al. (April 2019). "Bringing Open Data to Whole Slide Imaging". Digital Pathology. Lecture Notes in Computer Science. 2019. 3–10. doi:10.1007/978-3-030-23937-4_1. ISBN 978-3-030-23936-7. 
  16. ↑ Moore, Josh; Allan, Chris; Besson, Sébastien; Burel, Jean-Marie; Diel, Erin; Gault, David; Kozlowski, Kevin; Lindner, Dominik et al. (December 2021). "OME-NGFF: a next-generation file format for expanding bioimaging data-access strategies" (in en). Nature Methods 18 (12): 1496–1498. doi:10.1038/s41592-021-01326-w. ISSN 1548-7091. PMID 34845388. 
  17. ↑ "Zarr - chunked, compressed, N-dimensional arrays". https://zarr.dev/. 
  18. ↑ "Cloud-Optimized Geospatial Formats Guide: Zarr". https://guide.cloudnativegeo.org/zarr/intro.html. 
  19. ↑ 19.0 19.1 19.2 Moore, Josh; Basurto-Lozada, Daniela; Besson, Sébastien; Bogovic, John; Bragantini, Jordão; Brown, Eva M.; Burel, Jean-Marie; Casas Moreno, Xavier et al. (2023-09-01). "OME-Zarr: a cloud-optimized bioimaging file format with international community support" (in en). Histochemistry and Cell Biology 160 (3): 223–251. doi:10.1007/s00418-023-02209-1. ISSN 1432-119X. PMID 37428210. PMC 10492740. https://doi.org/10.1007/s00418-023-02209-1. 
  20. ↑ 20.0 20.1 Marconato, Luca; Palla, Giovanni; Yamauchi, Kevin A.; Virshup, Isaac; Heidari, Elyas; Treis, Tim; Vierdag, Wouter-Michiel; Toth, Marcella et al. (January 2025). "SpatialData: an open and universal data framework for spatial omics" (in en). Nature Methods 22 (1): 58–62. doi:10.1038/s41592-024-02212-x. ISSN 1548-7105. PMID 38509327. 
  21. ↑ 21.00 21.01 21.02 21.03 21.04 21.05 21.06 21.07 21.08 21.09 21.10 21.11 Gupta, Yubraj; Costa, Carlos; Pinho, Eduardo; Bastião Silva, Luís (2022-03-17). "DICOMization of Proprietary Files Obtained from Confocal, Whole-Slide, and FIB-SEM Microscope Scanners" (in en). Sensors 22 (6): 2322. doi:10.3390/s22062322. ISSN 1424-8220. PMID 35336492. Bibcode: 2022Senso..22.2322G. 
  22. ↑ "Supported Formats — Bio-Formats 8.4.0 documentation". https://bio-formats.readthedocs.io/en/v8.4.0/supported-formats.html. 
  23. ↑ "The Open Microscopy Environment" (in en). https://www.openmicroscopy.org/2019/06/25/formats.html. 
  24. ↑ "CZI Image File Format" (in en). https://www.zeiss.com/microscopy/en/products/software/zeiss-zen/czi-image-file-format.html. 
  25. ↑ "Leica LAS AF LIF (Leica Image File Format) — Bio-Formats 8.4.0 documentation". https://bio-formats.readthedocs.io/en/v8.4.0/formats/leica-lif.html. 
  26. ↑ "Zeiss AxioVision ZVI (Zeiss Vision Image) — Bio-Formats 8.3.0 documentation". https://bio-formats.readthedocs.io/en/v8.3.0/formats/zeiss-axiovision-zvi.html. 
  27. ↑ "Olympus FluoView FV1000 — Bio-Formats 8.4.0 documentation". https://bio-formats.readthedocs.io/en/v8.4.0/formats/olympus-fluoview-fv1000.html. 
  28. ↑ "Nikon NIS-Elements ND2 — Bio-Formats 8.3.0 documentation". https://bio-formats.readthedocs.io/en/v8.3.0/formats/nikon-nis-elements-nd2.html. 
  29. ↑ 29.0 29.1 "Files & file formats · Analyzing fluorescence microscopy images with ImageJ". https://petebankhead.gitbooks.io/imagej-intro/content/chapters/files/files.html. 
  30. ↑ ".OIR File Extension - How to open .oir files" (in en). https://fileinfo.com/extension/oir. 



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