[3i SlideBook]
extensions = .sld
owner = `Intelligent Imaging Innovations`_
developer = `Intelligent Imaging Innovations`_
bsd = no
versions = 4.1, 4.2, 5.0, 5.5, 6.0
weHave = * Numerous SlideBook datasets
weWant = * A SlideBook specification document \n
* More SlideBook datasets (preferably acquired with the most recent SlideBook software)
pixelsRating = Very good
metadataRating = Good
opennessRating = Fair
presenceRating = Very good
utilityRating = Fair
reader = SlidebookReader
mif = true
notes = We strongly encourage users to export their .sld files to OME-TIFF \n
using the SlideBook software.  Bio-Formats is not likely to support the full \n
range of metadata that is included in .sld files, and so exporting to \n
OME-TIFF from SlideBook is the best way to ensure that all metadata is \n
preserved. \n
Free software from 3i can export the files to OME-TIFF post-acquisition, see \n
https://www.intelligent-imaging.com/slidebook.\n
\n
3i also develops a native SlideBook reader which works with Bio-Formats. See \n
http://www.openmicroscopy.org/info/slidebook for details.\n
\n
.. seealso:: \n
  `Slidebook software overview <https://www.intelligent-imaging.com/slidebook>`_ \n
\n
.. _Intelligent Imaging Innovations: http://www.intelligent-imaging.com/

[3i SlideBook 7]
extensions = .sldy
owner = `Intelligent Imaging Innovations <http://www.intelligent-imaging.com/>`_
developer = `Intelligent Imaging Innovations <http://www.intelligent-imaging.com/>`_
bsd = yes
software = `SlideBook <https://www.intelligent-imaging.com/slidebook/>`_
weHave = * a small number of datasets
pixelsRating = Outstanding
metadataRating = Outstanding
opennessRating = Very good
presenceRating = Very good
utilityRating = Very good
privateSpecification = true
reader = SlideBook7Reader

[Adobe Photoshop PSD]
pagename = photoshop-psd
extensions = .psd
developer = `Adobe <https://www.adobe.com/>`_
bsd = no
versions = 1.0
weHave = * a PSD specification document (v3.0.4, 16 July 1995) \n
* a few PSD files
weWant = * more PSD files
pixelsRating = Good
metadataRating = Good
opennessRating = Good
presenceRating = Good
utilityRating = Fair
reader = PSDReader

[AIM]
extensions = .aim
developer = `SCANCO Medical AG <http://www.scanco.ch/>`_
bsd = no
weHave = * one .aim file
weWant = * an .aim specification document \n
* more .aim files
pixelsRating = Good
metadataRating = Fair
opennessRating = Fair
presenceRating = Poor
utilityRating = Fair
reader = AIMReader

[Alicona 3D]
extensions = .al3d
owner = `Alicona Imaging <https://www.alicona.com/>`_
bsd = no
versions = 1.0
weHave = * an AL3D specification document (v1.0, from 2003, in PDF)\n
* a few AL3D datasets
weWant = * more AL3D datasets (Z series, T series, 16-bit)
pixelsRating = Very good
metadataRating = Very good
opennessRating = Very good
presenceRating = Poor
utilityRating = Good
reader = AliconaReader
notes = Known deficiencies: \n
\n
- Support for 16-bit AL3D images is present, but has never been tested. \n
- Texture data is currently ignored.

[Amnis FlowSight]
extensions = .cif
owner = Amnis (now owned by `Merck <https://www.merckmillipore.com>`_)
bsd = yes
weHave = * a few sample datasets
pixelsRating = Good
metadataRating = Good
opennessRating = Good
presenceRating = Poor
utilityRating = Fair
reader = FlowSightReader
mif = true

[Amersham Biosciences Gel]
extensions = .gel
owner = `Cytiva <https://www.cytivalifesciences.com/en/us/shop/protein-analysis/molecular-imaging-for-proteins/imaging-systems>`_
developer = Molecular Dynamics
bsd = no
weHave = * a GEL specification document (Revision 2, from 2001 Mar 15, in PDF) \n
* a few GEL datasets
pixelsRating = Very good
metadataRating = Good
opennessRating = Good
presenceRating = Fair
utilityRating = Fair
reader = GelReader
privateSpecification = true
notes = .. seealso:: \n
  `GEL Technical Overview <https://web.archive.org/web/20231204123656/https://www.awaresystems.be/imaging/tiff/tifftags/docs/gel.html>`_

[Amira Mesh]
extensions = .am, .amiramesh, .grey, .hx, .labels
developer = `Visage Imaging <http://www.vsg3d.com/>`_
bsd = no
weHave = * a few Amira Mesh datasets \n
* `public sample images <https://downloads.openmicroscopy.org/images/AmiraMesh/>`__
weWant = * more Amira Mesh datasets
pixelsRating = Very good
metadataRating = Fair
opennessRating = Fair
presenceRating = Fair
utilityRating = Fair
reader = AmiraReader

[Analyze 7.5]
extensions = .img, .hdr
developer = `Mayo Foundation Biomedical Imaging Resource <https://www.mayo.edu/research/core-resources/biomedical-imaging-resource-core/overview>`_
bsd = no
weHave = * `an Analyze 7.5 specification document <http://web.archive.org/web/20070927191351/http://www.mayo.edu/bir/PDF/ANALYZE75.pdf>`_ \n
* several Analyze 7.5 datasets
pixelsRating = Very good
metadataRating = Very good
opennessRating = Very good
presenceRating = Good
utilityRating = Fair
reader = AnalyzeReader

[Andor Bio-Imaging Division (ABD) TIFF]
pagename = abd-tiff
extensions = .tif
owner = `Andor Technology <https://andor.oxinst.com/>`_
developer = Andor Bioimaging Department
bsd = no
weHave = * an ABD-TIFF specification document (from 2005 November, in PDF) \n
* a few ABD-TIFF datasets
pixelsRating = Very good
metadataRating = Very good
opennessRating = Good
presenceRating = Fair
utilityRating = Good
privateSpecification = true
reader = FluoviewReader
mif = true
notes = With a few minor exceptions, the ABD-TIFF format is identical to the \n
Fluoview TIFF format.

[Andor SIF]
extensions = .sif
owner = `Andor Technology <https://andor.oxinst.com/>`_
developer = Andor Bioimaging Department
bsd = no
weHave = * a small number of Andor SIF datasets
weWant = * an Andor SIF specification document
pixelsRating = Good
metadataRating = Fair
opennessRating = Fair
presenceRating = Fair
utilityRating = Fair
reader = SIFReader

[Animated PNG]
extensions = .png
developer = `The Animated PNG Project <https://animatedpngs.com/>`_
bsd = yes
software = `Firefox 3+ <https://www.mozilla.org/en-US/firefox>`_ \n
`Opera 9.5+ <http://www.opera.com>`_ \n
`KSquirrel <https://github.com/HappySeaFox/ksquirrel>`_
weHave = * `a specification document <http://wiki.mozilla.org/APNG_Specification>`_ \n
* several APNG files
pixelsRating = Very good
metadataRating = Very good
opennessRating = Outstanding
presenceRating = Good
utilityRating = Poor
reader = APNGReader
writer = APNGWriter

[Aperio AFI]
extensions = .afi, .svs
owner = `Leica Biosystems <https://www.leicabiosystems.com/>`_
bsd = no
versions =
weHave = * several AFI datasets
pixelsRating = Very good
metadataRating = Very good
opennessRating = Very good
presenceRating = Good
utilityRating = Good
pyramid = yes
reader = AFIReader
mif = true
notes = .. seealso:: \n
  `Aperio ImageScope <https://www.leicabiosystems.com/digital-pathology/manage/aperio-imagescope/>`_

[Aperio SVS TIFF]
extensions = .svs
owner = `Leica Biosystems <https://www.leicabiosystems.com/>`_
bsd = no
software = `OpenSlide <https://openslide.org>`_
versions = 8.0, 8.2, 9.0
weHave = * many SVS datasets\n
* `public sample images <https://downloads.openmicroscopy.org/images/SVS/>`__\n
* an SVS specification document \n
* the ability to generate additional SVS datasets
pixelsRating = Very good
metadataRating = Very good
opennessRating = Very good
presenceRating = Good
utilityRating = Good
privateSpecification = true
pyramid = yes
reader = SVSReader
mif = true
options = true
notes = .. seealso:: \n
  `Aperio ImageScope <https://www.leicabiosystems.com/digital-pathology/manage/aperio-imagescope/>`_

[Applied Precision CellWorX]
extensions = .htd, .pnl
developer = Applied Precision, Inc.
bsd = no
weHave = * a few CellWorX datasets\n
* `public sample datasets <https://downloads.openmicroscopy.org/images/CellWorX/>`__
weWant = * a CellWorX specification document \n
* more CellWorX datasets
pixelsRating = Very good
metadataRating = Very good
opennessRating = Good
presenceRating = Fair
utilityRating = Fair
reader = CellWorxReader
mif = true

[AVI (Audio Video Interleave)]
pagename = avi
extensions = .avi
developer = `Microsoft <https://www.microsoft.com/>`_
bsd = yes
software = `AVI Reader plugin for ImageJ <https://imagej.net/ij/plugins/avi-reader.html>`_ \n
`AVI Writer plugin for ImageJ <https://imagej.net/ij/plugins/avi.html>`_
weHave = * several AVI datasets
weWant = * more AVI datasets, including: \n
\n
  * files with audio tracks and/or multiple video tracks \n
  * files compressed with a common unsupported codec \n
  * 2+ GB files
pixelsRating = Good
metadataRating = Fair
opennessRating = Fair
presenceRating = Outstanding
utilityRating = Poor
reader = AVIReader
writer = AVIWriter
notes = * Bio-Formats can save image stacks as AVI (uncompressed). \n
* The following codecs are supported for reading: \n
\n
  * Microsoft Run-Length Encoding (MSRLE) \n
  * Microsoft Video (MSV1) \n
  * Raw (uncompressed) \n
  * JPEG \n
\n
.. seealso:: \n
  `AVI RIFF File Reference <https://msdn.microsoft.com/en-us/library/ms779636.aspx>`_ \n
  `AVI on Wikipedia <https://en.wikipedia.org/wiki/Audio_Video_Interleave>`_

[Axon Raw Format]
extensions = .arf
owner = `INDEC BioSystems <http://www.indecbiosystems.com/>`_
bsd = no
weHave = * one ARF dataset \n
* a `specification document <http://www.indecbiosystems.com/imagingworkbench/ApplicationNotes/IWAppNote11-ARF_File_Format.pdf>`_
weWant = * more ARF datasets
pixelsRating = Very good
metadataRating = Very good
opennessRating = Very good
presenceRating = Poor
utilityRating = Fair
reader = ARFReader

[BD Pathway]
extensions = .exp, .tif
owner = `BD Biosciences <http://www.bdbiosciences.com>`_
bsd = no
weHave = * a few BD Pathway datasets
weWant = * more BD Pathway datasets
pixelsRating = Very good
metadataRating = Very good
opennessRating = Good
presenceRating = Fair
utilityRating = Good
reader = BDReader
mif = true

[Becker & Hickl SPC FIFO]
pagename = becker-hickl-fifo
extensions = .spc
owner = `Becker-Hickl <https://www.becker-hickl.com/>`_
bsd = no
weHave = * an `SPC specification document <https://www.becker-hickl.com/literature/handbooks/>`_ \n
* `public sample images <https://downloads.openmicroscopy.org/images/SPC-FIFO/>`__
weWant = * more SPC sample files
pixelsRating = Poor
metadataRating = Poor
opennessRating = Good
presenceRating = Poor
utilityRating = Fair
reader = SPCReader
mif = true
notes = * Only files containing frame, line and pixel clock information \n
  are currently supported

[Becker & Hickl SPCImage]
extensions = .sdt
owner = `Becker-Hickl <https://www.becker-hickl.com/>`_
bsd = no
weHave = * an SDT specification document (from 2008 April, in PDF) \n
* an SDT specification document (from 2006 June, in PDF) \n
* Becker & Hickl's `SPCImage <https://www.becker-hickl.com/products/spcimage/>`_ software \n
* a large number of SDT datasets \n
* `public sample images <https://downloads.openmicroscopy.org/images/SDT/>`__ \n
* the ability to produce new datasets
pixelsRating = Very good
metadataRating = Good
opennessRating = Good
presenceRating = Poor
utilityRating = Fair
privateSpecification = true
reader = SDTReader
mif = true

[Big Data Viewer]
extensions = .xml, .h5
owner = `Tobias Pietzsch <https://imagej.net/BigDataViewer>`_
bsd = yes
weHave = * a BDV specification document\n
* `public sample images <https://downloads.openmicroscopy.org/images/BDV/>`__
pixelsRating = Good
metadataRating = Very good
opennessRating = Very Good
presenceRating = Good
utilityRating = Good
pyramid = yes
reader = BDVReader
mif = true

[Bio-Rad Gel]
extensions = .1sc
owner = `Bio-Rad <https://www.bio-rad.com>`_
bsd = no
weHave = * software that can read Bio-Rad Gel files \n
* several Bio-Rad Gel files \n
* reverse-engineered Bio-Rad Gel (1sc) file format specification \n
* Bio-Rad's `Image Lab 5.2.1 <https://www.bio-rad.com/en-ch/product/image-lab-software>`_ software
weWant = * more Bio-Rad Gel files
pixelsRating = Good
metadataRating = Fair
opennessRating = Fair
presenceRating = Poor
utilityRating = Fair
reader = BioRadGelReader
notes = * `Bio-Rad Gel Format (1sc) specification <https://biorad1sc-doc.readthedocs.io/>`_ \n
* Python3 package of a Bio-Rad Gel Format (1sc) reader \n
\n
  * ``pip3 install biorad1sc_reader`` \n
  * `biorad1sc_reader documentation <https://biorad1sc-reader.readthedocs.io/>`_ \n
  * Includes command-line utilities \n
\n
    * bio1sc2tiff - convert 1sc file image to tiff \n
    * bio1scmeta - report all metadata in a 1sc file \n
    * bio1scread - report details on internal 1sc file structure \n
\n
  * `biorad1sc_reader on pypi <https://pypi.org/project/biorad1sc-reader/>`_ \n
  * `biorad1sc_reader on github <https://github.com/itsayellow/biorad1sc_reader>`_

[Bio-Rad PIC]
extensions = .pic, .raw, .xml
owner = `ZEISS International <https://www.zeiss.com>`_
developer = Bio-Rad
bsd = no
software = `Bio-Rad PIC reader plugin for ImageJ <https://imagej.net/ij/plugins/biorad.html>`_
weHave = * a PIC specification document (v4.5, in PDF) \n
* an older PIC specification document (v4.2, from 1996 December 16, in DOC) \n
* a large number of PIC datasets \n
* the ability to produce new datasets
pixelsRating = Outstanding
metadataRating = Outstanding
opennessRating = Very good
presenceRating = Very good
utilityRating =  Very good
privateSpecification = true
reader = BioRadReader
notes = * Commercial applications that support this format include: \n
\n
  * `Bitplane Imaris <http://www.bitplane.com/>`_ \n
  * `SVI Huygens <https://svi.nl/>`_

[Bio-Rad SCN]
extensions = .scn
owner = `Bio-Rad <https://www.bio-rad.com>`_
developer = Bio-Rad
bsd = no
weHave = * a few Bio-Rad .scn files
pixelsRating = Very good
metadataRating = Fair
opennessRating = Fair
presenceRating = Poor
utilityRating = Fair
reader = BioRadSCNReader

[Bitplane Imaris]
extensions = .ims
owner = `Oxford Instruments <https://imaris.oxinst.com/>`_ (formerly Bitplane)
bsd = no
versions = 2.7, 3.0, 5.5
software = `Imaris writer <https://github.com/imaris/ImarisWriter>`_
weHave = * an Imaris (RAW) specification document (from no later than 1997 November 11, in HTML) \n
* an `Imaris 5.5 (HDF) specification document <https://imaris.oxinst.com/support/imaris-file-format>`_ \n
* Bitplane's bfFileReaderImaris3N code (from no later than 2005, in C++) \n
* several older Imaris (RAW) datasets \n
* one Imaris 3 (TIFF) dataset \n
* several Imaris 5.5 (HDF) datasets\n
* `public sample images <https://downloads.openmicroscopy.org/images/Imaris-IMS/>`__
weWant = * an Imaris 3 (TIFF) specification document \n
* more Imaris 3 (TIFF) datasets
pixelsRating = Very good
metadataRating = Very good
opennessRating = Very good
presenceRating = Fair
utilityRating = Fair
pyramid = yes
reader = ImarisHDFReader, ImarisTiffReader, ImarisReader
mif = true
notes = - There are three distinct Imaris formats: \n
    #. the old binary format (introduced in Imaris version 2.7) \n
    #. Imaris 3, a TIFF variant (introduced in Imaris version 3.0) \n
    #. Imaris 5.5, an HDF variant (introduced in Imaris version 5.5)

[Bruker MRI]
developer = `Bruker <https://www.bruker.com/>`_
bsd = no
software = `Bruker plugin for ImageJ <https://imagej.net/ij/plugins/bruker.html>`_
weHave = * a few Bruker MRI datasets
weWant = * an official specification document
pixelsRating = Good
metadataRating = Fair
opennessRating = Fair
presenceRating = Good
utilityRating = Fair
reader = BrukerReader
mif = true

[Burleigh]
extensions = .img
owner = Burleigh Instruments
bsd = no
weHave = * Pascal code that can read Burleigh files (from ImageSXM) \n
* a few Burleigh files
weWant = * a Burleigh file format specification \n
* more Burleigh files
pixelsRating = Good
metadataRating = Fair
opennessRating = Fair
presenceRating = Fair
utilityRating = Fair
reader = BurleighReader

[Canon DNG]
extensions = .cr2, .crw
developer = `Canon <https://global.canon/en/index.html>`_
bsd = no
software = `IrfanView <https://www.irfanview.com/>`_
weHave = * a few example datasets
weWant = * an official specification document
pixelsRating = Good
metadataRating = Fair
opennessRating = Fair
presenceRating = Fair
utilityRating = Fair
reader = DNGReader

[CellH5]
extensions = .ch5
developer = `CellH5 <http://cellh5.org/>`_
bsd = yes
software = `CellH5 <http://cellh5.org/>`_
weHave = * `public sample images <https://downloads.openmicroscopy.org/images/CellH5/>`__
pixelsRating = Very good
metadataRating = Outstanding
opennessRating = Outstanding
presenceRating = Fair
utilityRating = Very good
reader = CellH5Reader
writer = CellH5Writer
mif = true

[Cellomics]
extensions = .c01, .dib
developer = `Thermo Fisher Scientific <http://www.thermofisher.com/>`_
bsd = no
weHave = * a few Cellomics .c01 datasets\n
* `public sample images <https://downloads.openmicroscopy.org/images/Cellomics/>`__
weWant = * a Cellomics .c01 specification document \n
* more Cellomics .c01 datasets
pixelsRating = Very good
metadataRating = Very good
opennessRating = Fair
presenceRating = Poor
utilityRating = Poor
reader = CellomicsReader
mif = true

[cellSens VSI]
extensions = .vsi
developer = `Olympus <https://www.olympus-global.com>`_
bsd = no
weHave = * many example datasets \n
* `public sample images <https://downloads.openmicroscopy.org/images/CellSens/>`__ \n
* a VSI specification document (v1.6, 2012 November 27, in PDF) \n
* a VSI specification document (v1.3, 2010 February 5, in PDF)
pixelsRating = Fair
metadataRating = Very good
opennessRating = Good
presenceRating = Fair
utilityRating = Fair
pyramid = yes
reader = CellSensReader
mif = true
privateSpecification = true

[CellVoyager]
extensions = .xml, .tif
owner = `Yokogawa <https://www.yokogawa.com/>`_
bsd = no
weHave = * a few example datasets
pixelsRating = Very good
metadataRating = Very good
opennessRating = Good
presenceRating = Fair
utilityRating = Good
reader = CellVoyagerReader
mif = true

[CV7000]
extensions = .wpi, .tif
owner = `Yokogawa <http://www.yokogawa.com/>`_
bsd = no
weHave = * many example datasets \n
* `public sample images <https://downloads.openmicroscopy.org/images/CV7000/>`__
pixelsRating = Very good
metadataRating = Very good
opennessRating = Good
presenceRating = Fair
utilityRating = Fair
reader = CV7000Reader
mif = true
options = true

[DeltaVision]
extensions = .dv, .r3d, .rcpnl
owner = `Cytiva <https://www.cytivalifesciences.com/en/us/solutions/cellular-analysis/products-and-technology/microscopy>`_ (formerly GE Healthcare, Applied Precision)
bsd = no
software = `DeltaVision Opener plugin for ImageJ <https://imagej.net/ij/plugins/track/delta.html>`_
weHave = * a DV specification document (v2.10 or newer, in HTML) \n
* numerous DV datasets\n
* `public sample images <https://downloads.openmicroscopy.org/images/DV/>`__
pixelsRating = Outstanding
metadataRating = Good
opennessRating = Good
presenceRating = Good
utilityRating = Good
reader = DeltavisionReader, RCPNLReader
mif = true
privateSpecification = true
notes = - The Deltavision format is based on the Medical Research Council (MRC) file format. \n
- Commercial applications that support DeltaVision include: \n
\n
  * `Bitplane Imaris <http://www.bitplane.com/>`_ \n
  * `SVI Huygens <https://svi.nl/>`_ \n
  * `Image-Pro Plus <http://www.mediacy.com/>`_ \n
- RCPNL is a variant of the DeltaVision format and requires a separate reader. \n

[DICOM]
extensions = .dcm, .dicom
developer = `DICOM Standards Committee <https://www.dicomstandard.org/dsc/>`_
bsd = yes
software = `List of converters and viewers <https://www.dclunie.com/medical-image-faq/html/part8.html#DICOMFileConvertorsAndViewers>`_ \n
`List of libraries/toolkits <https://www.dclunie.com/medical-image-faq/html/part8.html#DICOMToolkits>`_ \n
`Wikipedia's list of freeware health software <https://en.wikipedia.org/wiki/List_of_freeware_health_software>`_
samples = `David Clunie's list of DICOM image samples <https://www.dclunie.com/medical-image-faq/html/part8.html#DICOMImageSamples>`_ \n
`Whole Slide Images from DICOM Working Group 26 <ftp://medical.nema.org/medical/dicom/DataSets/WG26/>`_ \n
`NCI Imaging Data Commons Portal <https://portal.imaging.datacommons.cancer.gov/>`_, `download instructions <https://learn.canceridc.dev/data/downloading-data>`_ \n
`Converted Whole Slide Images <https://wsi.orthanc-server.com/orthanc/app/explorer.html>`_ \n
`DICOM sample image sets from OsiriX web site <http://www.osirix-viewer.com/resources/dicom-image-library/>`_
weHave = * `DICOM specification documents <https://www.dicomstandard.org/current/>`_ \n
* numerous DICOM datasets (see above)\n
* `public sample images <https://downloads.openmicroscopy.org/images/DICOM/>`__
pixelsRating = Very good
metadataRating = Very good
opennessRating = Outstanding
presenceRating = Outstanding
utilityRating = Very good
reader = DicomReader
writer = DicomWriter
mif = true
pyramid = true
notes = * DICOM stands for "Digital Imaging and Communication in Medicine". \n
* Bio-Formats supports uncompressed, baseline JPEG, JPEG-2000 (lossy and lossless), and RLE lossless transfer syntaxes. \n
* Support for reading and writing DICOM whole slide images (DICOM WSI format) was implemented through collaboration with `NCI Imaging Data Commons <https://datacommons.cancer.gov/repository/imaging-data-commons/>`_  and has been funded in whole or in part with Federal funds from the National Cancer Institute, National Institutes of Health, under Task Order No. HHSN26110071 under Contract No. HHSN2612015000031. \n
\n
If you have a problematic DICOM file which you cannot send us for privacy \n
reasons, please send us the exact error message and be aware that it may take \n
several attempts to fix the problem blind. \n
\n
.. seealso:: \n
  `DICOM homepage <https://www.dicomstandard.org/>`_

[ECAT7]
extensions = .v
developer = `Siemens <https://www.siemens.com/global/en/home.html>`_
bsd = no
weHave = * a few ECAT7 files \n
* `public sample images <https://downloads.openmicroscopy.org/images/ECAT7/>`__
weWant = * an ECAT7 specification document \n
* more ECAT7 files
pixelsRating = Good
metadataRating = Fair
opennessRating = Fair
presenceRating = Fair
utilityRating = Fair
reader = Ecat7Reader

[EPS (Encapsulated PostScript)]
pagename = eps
extensions = .eps, .epsi, .ps
developer = `Adobe <https://www.adobe.com/>`_
bsd = yes
software = `EPS Writer plugin for ImageJ <https://imagej.net/ij/plugins/eps-writer.html>`_
weHave = * a few EPS datasets \n
* the ability to produce new datasets
pixelsRating = Good
metadataRating = Good
opennessRating = Good
presenceRating = Very good
utilityRating = Poor
reader = EPSReader
writer = EPSWriter
notes = * Bio-Formats can save individual planes as EPS. \n
* Certain types of compressed EPS files are not supported.

[Evotec/PerkinElmer Opera Flex]
extensions = .flex, .mea, .res
developer = Evotec Technologies, now `PerkinElmer <https://www.perkinelmer.com/>`_
bsd = no
weHave = * many Flex datasets\n
* `public sample images <https://downloads.openmicroscopy.org/images/Flex/>`__
pixelsRating = Outstanding
metadataRating = Outstanding
opennessRating = Poor
presenceRating = Poor
utilityRating = Poor
reader = FlexReader
mif = true

[FEI TIFF]
extensions = .tiff
developer = `FEI <https://www.fei.com/home/>`_
bsd = no
weHave = * a few FEI TIFF datasets
pixelsRating = Very good
metadataRating = Very good
opennessRating = Good
presenceRating = Fair
utilityRating = Fair
reader = FEITiffReader

[FEI]
extensions = .img
developer = `FEI <https://www.fei.com/home/>`_
bsd = no
weHave = * a few FEI files
weWant = * a specification document \n
* more FEI files
pixelsRating = Fair
metadataRating = Poor
opennessRating = Poor
presenceRating = Fair
utilityRating = Fair
reader = FEIReader

[FITS (Flexible Image Transport System)]
pagename = fits
extensions = .fits
developer = `National Radio Astronomy Observatory <http://www.nrao.edu/>`_
bsd = yes
weHave = * a `FITS specification document <http://archive.stsci.edu/fits/fits_standard/>`_ (NOST 100-2.0, from 1999 March 29, in HTML) \n
* several FITS datasets
pixelsRating = Very good
metadataRating = Very good
opennessRating = Very good
presenceRating = Good
utilityRating = Fair
reader = FitsReader
notes = .. seealso:: \n
  `MAST:FITS homepage <http://archive.stsci.edu/fits/>`_ \n
  `FITS Support Office <https://fits.gsfc.nasa.gov/>`_

[Gatan Digital Micrograph 2]
extensions = .dm2
developer = `Gatan <http://www.gatan.com>`_
bsd = no
versions = 2
weHave = * Pascal code that can read DM2 files (from ImageSXM) \n
* a few DM2 files
weWant = * an official DM2 specification document \n
* more DM2 files
pixelsRating = Good
metadataRating = Good
opennessRating = Fair
presenceRating = Fair
utilityRating = Good
reader = GatanDM2Reader

[Gatan Digital Micrograph]
extensions = .dm3, .dm4
owner = `Gatan <http://www.gatan.com/>`_
bsd = no
versions = 3, 4
software = `DM3 Reader plugin for ImageJ <https://imagej.net/ij/plugins/DM3_Reader.html>`_ \n
`EMAN <https://github.com/cryoem/eman2>`_
weHave = * Gatan's ImageReader2003 code (from 2003, in C++) \n
* numerous DM3 datasets\n
* `public sample images <https://downloads.openmicroscopy.org/images/Gatan/>`__
weWant = * a DM3 specification document
pixelsRating = Very good
metadataRating = Good
opennessRating = Fair
presenceRating = Fair
utilityRating = Fair
reader = GatanReader
notes = Applications that support .dm3 files include `Datasqueeze <https://www.sas.upenn.edu/~heiney/html-physics/datasqueeze/>`_. \n
\n
Note that the Gatan Reader does not currently support stacks.

[GE MicroCT]
extensions = .vff
developer = GE Healthcare
bsd = no
weHave = * several public MicroCT datasets from the `CIBC Dataset Archive <https://sci.utah.edu/archived-data/>`_
pixelsRating = Very good
metadataRating = Fair
opennessRating = Fair
presenceRating = Fair
utilityRating = Fair
reader = MicroCTReader

[GIF (Graphics Interchange Format)]
pagename = gif
extensions = .gif
owner = `Unisys <https://www.unisys.com/>`_
developer = `CompuServe <http://www.compuserve.com/>`_
bsd = yes
software = `Animated GIF Reader plugin for ImageJ <https://imagej.net/ij/plugins/agr.html>`_ \n
`GIF Stack Writer plugin for ImageJ <https://imagej.net/ij/plugins/gif-stack-writer.html>`_
weHave = * a `GIF specification document <https://www.w3.org/Graphics/GIF/spec-gif89a.txt>`_ (Version 89a, from 1990, in HTML) \n
* numerous GIF datasets \n
* the ability to produce new datasets
pixelsRating = Very good
metadataRating = Fair
opennessRating = Fair
presenceRating = Outstanding
utilityRating = Poor
reader = GIFReader

[Hamamatsu Aquacosmos NAF]
extensions = .naf
developer = `Hamamatsu <https://www.hamamatsu.com/>`_
bsd = no
weHave = * a few NAF files
weWant = * a specification document \n
* more NAF files
pixelsRating = Good
metadataRating = Poor
opennessRating = Poor
presenceRating = Fair
utilityRating = Fair
reader = NAFReader
mif = true

[Hamamatsu DCIMG]
extensions = .dcimg
owner = `Hamamatsu <https://www.hamamatsu.com/>`_
bsd = no
weHave = * `public sample images <https://downloads.openmicroscopy.org/images/DCIMG/>`__
pixelsRating = Good
metadataRating = Poor
opennessRating = Poor
presenceRating = Fair
utilityRating = Fair
reader = DCIMGReader
mif = false

[Hamamatsu HIS]
extensions = .his
owner = `Hamamatsu <https://www.hamamatsu.com/>`_
bsd = no
weHave = * Pascal code that can read HIS files (from ImageSXM) \n
* several HIS files
weWant = * an HIS specification \n
* more HIS files
pixelsRating = Good
metadataRating = Good
opennessRating = Fair
presenceRating = Fair
utilityRating = Fair
reader = HISReader
mif = true

[Hamamatsu ndpi]
extensions = .ndpi, .ndpis
developer = `Hamamatsu <https://www.hamamatsu.com/>`_
bsd = no
software = `NDP.view2 <https://www.hamamatsu.com/eu/en/product/life-science-and-medical-systems/digital-slide-scanner/U12388-01.html>`_ \n
`OpenSlide <https://openslide.org>`_
weHave = * many example datasets \n
* `public sample images <https://downloads.openmicroscopy.org/images/Hamamatsu-NDPI/>`__
pixelsRating = Very Good
metadataRating = Good
opennessRating = Good
presenceRating = Fair
utilityRating = Fair
reader = NDPIReader, NDPISReader
mif = true
pyramid = yes

[Hamamatsu VMS]
extensions = .vms
developer = `Hamamatsu <http://www.hamamatsu.com>`_
bsd = no
software = `OpenSlide <https://openslide.org>`_
weHave = * a few example datasets \n
* `public sample images <https://downloads.openmicroscopy.org/images/Hamamatsu-VMS/>`__ \n
* `developer documentation from the OpenSlide project <https://openslide.org/Hamamatsu%20format/>`_
weWant = * an official specification document \n
* more example datasets
pixelsRating = Good
metadataRating = Good
opennessRating = Fair
presenceRating = Fair
utilityRating = Fair
reader = HamamatsuVMSReader
mif = true

[Hitachi S-4800]
extensions = .txt, .tif, .bmp, .jpg
developer = `Hitachi <https://www.hitachi-hightech.com/file/us/pdf/library/technical/Hitachi_4800_STEM.pdf>`_
bsd = no
weHave = * several Hitachi S-4800 datasets
pixelsRating = Very good
metadataRating = Very good
opennessRating = Very good
presenceRating = Fair
utilityRating = Fair
reader = HitachiReader

[I2I]
extensions = .i2i
developer = `Biomedical Imaging Group, UMass Medical School <https://www.umassmed.edu/>`_
bsd = no
weHave = * several example datasets \n
* a specification document \n
* an ImageJ plugin that can read I2I data
pixelsRating = Very Good
metadataRating = Very good
opennessRating = Very Good
presenceRating = Poor
utilityRating = Fair
reader = I2IReader

[ICS (Image Cytometry Standard)]
pagename = ics
extensions = .ics, .ids
developer = P. Dean et al.
bsd = yes
versions = 1.0, 2.0
software = `Libics (ICS reference library) <https://svi-opensource.github.io/libics/>`_ \n
`ICS Opener plugin for ImageJ <https://valelab4.ucsf.edu/~nstuurman/IJplugins/Ics_Opener.html>`_ \n
`IrfanView <https://www.irfanview.com/>`_
weHave = * numerous ICS datasets\n
* `public sample images <https://downloads.openmicroscopy.org/images/ICS/>`__
pixelsRating = Outstanding
metadataRating = Outstanding
opennessRating = Outstanding
presenceRating = Very good
utilityRating = Very good
reader = ICSReader
writer = ICSWriter
notes = * ICS version 1.0 datasets have two files - an .ics file that contains \n
  all of the metadata in plain-text format, and an .ids file that \n
  contains all of the pixel data. \n
* ICS version 2.0 datasets are a single .ics file that contains both \n
  pixels and metadata. \n
\n
Commercial applications that can support ICS include: \n
\n
* `Bitplane Imaris <http://www.bitplane.com/>`_ \n
* `SVI Huygens <https://svi.nl/>`_

[Imacon]
extensions = .fff
owner = `Hasselblad <https://www.hasselblad.com/>`_
bsd = no
weHave = * one Imacon file
weWant = * more Imacon files
pixelsRating = Poor
metadataRating = Poor
opennessRating = Fair
presenceRating = Poor
utilityRating = Good
reader = ImaconReader
mif = true

[ImagePro Sequence]
extensions = .seq
owner = `Media Cybernetics <http://www.mediacy.com/>`_
bsd = no
weHave = * the `Image-Pro Plus <http://www.mediacy.com/imageproplus>`_ software \n
* a few SEQ datasets \n
* the ability to produce more datasets
weWant = * an official SEQ specification document
pixelsRating = Very good
metadataRating = Fair
opennessRating = Fair
presenceRating = Fair
utilityRating = Fair
reader = SEQReader

[ImagePro Workspace]
extensions = .ipw
owner = `Media Cybernetics <http://www.mediacy.com/>`_
bsd = no
weHave = * the `Image-Pro Plus <http://www.mediacy.com/imageproplus>`_ software \n
* a few IPW datasets \n
* the ability to produce more datasets
weWant = * an official IPW specification document \n
* more IPW datasets: \n
\n
  * multiple datasets in one file \n
  * 2+ GB files
pixelsRating = Very good
metadataRating = Poor
opennessRating = Poor
presenceRating = Poor
utilityRating = Poor
reader = IPWReader
notes = Bio-Formats uses a modified version of the `Apache Jakarta \n
POI <http://poi.apache.org/>`_ library to read IPW files.

[IMAGIC]
extensions = .hed, .img
developer = `Image Science <http://www.imagescience.de>`_
bsd = no
software = `em2em <http://www.imagescience.de/em2em.html>`_
weHave = * one example dataset \n
* official file format documentation
weWant = * more example datasets
pixelsRating = Very good
metadataRating = Very good
opennessRating = Very good
presenceRating = Good
utilityRating = Good
reader = ImagicReader
notes = .. seealso:: \n
  `IMAGIC specification <http://www.imagescience.de/em2em.html>`_

[IMOD]
extensions = .mod
owner = `Boulder Laboratory for 3-Dimensional Electron Microscopy of Cells <http://bio3d.colorado.edu>`_
developer = `Boulder Laboratory for 3-Dimensional Electron Microscopy of Cells <http://bio3d.colorado.edu>`_
bsd = no
software = `IMOD <http://bio3d.colorado.edu/imod/>`_
weHave = * a few sample datasets \n
* `official documentation <http://bio3d.colorado.edu/imod/doc/binspec.html>`_
pixelsRating = Good
metadataRating = Good
opennessRating = Outstanding
presenceRating = Fair
utilityRating = Fair
reader = IMODReader

[Improvision Openlab LIFF]
extensions = .liff
owner = `PerkinElmer <https://www.perkinelmer.com/>`_
developer = Improvision, now `PerkinElmer <https://www.perkinelmer.com/>`_
bsd = no
versions = 2.0, 5.0
weHave = * an Openlab specification document (from 2000 February 8, in DOC) \n
* Improvision's XLIFFFileImporter code for reading Openlab LIFF v5 files (from 2006, in C++) \n
* several Openlab datasets
weWant = * more Openlab datasets (preferably with 32-bit integer data)
pixelsRating = Very good
metadataRating = Very good
opennessRating = Very good
presenceRating = Good
utilityRating = Fair
privateSpecification = true
reader = OpenlabReader
mif = true

[Improvision Openlab Raw]
extensions = .raw
owner = `PerkinElmer <https://www.perkinelmer.com/>`_
developer = Improvision, now `PerkinElmer <https://www.perkinelmer.com/>`_
bsd = no
weHave = * an Openlab Raw specification document (from 2004 November 09, in HTML) \n
* a few Openlab Raw datasets
pixelsRating = Outstanding
metadataRating = Very good
opennessRating = Very good
presenceRating = Poor
utilityRating = Fair
reader = OpenlabRawReader

[Improvision TIFF]
extensions = .tif
owner = `PerkinElmer <https://www.perkinelmer.com/>`_
developer = Improvision, now `PerkinElmer <https://www.perkinelmer.com/>`_
bsd = no
weHave = * an Improvision TIFF specification document \n
* a few Improvision TIFF datasets
pixelsRating = Very good
metadataRating = Very good
opennessRating = Very good
presenceRating = Fair
utilityRating = Good
privateSpecification = true
reader = ImprovisionTiffReader

[Imspector OBF]
extensions = .obf, .msr
owner = `MPI-BPC <http://www.mpibpc.mpg.de/de>`_
developer = `Department of NanoBiophotonics, MPI-BPC <https://imspector.mpibpc.mpg.de>`_
bsd = yes
weHave = * a few OBF datasets \n
* `public OBF sample images <https://downloads.openmicroscopy.org/images/OBF/>`_ \n
* `a specification document <https://imspectordocs.readthedocs.io/en/latest/fileformat.html>`_
pixelsRating = Very good
metadataRating = Very good
opennessRating = Very good
presenceRating = Poor
utilityRating = Fair
reader = OBFReader
mif = true

[InCell 1000/2000]
pagename = incell-1000
extensions = .xdce, .tif
developer = GE Healthcare
owner = `Cytiva <https://www.cytivalifesciences.com/en/us/solutions/cellular-analysis/products-and-technology/high-content-analysis>`_
bsd = no
weHave = * a few InCell 1000 datasets\n
* `public InCell 2000 sample images <https://downloads.openmicroscopy.org/images/InCell2000/>`_
weWant = * an InCell 1000 specification document \n
* more InCell 1000 datasets
pixelsRating = Very good
metadataRating = Very good
opennessRating = Good
presenceRating = Fair
utilityRating = Good
reader = InCellReader
mif = true
options = true

[InCell 3000]
extensions = .frm
developer = GE Healthcare
owner = `Cytiva <https://www.cytivalifesciences.com/en/us/solutions/cellular-analysis/products-and-technology/high-content-analysis>`_
bsd = no
weHave = * a few example datasets \n
* `public sample images <https://downloads.openmicroscopy.org/images/InCell3000/>`__
weWant = * an official specification document
pixelsRating = Good
metadataRating = Fair
opennessRating = Fair
presenceRating = Fair
utilityRating = Poor
reader = InCell3000Reader

[INR]
extensions = .inr
bsd = no
weHave = * several sample .inr datasets
pixelsRating = Very good
metadataRating = Fair
opennessRating = Fair
presenceRating = Poor
utilityRating = Fair
reader = INRReader

[Inveon]
extensions = .hdr
bsd = no
weHave = a few Inveon datasets
pixelsRating = Very good
metadataRating = Very good
opennessRating = Good
presenceRating = Poor
utilityRating = Fair
reader = InveonReader
mif = true

[Ionpath MIBI]
extensions = .tif, .tiff
owner = `IonPath`
developer = `IonPath`
versions = 0.1
bsd = no
weHave = * a few sample datasets\n
* a specification document
weWant = * more sample datasets
privateSpecification = true
pixelsRating = Very good
metadataRating = Very good
opennessRating = Very good
presenceRating = Poor
utilityRating = Fair
reader = IonpathMIBITiffReader

[IVision]
pagename = iplab-mac
extensions = .ipm
owner = `BioVision Technologies <https://www.biovis.com/>`_
bsd = no
weHave = * a few iVision-Mac datasets\n
* a specification document
weWant = * more iVision-Mac datasets
pixelsRating = Very good
metadataRating = Very good
opennessRating = Very good
presenceRating = Poor
utilityRating = Fair
privateSpecification = true
reader = IvisionReader
notes = iVision-Mac was formerly called IPLab for Macintosh.

[IPLab]
extensions = .ipl
owner = was `BD Biosystems <http://www.bdbiosciences.com/>`_, now `BioVision Technologies <https://www.biovis.com/iplab.htm>`_
developer = Scanalytics
bsd = no
software = `IPLab Reader plugin for ImageJ <https://imagej.net/ij/plugins/iplab-reader.html>`_
weHave = * an IPLab specification document (v3.6.5, from 2004 December 1, in PDF) \n
* several IPLab datasets
weWant = * more IPLab datasets (preferably with 32-bit integer or floating point data)
pixelsRating = Outstanding
metadataRating = Very good
opennessRating = Very good
presenceRating = Fair
utilityRating = Fair
privateSpecification = true
reader = IPLabReader
notes = Commercial applications that support IPLab include: \n
\n
* `Bitplane Imaris <http://www.bitplane.com/>`_ \n
* `SVI Huygens <https://svi.nl/>`_ \n
\n
.. seealso:: \n
  `IPLab software review <https://www.biovis.com/iplab.htm>`_

[JDCE]
extensions = .jdce, .tif
owner = `Molecular Devices <https://www.moleculardevices.com/>`_
bsd = no
weHave = * a few public JDCE plates: https://downloads.openmicroscopy.org/images/JDCE/
pixelsRating = Very good
metadataRating = Very good
opennessRating = Very good
presenceRating = Fair
utilityRating = Good
reader = JDCEReader
mif = true

[JEOL]
extensions = .dat, .img, .par
owner = `JEOL <https://www.jeol.co.jp/en/>`_
bsd = no
weHave = * Pascal code that reads JEOL files (from ImageSXM) \n
* a few JEOL files
weWant = * an official specification document \n
* more JEOL files
pixelsRating = Good
metadataRating = Fair
opennessRating = Fair
presenceRating = Fair
utilityRating = Fair
reader = JEOLReader

[JPEG 2000]
extensions = .jp2, .j2k, .jpf
developer = `Independent JPEG Group <http://www.ijg.org/>`_
bsd = yes
software = `JJ2000 (JPEG 2000 library for Java) <https://code.google.com/archive/p/jj2000/>`_
weHave = * a JPEG 2000 specification document (free draft from 2000, no longer available online) \n
* a few .jp2 files
pixelsRating = Very good
metadataRating = Outstanding
opennessRating = Outstanding
presenceRating = Good
utilityRating = Poor
pyramid = yes
reader = JPEG2000Reader
writer = JPEG2000Writer
mif = true
notes = Bio-Formats uses the `JAI Image I/O Tools <https://github.com/jai-imageio/jai-imageio-core>`_ library to read JP2 files. \n
Conflicting versions of this no-longer-maintained library may cause errors, \n
see :ref:`JAI ImageIO component <forks-jai>` for details. \n
\n
JPEG stands for "Joint Photographic Experts Group".

[JPEG]
extensions = .jpg
developer = `Independent JPEG Group <http://www.ijg.org/>`_
bsd = yes
weHave = * a `JPEG specification document <http://www.w3.org/Graphics/JPEG/jfif3.pdf>`_ (v1.04, from 1992 September 1, in PDF) \n
* numerous JPEG datasets \n
* the ability to produce more datasets
pixelsRating = Very good
metadataRating = Very good
opennessRating = Outstanding
presenceRating = Outstanding
utilityRating = Poor
reader = JPEGReader
writer = JPEGWriter
notes = Bio-Formats can save individual planes as JPEG. \n
Bio-Formats uses the `Java Image I/O <https://docs.oracle.com/javase/7/docs/technotes/guides/imageio/>`_ API to read and write JPEG files. \n
JPEG stands for "Joint Photographic Experts Group". \n
\n
.. seealso:: \n
  `JPEG homepage <https://www.jpeg.org/jpeg/index.html>`_

[JPK]
extensions = .jpk
developer = `JPK Instruments <https://www.jpk.com>`_
bsd = no
weHave = * Pascal code that can read JPK files (from ImageSXM) \n
* a few JPK files
weWant = * an official specification document \n
* more JPK files
pixelsRating = Good
metadataRating = Fair
opennessRating = Fair
presenceRating = Fair
utilityRating = Fair
reader = JPKReader
mif = true

[JPX]
extensions = .jpx
developer = `JPEG Committee <https://jpeg.org/jpeg2000/>`_
bsd = no
weHave = * a few .jpx files
pixelsRating = Very good
metadataRating = Very good
opennessRating = Outstanding
presenceRating = Good
utilityRating = Fair
reader = JPXReader
mif = true

[Keller Lab Block]
extensions = .klb
developer = `Keller Lab (Janelia Research Campus) <https://bitbucket.org/fernandoamat/keller-lab-block-filetype/overview>`_
bsd = yes
pyramid = yes
mif = true
weHave = * `public sample images <https://downloads.openmicroscopy.org/images/KLB/>`__
pixelsRating = Good
metadataRating = Very good
opennessRating = Very good
presenceRating = Good
utilityRating = Fair
reader = KLBReader

[Khoros VIFF (Visualization Image File Format) Bitmap]
pagename = khoros-viff-bitmap
extensions = .xv
owner = `AccuSoft <https://www.accusoft.com/company/>`_
developer = Khoral
bsd = no
samples = `VIFF Images <http://netghost.narod.ru/gff/sample/images/viff/index.htm>`_
weHave = * several VIFF datasets
pixelsRating = Good
metadataRating = Poor
opennessRating = Poor
presenceRating = Poor
utilityRating = Poor
reader = KhorosReader

[Kodak BIP]
extensions = .bip
developer = `Kodak/Carestream <https://www.carestream.com/en/us>`_
bsd = no
weHave = * a few .bip datasets
weWant = * an official specification document
pixelsRating = Very good
metadataRating = Good
opennessRating = Fair
presenceRating = Poor
utilityRating = Fair
reader = KodakReader

[Lambert Instruments FLIM]
extensions = .fli
developer = `Lambert Instruments <https://www.lambertinstruments.com>`_
bsd = no
versions = 1.0, 2.0
weHave = * an LI-FLIM specification document \n
* several example LI-FLIM datasets
pixelsRating = Very good
metadataRating = Very good
opennessRating = Very good
presenceRating = Fair
utilityRating = Good
privateSpecification = true
reader = LiFlimReader
mif = true

[Leica LAS AF LIF (Leica Image File Format)]
pagename = leica-lif
extensions = .lif
owner = `Leica Microsystems <https://www.leica-microsystems.com/>`_
developer = `Leica Microsystems CMS GmbH <https://www.leica-microsystems.com/>`_
bsd = no
versions = 1.0, 2.0
software = `Leica Application Suite X <https://www.leica-microsystems.com/products/microscope-software/p/leica-las-x-ls/>`_
weHave = * a LIF/XLLF/XLEF/LOF specification document (version 3.2, from no later than 2016 December 15, in PDF) \n
* a LIF specification document (version 2, from no later than 2007 July 26, in PDF) \n
* a LIF specification document (version 1, from no later than 2006 April 3, in PDF) \n
* numerous LIF datasets \n
* `public sample images <https://downloads.openmicroscopy.org/images/Leica-LIF/>`__
pixelsRating = Outstanding
metadataRating = Outstanding
opennessRating = Very good
presenceRating = Good
utilityRating = Very good
privateSpecification = true
reader = LIFReader
mif = true
options = true
notes = LAS stands for "Leica Application Suite". \n
AF stands for "Advanced Fluorescence". \n
\n
Commercial applications that support LIF include: \n
\n
* `Bitplane Imaris <http://www.bitplane.com/>`_ \n
* `SVI Huygens <https://svi.nl/>`_ \n
* `Amira <https://www.fei.com/software/amira-avizo/>`_ \n
\n
Versions of Bio-Formats prior to 5.3.3 incorrectly calculated the physical \n
pixel width and height.  The physical image width and height were divided by \n
the number of pixels, which was inconsistent with the official Leica LIF \n
specification documents.  Versions 5.3.3 and later correctly calculate \n
physical pixel sizes by dividing the physical image size by the number of \n
pixels minus one.  To revert to the old method of physical pixel size \n
calculation in 5.3.3 and later, set the ``leicalif.old_physical_size`` option \n
to ``true`` as described in :doc:`options`.

[Leica LOF]
pagename = leica-lof
extensions = .lof
owner = `Leica Microsystems <https://www.leica-microsystems.com/>`_
developer = `Leica Microsystems CMS GmbH <https://www.leica-microsystems.com/>`_
bsd = no
software = `Leica Application Suite X <https://www.leica-microsystems.com/products/microscope-software/p/leica-las-x-ls/>`_
weHave = * numerous LOF datasets \n
* `public sample images <https://downloads.openmicroscopy.org/images/Leica-XLEF/>`__
pixelsRating = Outstanding
metadataRating = Very good
opennessRating = Very good
presenceRating = Very good
utilityRating = Very good
privateSpecification = true
reader = LOFReader

[Leica XLEF]
pagename = leica-xlef
extensions = .xlef
owner = `Leica Microsystems <https://www.leica-microsystems.com/>`_
developer = `Leica Microsystems CMS GmbH <https://www.leica-microsystems.com/>`_
bsd = no
software = `Leica Application Suite X <https://www.leica-microsystems.com/products/microscope-software/p/leica-las-x-ls/>`_
weHave = * numerous XLEF datasets \n
* `public sample images <https://downloads.openmicroscopy.org/images/Leica-XLEF/>`__
pixelsRating = Outstanding
metadataRating = Very good
opennessRating = Very good
presenceRating = Very good
utilityRating = Very good
privateSpecification = true
reader = XLEFReader
mif = true

[LaVision Imspector]
extensions = .msr
developer = `LaVision BioTec <http://www.lavisionbiotec.com/>`_
versions = 4.0, 4.1
bsd = no
weHave = * a few .msr files \n
* `public sample images <https://downloads.openmicroscopy.org/images/Imspector/>`__
pixelsRating = Fair
metadataRating = Poor
opennessRating = Poor
presenceRating = Poor
utilityRating = Fair
reader = ImspectorReader
mif = true

[Leica LCS LEI]
extensions = .lei, .tif
owner = `Leica Microsystems <https://www.leica-microsystems.com/>`_
developer = `Leica Microsystems CMS GmbH <https://www.leica-microsystems.com/>`_
bsd = no
software = `Leica LCS Lite <ftp://ftp.llt.de/softlib/LCSLite/LCSLite2611537.exe>`_
weHave = * an LEI specification document (beta 2.000, from no later than 2004 February 17, in PDF) \n
* many LEI datasets
pixelsRating = Outstanding
metadataRating = Outstanding
opennessRating = Very good
presenceRating = Very good
utilityRating = Very good
privateSpecification = true
reader = LeicaReader
mif = true
notes = LCS stands for "Leica Confocal Software". \n
LEI presumably stands for "Leica Experimental Information". \n
\n
Commercial applications that support LEI include: \n
\n
* `Bitplane Imaris <http://www.bitplane.com/>`_ \n
* `SVI Huygens <https://svi.nl/>`_ \n
* `Image-Pro Plus <http://www.mediacy.com/>`_

[Leica SCN]
extensions = .scn
developer = `Leica Microsystems <https://www.leica-microsystems.com/>`_
bsd = no
software = `OpenSlide <https://openslide.org>`_
versions = 2012-03-10
weHave = * a few sample datasets\n
* `public sample images <https://downloads.openmicroscopy.org/images/Leica-SCN/>`__
weWant = * an official specification document \n
* sample datasets that cannot be opened
pixelsRating = Good
metadataRating = Good
opennessRating = Good
presenceRating = Fair
utilityRating = Good
pyramid = yes
reader = LeicaSCNReader
mif = true

[LEO]
extensions = .sxm, .tif, .tiff
owner = `ZEISS International <https://www.zeiss.com>`_
bsd = no
weHave = * Pascal code that can read LEO files (from ImageSXM) \n
* a few LEO files\n
* `public sample images <https://downloads.openmicroscopy.org/images/LEO/>`__
weWant = * an official specification document \n
* more LEO files
pixelsRating = Good
metadataRating = Good
opennessRating = Good
presenceRating = Fair
utilityRating = Fair
reader = LEOReader

[Li-Cor L2D]
extensions = .l2d, .tif, .scn
owner = `LiCor Biosciences <http://www.licor.com/>`_
bsd = no
weHave = * a few L2D datasets
weWant = * an official specification document \n
* more L2D datasets
pixelsRating = Very good
metadataRating = Very good
opennessRating = Good
presenceRating = Good
utilityRating = Good
reader = L2DReader
mif = true
notes = L2D datasets cannot be imported into OME using server-side import. \n
They can, however, be imported from ImageJ, or using the omeul utility.

[LIM (Laboratory Imaging/Nikon)]
pagename = lim
extensions = .lim
owner = `Laboratory Imaging <http://www.lim.cz/>`_
bsd = no
weHave = * several LIM files \n
* the ability to produce more LIM files
weWant = * an official specification document
pixelsRating = Good
metadataRating = Poor
opennessRating = Poor
presenceRating = Poor
utilityRating = Poor
reader = LIMReader
notes = Bio-Formats only supports uncompressed LIM files. \n
\n
Commercial applications that support LIM include: \n
\n
* `NIS Elements <https://www.nis-elements.com/>`_

[MetaMorph 7.5 TIFF]
extensions = .tiff
owner = `Molecular Devices <https://www.moleculardevices.com/>`_
bsd = no
weHave = * a few Metamorph 7.5 TIFF datasets
pixelsRating = Very good
metadataRating = Very good
opennessRating = Very good
presenceRating = Fair
utilityRating = Good
reader = MetamorphTiffReader
mif = true

[MetaMorph Stack (STK)]
extensions = .stk, .nd
owner = `Molecular Devices <https://www.moleculardevices.com/>`_
bsd = no
weHave = * an STK specification document (from 2006 November 21, in DOC) \n
* an older STK specification document (from 2005 March 25, in DOC) \n
* an ND specification document (from 2002 January 24, in PDF) \n
* a large number of datasets \n
* `public sample images <https://downloads.openmicroscopy.org/images/Metamorph/>`__
pixelsRating = Very good
metadataRating = Very good
opennessRating = Very good
presenceRating = Very good
utilityRating = Good
privateSpecification = true
reader = MetamorphReader
notes = Commercial applications that support STK include: \n
\n
* `Bitplane Imaris <http://www.bitplane.com/>`_ \n
* `SVI Huygens <https://svi.nl/>`_ \n
* `DIMIN <http://dimin.net/>`_ \n
\n
.. seealso:: \n
  `Metamorph imaging system overview <https://www.moleculardevices.com/systems/metamorph-research-imaging/metamorph-microscopy-automation-and-image-analysis-software>`_

[MetaXpress]
extensions = .htd, .tif, .tiff
owner = `Molecular Devices <https://www.moleculardevices.com/>`_
bsd = no
weHave = * several MetaXpress datasets\n
* `public sample datasets <https://downloads.openmicroscopy.org/images/MetaXpress/>`__
weWant = * a MetaXpress specification document
pixelsRating = Very good
metadataRating = Good
opennessRating = Good
presenceRating = Fair
utilityRating = Fair
reader = MetaxpressTiffReader
mif = true

[MIAS (Maia Scientific)]
extensions = .tif
developer = `Maia Scientific <https://www.selectscience.net/company/maia-scientific>`_
bsd = no
weHave = * several MIAS datasets
pixelsRating = Very good
metadataRating = Very good
opennessRating = Fair
presenceRating = Poor
utilityRating = Poor
reader = MIASReader
mif = true

[Micro-Manager]
extensions = .tif, .txt, .xml
developer = `Vale Lab <https://valelab.ucsf.edu/>`_
bsd = yes
versions = Up to 1.4.22
software = `Micro-Manager <https://micro-manager.org/>`_
weHave = * many Micro-manager datasets\n
* `public sample images <https://downloads.openmicroscopy.org/images/Micro-Manager/>`__
pixelsRating = Outstanding
metadataRating = Outstanding
opennessRating = Outstanding
presenceRating = Fair
utilityRating = Good
reader = MicromanagerReader
mif = true
notes = - Bio-Formats will recognize a :file:`*metadata.txt` file as part of a\n
  Micro-Manager fileset if pointed at it and will load the fileset including\n
  the companion TIFF files.\n
- If pointed at a companion :file:`.ome.tif` file, Bio-Formats will recognize\n
  an OME-TIFF format instead. This means it may load the fileset if there are\n
  multiple .ome.tif but it will not include :file:`*metadata.txt` in this\n
  fileset and therefore the extended Micro-Manager metadata will be skipped.\n
- See :doc:`/users/micromanager/index` for more information.

[Mikroscan TIFF]
extensions = .tif, .tiff
owner = `Mikroscan <https://www.mikroscan.com/>`_
bsd = no
weHave = * some Mikroscan datasets
pixelsRating = Good
metadataRating = Good
opennessRating = Good
presenceRating = Fair
utilityRating = Fair
privateSpecification = true
pyramid = yes
reader = MikroscanTiffReader

[MINC MRI]
extensions = .mnc
developer = `McGill University <http://www.bic.mni.mcgill.ca/ServicesSoftware/MINC>`_
bsd = no
software = `MINC <http://www.bic.mni.mcgill.ca/ServicesSoftware/MINC>`_
weHave = * a few MINC files
pixelsRating = Very good
metadataRating = Good
opennessRating = Good
presenceRating = Good
utilityRating = Fair
reader = MINCReader

[Minolta MRW]
extensions = .mrw
developer = `Minolta <https://www.konicaminolta.com/uk-en/index.html>`_
bsd = no
software = `dcraw <https://en.wikipedia.org/wiki/Dcraw>`_
weHave = * several .mrw files
pixelsRating = Very good
metadataRating = Fair
opennessRating = Fair
presenceRating = Fair
utilityRating = Fair
reader = MRWReader

[MNG (Multiple-image Network Graphics)]
pagename = mng
extensions = .mng
developer = `MNG Development Group <http://www.libpng.org/pub/mng/mngnews.html>`_
bsd = yes
software = `libmng (MNG reference library) <https://sourceforge.net/projects/libmng/>`_
samples = `MNG sample files <https://sourceforge.net/projects/libmng/files/libmng-testsuites/MNGsuite-1.0/MNGsuite.zip/>`_
weHave = * the `libmng-testsuites <https://sourceforge.net/projects/libmng/files/libmng-testsuites/Release-20030305/MNGsuite-20030305.zip/>`_ package (from 2003 March 05, in C) \n
* a large number of MNG datasets
pixelsRating = Good
metadataRating = Good
opennessRating = Outstanding
presenceRating = Fair
utilityRating = Poor
reader = MNGReader
mif = true
notes = .. seealso:: \n
  `MNG homepage <http://www.libpng.org/pub/mng/>`_  \n
  `MNG specification <http://www.libpng.org/pub/mng/spec>`_

[Molecular Imaging]
extensions = .stp
owner = Molecular Imaging Corp, San Diego CA (closed)
bsd = no
weHave = * Pascal code that reads Molecular Imaging files (from ImageSXM) \n
* a few Molecular Imaging files
weWant = * an official specification document \n
* more Molecular Imaging files
pixelsRating = Good
metadataRating = Fair
opennessRating = Fair
presenceRating = Fair
utilityRating = Fair
reader = MolecularImagingReader

[MRC (Medical Research Council)]
pagename = mrc
extensions = .mrc, .st, .ali, .map, .rec, .mrcs
developer = * `MRC Laboratory of Molecular Biology <https://www2.mrc-lmb.cam.ac.uk/>`_ \n
* `CCP-EM <https://www.ccpem.ac.uk/mrc_format/mrc_format.php>`_
bsd = no
samples = `golgi.mrc <http://bio3d.colorado.edu/imod/files/imod_data.tar.gz>`_
weHave = * `specification documents for MRC2000 and MRC2014 <https://www.ccpem.ac.uk/mrc_format/mrc_format.php>`_ \n
* an `IMOD-specific MRC specification document <http://bio3d.colorado.edu/imod/doc/mrc_format.txt>`_ (in TXT) \n
* `public sample images <https://downloads.openmicroscopy.org/images/MRC/>`__\n
* a few MRC datasets
pixelsRating = Outstanding
metadataRating = Very good
opennessRating = Very good
presenceRating = Good
utilityRating = Good
reader = MRCReader
notes = Commercial applications that support MRC include: \n
\n
* `Bitplane Imaris <http://www.bitplane.com/>`_ \n
\n
Bio-Formats provides support for the base MRC2000/MRC2014 specifications. Limited support is provided for vendor-specific \n
extended headers, as described in the `MRC2014 specification <https://www.ccpem.ac.uk/mrc_format/mrc2014.php#8>`_. \n
`IMOD <https://bio3d.colorado.edu/imod/doc/mrc_format.txt>`_ extended metadata is perhaps the best-supported variant. \n
\n
.. seealso:: \n
  `MRC on Wikipedia <https://en.wikipedia.org/wiki/MRC_%28file_format%29>`_

[NEF (Nikon Electronic Format)]
pagename = nef
extensions = .nef, .tif
developer = `Nikon <http://www.nikon.com/>`_
bsd = no
samples = `neffile1.zip <https://www.outbackphoto.com/workshop/NEF_conversion/neffile1.zip>`_ \n
`Sample NEF images <http://www.nikondigital.org/articles/library/nikon_d2x_first_impressions.htm>`_
weHave = * a NEF specification document (v0.1, from 2003, in PDF) \n
* several NEF datasets
pixelsRating = Very good
metadataRating = Poor
opennessRating = Poor
presenceRating = Poor
utilityRating = Poor
privateSpecification = true
reader = NikonReader
notes = .. seealso:: \n
  `NEF Conversion <https://www.outbackphoto.com/workshop/NEF_conversion/nefconversion.html>`_

[NIfTI]
extensions = .img, .hdr, .nii, .nii.gz
developer = `National Institutes of Health <https://www.nih.gov/>`_
bsd = no
weHave = * `NIfTI specification documents <https://www.nitrc.org/docman/view.php/26/204/TheNIfTI>`_\n
* several NIfTI datasets \n
* `public sample images <https://downloads.openmicroscopy.org/images/NIfTI/>`__
pixelsRating = Very good
metadataRating = Very good
opennessRating = Very good
presenceRating = Good
utilityRating = Fair
reader = NiftiReader

[Nikon Elements TIFF]
extensions = .tiff
developer = `Nikon <http://www.nikon.com>`_
bsd = no
weHave = * a few Nikon Elements TIFF files
weWant = * more Nikon Elements TIFF files
pixelsRating = Good
metadataRating = Good
opennessRating = Fair
presenceRating = Fair
utilityRating = Fair
reader = NikonElementsTiffReader

[Nikon EZ-C1 TIFF]
extensions = .tiff
developer = `Nikon <http://www.nikon.com/>`_
bsd = no
weHave = * a few Nikon EZ-C1 TIFF files
pixelsRating = Very good
metadataRating = Very good
opennessRating = Good
presenceRating = Poor
utilityRating = Fair
reader = NikonTiffReader

[Nikon NIS-Elements ND2]
extensions = .nd2
developer = `Nikon USA <https://www.nikonusa.com/en/index.page>`_
bsd = no
software = `NIS-Elements Viewer from Nikon <https://www.microscope.healthcare.nikon.com/products/software/nis-elements>`_
weHave = * many ND2 datasets\n
* `public sample images <https://downloads.openmicroscopy.org/images/ND2/>`__
weWant = * an official specification document
pixelsRating = Very good
metadataRating = Good
opennessRating = Fair
presenceRating = Very good
utilityRating = Very good
reader = ND2Reader
mif = true
options = true
notes = There are two distinct versions of ND2: an old version, which uses \n
JPEG-2000 compression, and a new version which is either uncompressed or \n
Zip-compressed.  We are not aware of the version number or release date \n
for either format. \n
\n
Bio-Formats uses the `JAI Image I/O Tools <https://github.com/jai-imageio/jai-imageio-core>`_ \n
library to read ND2 files compressed with JPEG-2000. \n

[NRRD (Nearly Raw Raster Data)]
pagename = nrrd
extensions = .nrrd, .nhdr, .raw, .txt
developer = `Teem developers <https://teem.sourceforge.net/>`_
bsd = yes
software = `nrrd (NRRD reference library) <https://teem.sourceforge.net/nrrd/>`_
samples = `Diffusion tensor MRI datasets <http://www.sci.utah.edu/%7Egk/DTI-data/>`_
weHave = * an `nrrd specification document <https://teem.sourceforge.net/nrrd/format.html>`_ (v1.9, from 2005 December 24, in HTML) \n
* a few nrrd datasets \n
* `public sample images <https://downloads.openmicroscopy.org/images/NRRD/>`__
pixelsRating = Very good
metadataRating = Very good
opennessRating = Outstanding
presenceRating = Fair
utilityRating = Very good
reader = NRRDReader

[Olympus CellR/APL]
extensions = .apl, .mtb, .tnb, .tif, .obsep
owner = `Olympus <https://www.olympus-global.com>`_
bsd = no
weHave = * a few CellR datasets
weWant = * more Cellr datasets \n
* an official specification document
pixelsRating = Very good
metadataRating = Fair
opennessRating = Fair
presenceRating = Poor
utilityRating = Fair
reader = APLReader
mif = true

[Olympus FluoView FV1000]
extensions = .oib, .oif
owner = `Olympus <https://www.olympus-global.com>`_
bsd = no
versions = 1.0, 2.0
software = `FV-Viewer from Olympus <https://www.olympus-lifescience.com/en/>`_
weHave = * an OIF specification document (v2.0.0.0, from 2008, in PDF) \n
* an FV1000 specification document (v1.0.0.0, from 2004 June 22, in PDF) \n
* older FV1000 specification documents (draft, in DOC and XLS) \n
* `public sample images <https://downloads.openmicroscopy.org/images/Olympus-FluoView/>`__\n
* many FV1000 datasets
weWant = * more OIB datasets (especially 2+ GB files) \n
* more FV1000 version 2 datasets
pixelsRating = Very good
metadataRating = Very good
opennessRating = Good
presenceRating = Good
utilityRating = Very good
privateSpecification = true
reader = FV1000Reader
mif = true
notes = Bio-Formats uses a modified version of the `Apache POI \n
<http://poi.apache.org/>`_ library to read OIB files. \n
OIF stands for "Original Imaging Format". \n
OIB stands for "Olympus Image Binary". \n
OIF is a multi-file format that includes an .oif file and a directory of \n
.tif, .roi, .pty, .lut, and .bmp files. \n
OIB is a single file format. \n
\n
Commercial applications that support this format include: \n
\n
* `Bitplane Imaris <http://www.bitplane.com/>`_ \n
* `SVI Huygens <https://svi.nl/>`_ \n
\n
.. seealso:: \n
  `Olympus FluoView Resource Center <https://www.olympus-lifescience.com/en/>`_

[Olympus FluoView TIFF]
extensions = .tif
owner = `Olympus <https://www.olympus-global.com>`_
bsd = no
software = `DIMIN <http://www.dimin.net/>`_
weHave = * a FluoView specification document (from 2002 November 14, in DOC) \n
* Olympus' FluoView Image File Reference Suite (from 2002 March 1, in DOC) \n
* several FluoView datasets
pixelsRating = Very good
metadataRating = Very good
opennessRating = Very good
presenceRating = Good
utilityRating = Good
privateSpecification = true
reader = FluoviewReader
mif = true
notes = Commercial applications that support this format include: \n
\n
* `Bitplane Imaris <http://www.bitplane.com/>`_ \n
* `SVI Huygens <https://svi.nl/>`_

[Olympus OIR]
extensions = .oir
owner = `Olympus <https://www.olympus-global.com>`_
bsd = no
software = `Olympus Viewer Plugin for ImageJ <http://imagej.net/OlympusImageJPlugin>`_
weHave = * several OIR datasets \n
* `public sample images <https://downloads.openmicroscopy.org/images/Olympus-OIR>`_
pixelsRating = Very good
metadataRating = Good
opennessRating = Fair
presenceRating = Poor
utilityRating = Fair
reader = OIRReader
notes = Support for this format was added in partnership with OLYMPUS EUROPA SE & Co. KG

[Olympus OMP2INFO]
extensions = .omp2info
owner = `Olympus <https://www.olympus-global.com>`_
bsd = no
software = `Olympus Viewer Plugin for ImageJ <http://imagej.net/OlympusImageJPlugin>`_
weHave = * several OMP2INFO datasets
pixelsRating = Very good
metadataRating = Fair
opennessRating = Fair
presenceRating = Poor
utilityRating = Fair
reader = OlympusTileReader
notes = Support for this format was added in partnership with OLYMPUS EUROPA SE & Co. KG

[Olympus ScanR]
extensions = .xml, .dat, .tif
owner = `Olympus <https://www.olympus-global.com>`_
developer = `Olympus <https://www.olympus-global.com>`_
bsd = no
versions = Up to 2.5.1
weHave = * several ScanR datasets \n
* `public sample images <https://downloads.openmicroscopy.org/images/ScanR/>`__
pixelsRating = Very good
metadataRating = Very good
opennessRating = Good
presenceRating = Poor
utilityRating = Fair
reader = ScanrReader
mif = true

[Olympus SIS TIFF]
extensions = .tiff
developer = `Olympus <https://www.olympus-sis.com/>`_
bsd = no
weHave = * a few example SIS TIFF files
pixelsRating = Good
metadataRating = Good
opennessRating = Good
presenceRating = Fair
utilityRating = Good
reader = SISReader

[OMERO Pyramid]
developer = `Open Microscopy Environment <http://www.openmicroscopy.org/>`_
bsd = yes
versions = 1.0.0
weHave = * a :ref:`specification document <omero-pyramid>`\n
* several OMERO Pyramid datasets\n
* the ability to produce additional datasets
pixelsRating = Outstanding
metadataRating = Outstanding
opennessRating = Outstanding
presenceRating = Fair
utilityRating = Fair
reader = TiffReader
mif = true
pyramid = yes

[OME-TIFF]
indexExtensions = .ome.tiff, .ome.tif, .ome.tf2, .ome.tf8, .ome.btf
extensions = :model_doc:`.ome.tiff, .ome.tif, .ome.tf2, .ome.tf8, .ome.btf <ome-tiff/index.html>`
developer = `Open Microscopy Environment <http://www.openmicroscopy.org/>`_
bsd = yes
versions = 2003FC, 2007-06, 2008-02, 2008-09, 2009-09, 2010-04, 2010-06, 2011-06, 2012-06, 2013-06, 2015-01, 2016-06
weHave = * an :model_doc:`OME-TIFF specification document <ome-tiff/specification.html>`\n
* many OME-TIFF datasets\n
* `public sample images <https://downloads.openmicroscopy.org/images/OME-TIFF/>`__\n
* the ability to produce additional datasets
pixelsRating = Outstanding
metadataRating = Outstanding
opennessRating = Outstanding
presenceRating = Fair
utilityRating = Outstanding
reader = OMETiffReader
writer = OMETiffWriter
mif = true
pyramid = yes
options = true
notes = Bio-Formats can save image stacks as OME-TIFF. \n
\n
Commercial applications that support OME-TIFF are listed on our :oo_root:`commercial partners page <commercial-partners/#partnerships>`\n
\n
.. seealso:: \n
  :model_doc:`OME-TIFF technical overview <ome-tiff/index.html>`

[OME-XML]
indexExtensions = .ome, .ome.xml
extensions = :model_doc:`.ome, .ome.xml <ome-xml/index.html>`
developer = `Open Microscopy Environment <http://www.openmicroscopy.org/>`_
bsd = yes
versions = 2003FC, 2007-06, 2008-02, 2008-09, 2009-09, 2010-04, 2010-06, 2011-06, 2012-06, 2013-06, 2015-01, 2016-06
weHave = * `OME-XML specification documents <http://www.openmicroscopy.org/Schemas/>`_\n
* many OME-XML datasets\n
* `public sample images <https://downloads.openmicroscopy.org/images/OME-XML/>`__\n
* the ability to produce more datasets
pixelsRating = Outstanding
metadataRating = Outstanding
opennessRating = Outstanding
presenceRating = Fair
utilityRating = Outstanding
reader = OMEXMLReader
writer = OMEXMLWriter
mif = true
notes = Bio-Formats uses the :model_doc:`OME-XML Java library <ome-xml/java-library.html>` \n
to read OME-XML files. \n
\n
Commercial applications that support OME-XML include: \n
\n
* `Bitplane Imaris <http://www.bitplane.com/>`_ \n
* `SVI Huygens <https://svi.nl/>`_

[Oxford Instruments]
extensions = .top
owner = `Oxford Instruments <https://www.oxinst.com/>`_
bsd = no
weHave = * Pascal code that can read Oxford Instruments files (from ImageSXM) \n
* a few Oxford Instruments files
weWant = * an official specification document \n
* more Oxford Instruments files
pixelsRating = Good
metadataRating = Fair
opennessRating = Fair
presenceRating = Fair
utilityRating = Fair
reader = OxfordInstrumentsReader

[PCX (PC Paintbrush)]
extensions = .pcx
developer = ZSoft Corporation
bsd = yes
weHave = * several .pcx files \n
* the ability to generate additional .pcx files
pixelsRating = Very good
metadataRating = Fair
opennessRating = Fair
presenceRating = Poor
utilityRating = Fair
reader = PCXReader
notes = Commercial applications that support PCX include `Zeiss LSM Image Browser <https://www.zeiss.com/microscopy/en/service-support/downloads.html>`_.

[PCORAW]
extensions = .pcoraw, .rec
developer = `PCO <https://www.excelitas.com/product-category/pco-camera-software>`_
bsd = no
weHave = * a few example datasets
pixelsRating = Very good
metadataRating = Very good
opennessRating = Very good
presenceRating = Fair
utilityRating = Good
reader = PCORAWReader

[PicoQuant Bin]
extensions = .bin
developer = `PicoQuant <http://www.picoquant.com/>`_
bsd = no
software = `SymphoTime64 <http://www.picoquant.com/products/category/software/symphotime-64-fluorescence-lifetime-imaging-and-correlation-software>`_
weHave = * a few example datasets
pixelsRating = Good
metadataRating = Fair
opennessRating = Fair
presenceRating = Fair
utilityRating = Poor
reader = PQBinReader

[PerkinElmer Columbus]
extensions = .xml, .csv, .tif
owner = `PerkinElmer <https://www.perkinelmer.com/>`_
bsd = no
weHave = * a few example datasets\n
* `public sample images <https://downloads.openmicroscopy.org/images/PerkinElmer-Columbus/>`__
weWant = * an official specification document
pixelsRating = Good
metadataRating = Good
opennessRating = Fair
presenceRating = Good
utilityRating = Fair
reader = ColumbusReader
mif = true

[Perkin Elmer Densitometer]
extensions = .pds
developer = `Perkin Elmer <https://www.perkinelmer.com>`_
bsd = no
weHave = * a few PDS datasets
weWant = * an official specification document \n
* more PDS datasets
pixelsRating = Good
metadataRating = Good
opennessRating = Good
presenceRating = Poor
utilityRating = Fair
reader = PDSReader

[PerkinElmer Nuance]
extensions = .im3
developer = `PerkinElmer <https://www.perkinelmer.com/>`_
bsd = yes
weHave = * a few sample datasets
pixelsRating = Good
metadataRating = Poor
opennessRating = Poor
presenceRating = Poor
utilityRating = Fair
reader = IM3Reader
mif = true

[PerkinElmer Operetta]
extensions = .tiff, .xml
developer = `PerkinElmer <https://www.perkinelmer.com/>`_
bsd = no
weHave = * a few sample datasets\n
* `public sample images <https://downloads.openmicroscopy.org/images/PerkinElmer-Operetta/>`__
weWant = * an official specification document \n
* more sample datasets
pixelsRating = Very good
metadataRating = Very good
opennessRating = Good
presenceRating = Fair
utilityRating = Good
reader = OperettaReader
mif = true

[PerkinElmer UltraVIEW]
indexExtensions = .tif, .2, .3, .4
extensions = .tif, .2, .3, .4, etc.
owner = `PerkinElmer <https://www.perkinelmer.com/>`_
bsd = no
weHave = * several UltraVIEW datasets
pixelsRating = Very good
metadataRating = Good
opennessRating = Fair
presenceRating = Fair
utilityRating = Fair
reader = PerkinElmerReader
notes = Other associated extensions include: .tim, .zpo, .csv, .htm, \n
.cfg, .ano, .rec \n
\n
Commercial applications that support this format include: \n
\n
* `Bitplane Imaris <http://www.bitplane.com/>`_ \n
* `Image-Pro Plus <http://www.mediacy.com/>`_ \n
\n
.. seealso:: \n
  `PerkinElmer UltraVIEW system overview (pdf) <https://www.perkinelmer.com/lab-solutions/resources/PDFs/LST/Brochures/BRO_UltraVIEW-VoX-Product-Brochure.pdf>`_

[Portable Any Map]
pagename = pgm
extensions = .pbm, .pgm, .ppm
developer = Netpbm developers
bsd = yes
software = `Netpbm graphics filter <https://netpbm.sourceforge.net/>`_
weHave = * a `PGM specification document <https://netpbm.sourceforge.net/doc/pgm.html>`_ (from 2003 October 3, in HTML) \n
* a few PBM, PPM and PGM files
pixelsRating = Very good
metadataRating = Very good
opennessRating = Outstanding
presenceRating = Good
utilityRating = Poor
reader = PGMReader

[Photoshop TIFF]
extensions = .tif, .tiff
developer = `Adobe <https://www.adobe.com>`_
bsd = no
weHave = * a Photoshop TIFF specification document \n
* a few Photoshop TIFF files
pixelsRating = Good
metadataRating = Good
opennessRating = Good
presenceRating = Good
utilityRating = Good
reader = PhotoshopTiffReader
mif = true

[PICT (Macintosh Picture)]
extensions = .pict
developer = `Apple Computer <https://www.apple.com>`_
bsd = yes
weHave = * many PICT datasets
pixelsRating = Very good
metadataRating = Fair
opennessRating = Fair
presenceRating = Very good
utilityRating = Poor
reader = PictReader
\n
.. seealso:: \n
  `PICT technical overview <http://www.faqs.org/faqs/graphics/fileformats-faq/part3/section-107.html>`_ \n
  `Another PICT technical overview <http://www.fileformat.info/format/macpict/egff.htm>`_

[PNG (Portable Network Graphics)]
pagename = png
extensions = .png
developer = `PNG Development Group <http://www.libpng.org/pub/png/pngnews.html>`_
bsd = yes
software = `PNG Writer plugin for ImageJ <https://imagej.net/ij/plugins/png-writer.html>`_
weHave = * a `PNG specification document <http://www.libpng.org/pub/png/spec/iso/>`_ (W3C/ISO/IEC version, from 2003 November 10, in HTML) \n
* several PNG datasets\n
* `public sample images <https://downloads.openmicroscopy.org/images/PNG/>`__
pixelsRating = Very good
metadataRating = Very good
opennessRating = Outstanding
presenceRating = Outstanding
utilityRating = Poor
reader = APNGReader
writer = APNGWriter
notes = Bio-Formats uses the `Java Image I/O <https://docs.oracle.com/javase/7/docs/technotes/guides/imageio/>`_  \n
API to read and write PNG files. \n
\n
.. seealso:: \n
  `PNG technical overview <http://www.libpng.org/pub/png/>`_

[Prairie Technologies TIFF]
pagename = prairie-tech-tiff
extensions = .tif, .xml, .cfg
developer = `Prairie Technologies <https://www.bruker.com/products/fluorescence-microscopes/ultima-multiphoton-microscopy/ultima-in-vitro/overview.html>`_
bsd = no
weHave = * many Prairie datasets
pixelsRating = Very good
metadataRating = Very good
opennessRating = Good
presenceRating = Fair
utilityRating = Good
reader = PrairieReader
mif = true

[Princeton Instruments SPE]
extensions = .spe
developer = `Princeton Instruments <https://www.princetoninstruments.com/>`_
bsd = no
versions = 3.0
weHave = * `An official specification document <ftp://ftp.princetoninstruments.com/public/Manuals/Princeton%20Instruments/SPE%203.0%20File%20Format%20Specification.pdf>`_ \n
* two SPE files
weWant = * more SPE files
pixelsRating = Good
metadataRating = Good
opennessRating = Very good
presenceRating = Fair
utilityRating = Good
reader = SPEReader
mif = true

[Quesant]
extensions = .afm
owner = `KLA-Tencor Corporation <https://www.kla-tencor.com/>`_
developer = Quesant Instrument Corporation
bsd = no
weHave = * Pascal code that can read Quesant files (from ImageSXM) \n
* several Quesant files
weWant = * an official specification document \n
* more Quesant files
pixelsRating = Good
metadataRating = Fair
opennessRating = Fair
presenceRating = Fair
utilityRating = Fair
reader = QuesantReader

[QuickTime Movie]
extensions = .mov
owner = `Apple Computer <https://www.apple.com/>`_
bsd = yes
software = `QuickTime Player <https://support.apple.com/downloads/quicktime>`_
weHave = * a `QuickTime specification document <https://developer.apple.com/documentation/quicktime-file-format>`_ \n
* several QuickTime datasets \n
* the ability to produce more datasets
weWant = * more QuickTime datasets, including: \n
\n
  * files compressed with a common, unsupported codec \n
  * files with audio tracks and/or multiple video tracks
pixelsRating = Good
metadataRating = Fair
opennessRating = Fair
presenceRating = Outstanding
utilityRating = Poor
reader = QTReader
writer = QTWriter
notes = Bio-Formats can save image stacks as QuickTime movies. \n
The following table shows supported codecs: \n
\n
====== ================================== =================== \n
Codec  Description                        Native              \n
====== ================================== =================== \n
raw    Full Frames (Uncompressed)         read & write        \n
iraw   Intel YUV Uncompressed             read only           \n
rle    Animation (run length encoded RGB) read only           \n
jpeg   Still Image JPEG DIB               read only           \n
rpza   Apple Video 16 bit "road pizza"    read only (partial) \n
mjpb   Motion JPEG codec                  read only           \n
====== ================================== =================== \n
\n
.. seealso:: \n
    `QuickTime software overview <https://support.apple.com/quicktime>`_

[RHK]
extensions = .sm2, .sm3
owner = `RHK Technologies <http://www.rhk-tech.com>`_
bsd = no
weHave = * Pascal code that can read RHK files (from ImageSXM) \n
* a few RHK files
weWant = * an official specification document \n
* more RHK files
pixelsRating = Good
metadataRating = Fair
opennessRating = Fair
presenceRating = Fair
utilityRating = Fair
reader = RHKReader

[SBIG]
owner = `Diffraction Limited <https://diffractionlimited.com/>`_ (formerly Santa Barbara Instrument Group)
bsd = no
weHave = * an `official SBIG specification document <https://diffractionlimited.com/downloads/sbig/AppNoteArchive.zip>`_ \n
* a few SBIG files
weWant = * more SBIG files
pixelsRating = Very good
metadataRating = Very good
opennessRating = Very good
presenceRating = Fair
utilityRating = Fair
reader = SBIGReader

[Seiko]
extensions = .xqd, .xqf
owner = `Seiko <https://www.seiko.co.jp/en>`_
bsd = no
weHave = * Pascal code that can read Seiko files (from ImageSXM) \n
* a few Seiko files
weWant = * an official specification document \n
* more Seiko files
pixelsRating = Good
metadataRating = Fair
opennessRating = Fair
presenceRating = Fair
utilityRating = Fair
reader = SeikoReader

[SimplePCI & HCImage TIFF]
extensions = .tiff
developer = `Hamamatsu <https://hcimage.com/simple-pci-legacy/>`_
bsd = no
weHave = * a few SimplePCI TIFF datasets
weWant = * more SimplePCI TIFF datasets
pixelsRating = Very good
metadataRating = Very good
opennessRating = Very good
presenceRating = Fair
utilityRating = Good
reader = SimplePCITiffReader

[SimplePCI & HCImage]
extensions = .cxd
developer = `Compix <https://hcimage.com>`_
bsd = no
weHave = * several SimplePCI files
pixelsRating = Outstanding
metadataRating = Outstanding
opennessRating = Very good
presenceRating = Poor
utilityRating = Fair
reader = PCIReader
notes = Bio-Formats uses a modified version of the `Apache \n
POI library <http://poi.apache.org/>`_ to read CXD files. \n
\n
.. seealso:: \n
  `SimplePCI software overview <https://hcimage.com/simple-pci-legacy/>`_

[SM Camera]
bsd = no
weHave = * Pascal code that can read SM-Camera files (from ImageSXM) \n
* a few SM-Camera files
weWant = * an official specification document \n
* more SM-Camera files
pixelsRating = Good
metadataRating = Fair
opennessRating = Fair
presenceRating = Fair
utilityRating = Fair
reader = SMCameraReader

[SPIDER]
extensions = .spi, .stk
developer = `Wadsworth Center <https://spider.wadsworth.org/spider_doc/spider/docs/spider.html>`_
bsd = no
software = `SPIDER <https://spider.wadsworth.org/spider_doc/spider/docs/spider.html>`_
weHave = * a few example datasets \n
* `official file format documentation <https://spider.wadsworth.org/spider_doc/spider/docs/image_doc.html>`_
pixelsRating = Very good
metadataRating = Very good
opennessRating = Outstanding
presenceRating = Good
utilityRating = Good
reader = SpiderReader

[Targa]
extensions = .tga
developer = `Truevision <https://en.wikipedia.org/wiki/Truevision>`_
bsd = no
weHave = * a Targa specification document \n
* a few Targa files
pixelsRating = Very good
metadataRating = Very good
opennessRating = Very good
presenceRating = Good
utilityRating = Poor
reader = TargaReader

[Tecan Spark Cyto Workspace]
extensions = .db, .tif
owner = `Tecan Trading <https://www.tecan.com/>`_
bsd = no
weHave = * a few Tecan Spark Cyto workspaces
pixelsRating = Very good
metadataRating = Very good
opennessRating = Good
presenceRating = Fair
utilityRating = Good
reader = TecanReader
mif = true
notes = Fiji users will need to enable the "Tissue Analyzer" update site and install "sqlite-jdbc.jar"

[Text]
extensions = .txt
bsd = yes
pixelsRating = Good
metadataRating = Fair
opennessRating = Fair
presenceRating = Fair
utilityRating = Poor
reader = TextReader
notes = Reads tabular pixel data produced by a variety of software.

[TIFF (Tagged Image File Format)]
pagename = tiff
extensions = .tiff, .tif, .tf2, .tf8, .btf
owner = `Adobe <https://www.adobe.com>`_
developer = Aldus and Microsoft
bsd = yes
samples = `Big TIFF <https://web.archive.org/web/20240706160214/https://www.awaresystems.be/imaging/tiff/bigtiff.html#samples>`_
weHave = * `TIFF specification documents from Adobe <https://www.loc.gov/preservation/digital/formats/fdd/fdd000022.shtml>`_ \n
* a `TIFF specification document <https://web.archive.org/web/20240329145220/https://www.awaresystems.be/imaging/tiff.html>`_ \n
* `public sample images <https://downloads.openmicroscopy.org/images/TIFF/>`__\n
* many TIFF datasets \n
* a few BigTIFF datasets
pixelsRating = Very good
metadataRating = Outstanding
opennessRating = Outstanding
presenceRating = Outstanding
utilityRating = Fair
pyramid = yes
reader = TiffReader
writer = TiffWriter
mif = true
notes = Bio-Formats can also read BigTIFF files (TIFF files larger than 4 GB). \n
Bio-Formats can save image stacks as TIFF or BigTIFF. \n
\n
TIFF files written by ImageJ are also supported, including ImageJ TIFFs larger \n
than 4GB.  ImageJ TIFFs are detected based upon the text in the first IFD's \n
"ImageDescription" tag; this tag's value is then used to determine Z, C, and T \n
sizes as well as physical sizes and timestamps.  For ImageJ TIFFs larger than \n
4GB, a single IFD is expected (instead of one IFD per image plane).  The \n
"ImageDescription" is used to determine the number of images, the pixel data \n
for which are expected to be stored contiguously at the offset indicated in \n
the sole IFD.  This differs from standard TIFF and BigTIFF; if the \n
"ImageDescription" tag is missing or invalid, only the first image will be \n
read. \n
\n
.. seealso:: \n
  `TIFF technical overview <https://web.archive.org/web/20240702055230/https://www.awaresystems.be/imaging/tiff/faq.html#q3>`_ \n
  `BigTIFF technical overview <https://web.archive.org/web/20240706160214/https://www.awaresystems.be/imaging/tiff/bigtiff.html>`_ \n
  `ImageJ TIFF overview <https://imagej.net/TIFF>`_ \n
  `Source code for ImageJ's native TIFF reader <https://imagej.net/ij/developer/source/ij/io/TiffDecoder.java.html>`_

[TillPhotonics TillVision]
extensions = .vws
developer = `TILL Photonics <https://www.fei.com/service-support/Light-Microscopy/>`_
bsd = no
weHave = * several TillVision datasets
weWant = * an official specification document
pixelsRating = Good
metadataRating = Poor
opennessRating = Poor
presenceRating = Poor
utilityRating = Fair
reader = TillVisionReader
mif = true

[Topometrix]
extensions = .tfr, .ffr, .zfr, .zfp, .2fl
owner = `TopoMetrix (now Veeco) <http://www.veeco.com/>`_
bsd = no
weHave = * Pascal code that reads Topometrix files (from ImageSXM) \n
* a few Topometrix files
weWant = * an official specification document \n
* more Topometrix files
pixelsRating = Good
metadataRating = Fair
opennessRating = Fair
presenceRating = Fair
utilityRating = Fair
reader = TopometrixReader

[Trestle]
extensions = .tif, .sld, .jpg
bsd = no
samples = `OpenSlide <http://openslide.cs.cmu.edu/download/openslide-testdata/Trestle/>`_
weHave = * a few example datasets \n
* `public sample images <https://downloads.openmicroscopy.org/images/Trestle/>`__\n
* `developer documentation from the OpenSlide project <https://openslide.org/Trestle%20format/>`_
pixelsRating = Good
metadataRating = Good
opennessRating = Good
presenceRating = Fair
utilityRating = Fair
pyramid = yes
reader = TrestleReader
mif = true

[UBM]
extensions = .pr3
bsd = no
weHave = * Pascal code that can read UBM files (from ImageSXM) \n
* one UBM file
weWant = * an official specification document \n
* more UBM files
pixelsRating = Good
metadataRating = Fair
opennessRating = Fair
presenceRating = Poor
utilityRating = Fair
reader = UBMReader

[Unisoku]
extensions = .dat, .hdr
owner = `Unisoku <http://www.unisoku.com>`_
bsd = no
weHave = * Pascal code that can read Unisoku files (from ImageSXM) \n
* a few Unisoku files
weWant = * an official specification document \n
* more Unisoku files
pixelsRating = Good
metadataRating = Fair
opennessRating = Fair
presenceRating = Fair
utilityRating = Fair
reader = UnisokuReader

[Varian FDF]
extensions = .fdf
owner = `Agilent Technologies <https://www.agilent.com/home>`_
developer = Varian, Inc.
bsd = no
weHave = * a few Varian FDF datasets
weWant = * an official specification document \n
* more Varian FDF datasets
pixelsRating = Good
metadataRating = Fair
opennessRating = Fair
presenceRating = Fair
utilityRating = Fair
reader = VarianFDFReader

[Vectra QPTIFF]
extensions = .tif, .qptiff
owner = `Akoya Biosciences <https://www.akoyabio.com>`_, formerly owned by PerkinElmer
bsd = no
pyramid = yes
weHave = * a `specification document <https://downloads.openmicroscopy.org/images/Vectra-QPTIFF/perkinelmer/PKI_Image%20Format.docx>`__\n
* `public sample images <https://downloads.openmicroscopy.org/images/Vectra-QPTIFF/>`__\n
* several datasets
pixelsRating = Very good
metadataRating = Outstanding
opennessRating = Outstanding
presenceRating = Fair
utilityRating = Fair
reader = VectraReader
notes = Support for this format was added in partnership with PerkinElmer and updated \n
in partnership with `Akoya Biosciences <https://www.akoyabio.com>`_

[Veeco AFM]
extensions = .hdf
developer = `Veeco <http://www.veeco.com>`_
bsd = no
weHave = * a few sample datasets
pixelsRating = Good
metadataRating = Good
opennessRating = Very Good
presenceRating = Fair
utilityRating = Good
reader = VeecoReader

[Ventana BIF]
extensions = .bif
owner = `Roche Digital Diagnostics <https://diagnostics.roche.com/global/en/home.html>`_
bsd = no
weHave = * some Ventana datasets\n
* `public sample images <https://downloads.openmicroscopy.org/images/Ventana/>`__
pixelsRating = Good
metadataRating = Good
opennessRating = Fair
presenceRating = Fair
utilityRating = Good
pyramid = yes
reader = VentanaReader

[VG SAM]
extensions = .dti
bsd = no
weHave = * a few VG-SAM files
weWant = * an official specification document \n
* more VG-SAM files
pixelsRating = Good
metadataRating = Fair
opennessRating = Fair
presenceRating = Poor
utilityRating = Fair
reader = VGSAMReader

[VisiTech XYS]
extensions = .xys, .html
developer = `VisiTech International <http://www.visitech.co.uk/>`_
bsd = no
weHave = * several VisiTech datasets
weWant = * an official specification document
pixelsRating = Very good
metadataRating = Fair
opennessRating = Fair
presenceRating = Poor
utilityRating = Good
reader = VisitechReader
mif = true

[Volocity Library Clipping]
extensions = .acff
developer = `PerkinElmer <https://www.perkinelmer.com/>`_
bsd = no
weHave = * several Volocity library clipping datasets
weWant = * any datasets that do not open correctly \n
* an official specification document
pixelsRating = Good
metadataRating = Fair
opennessRating = Fair
presenceRating = Poor
utilityRating = Poor
reader = VolocityClippingReader
notes = RGB .acff files are not yet supported.  See :ticket:`6413`.

[Volocity]
extensions = .mvd2
developer = `PerkinElmer <https://www.perkinelmer.com>`_
bsd = no
samples = `PerkinElmer Downloads <http://cellularimaging.perkinelmer.com/downloads/>`_
weHave = * many example Volocity datasets
weWant = * an official specification document \n
* any Volocity datasets that do not open correctly
pixelsRating = Good
metadataRating = Good
opennessRating = Fair
presenceRating = Poor
utilityRating = Fair
reader = VolocityReader
mif = true
notes = .mvd2 files are `Metakit database files <https://wiki.tcl-lang.org/page/Metakit/>`_.

[WA-TOP]
extensions = .wat
owner = `Oxford Instruments <https://www.oxinst.com/>`_
developer = WA Technology
bsd = no
weHave = * Pascal code that can read WA-TOP files (from ImageSXM) \n
* a few WA-TOP files
weWant = * an official specification document \n
* more WA-TOP files
pixelsRating = Good
metadataRating = Fair
opennessRating = Fair
presenceRating = Fair
utilityRating = Fair
reader = WATOPReader

[Windows Bitmap]
extensions = .bmp
developer = Microsoft and IBM
bsd = yes
software = `BMP Writer plugin for ImageJ <https://imagej.net/ij/plugins/bmp-writer.html>`_
weHave = * many BMP datasets
pixelsRating = Very good
metadataRating = Fair
opennessRating = Fair
presenceRating = Outstanding
utilityRating = Poor
reader = BMPReader
notes = Compressed BMP files are currently not supported. \n
\n
.. seealso:: \n
  `Technical Overview <http://www.faqs.org/faqs/graphics/fileformats-faq/part3/section-18.html>`_ \n

[Zeiss Axio CSM]
extensions = .lms
owner = `ZEISS International <https://www.zeiss.com>`_
developer = `ZEISS International <https://www.zeiss.com>`_
bsd = no
weHave = * one example dataset
pixelsRating = Good
metadataRating = Poor
opennessRating = Poor
presenceRating = Poor
utilityRating = Fair
reader = ZeissLMSReader
notes = This should not be confused with the more common Zeiss LSM format, \n
which has a similar extension.  As far as we know, the Axio CSM 700 system is \n
the only one which saves files in the .lms format. \n

[Zeiss AxioVision TIFF]
extensions = .xml, .tif
owner = `ZEISS International <https://www.zeiss.com>`_
developer = `ZEISS International <https://www.zeiss.com>`_
bsd = no
software = `Zeiss ZEN Lite <https://www.zeiss.com/microscopy/en/products/software/zeiss-zen-lite.html>`_
weHave = * many example datasets
weWant = * an official specification document
pixelsRating = Very good
metadataRating = Good
opennessRating = Good
presenceRating = Fair
utilityRating = Fair
reader = ZeissTIFFReader
mif = true

[Zeiss AxioVision ZVI (Zeiss Vision Image)]
pagename = zeiss-axiovision-zvi
extensions = .zvi
owner = `ZEISS International <https://www.zeiss.com>`_
developer = `Carl Zeiss Microscopy GmbH <https://www.zeiss.com/microscopy>`_
bsd = no
versions = 1.0, 2.0
software = `Zeiss Zen <https://www.zeiss.com/microscopy/en/products/software/zeiss-zen.html>`_
weHave = * a ZVI specification document (v2.0.5, from 2010 August, in PDF) \n
* an older ZVI specification document (v2.0.2, from 2006 August 23, in PDF) \n
* an older ZVI specification document (v2.0.1, from 2005 April 21, in PDF) \n
* an older ZVI specification document (v1.0.26.01.01, from 2001 January 29, in DOC) \n
* Zeiss' ZvImageReader code (v1.0, from 2001 January 25, in C++) \n
* many ZVI datasets
pixelsRating = Outstanding
metadataRating = Very good
opennessRating = Very good
presenceRating = Good
utilityRating = Good
privateSpecification = true
reader = ZeissZVIReader
notes = Bio-Formats uses a modified version of the `Apache POI library <http://poi.apache.org/>`_ to read ZVI files. \n
ImageJ/FIJI will use the ZVI reader plugin in preference to Bio-Formats if \n
both are installed. If you have a problem which is solved by opening the file \n
using the Bio-Formats Importer plugin, you can just remove the \n
ZVI_Reader.class from the plugins folder. \n
\n
Commercial applications that support ZVI include `Bitplane Imaris <http://www.bitplane.com/>`_. \n
\n
As of May 2021, the proprietary ZEISS AxioVision software is classed as `End of Support <https://www.zeiss.com/microscopy/en/service-support/support/discontinued-products.html>`_. Zeiss ZEN is the successor programme to AxioVision. \n

[Zeiss CZI]
indexExtensions = .czi
extensions = `.czi <https://www.zeiss.com/microscopy/en/products/software/zeiss-zen/czi-image-file-format.html>`_
developer = `ZEISS International <https://www.zeiss.com>`_
bsd = no
software = `Zeiss ZEN <https://www.zeiss.com/microscopy/en/products/software/zeiss-zen.html>`_ \n
`libCZI <https://github.com/zeiss-microscopy/libCZI>`_
weHave = * many example datasets \n
* `public sample images <https://downloads.openmicroscopy.org/images/Zeiss-CZI/>`__
* official specification documents
pixelsRating = Outstanding
metadataRating = Outstanding
opennessRating = Very good
presenceRating = Fair
utilityRating = Good
privateSpecification = true
pyramid = yes
reader = ZeissCZIReader
mif = true
options = true
notes = JPEG-XR compressed CZI files are supported on the following 64-bit platforms:\n
\n
* Windows 7 and above with `Visual Studio 2015 C++ Redistributable <https://www.microsoft.com/en-us/download/details.aspx?id=48145>`_\n
* CentOS 6 and above, Ubuntu 12.04 and above\n
* OS X 10.10 and above

[Zeiss LSM (Laser Scanning Microscope) 510/710]
pagename = zeiss-lsm
extensions = .lsm, .mdb
owner = `ZEISS International <https://www.zeiss.com>`_
bsd = no
software = `Zeiss LSM Image Browser <https://www.zeiss.com/microscopy/en/service-support/downloads.html>`_ \n
`LSM Toolbox plugin for ImageJ <https://imagej.net/LSM_Toolbox>`_ \n
`LSM Reader plugin for ImageJ <https://imagej.net/ij/plugins/lsm-reader.html>`_ \n
`DIMIN <http://www.dimin.net/>`_
weHave = * LSM specification v3.2, from 2003 March 12, in PDF \n
* LSM specification v5.5, from 2009 November 23, in PDF \n
* LSM specification v6.0, from 2010 September 28, in PDF \n
* many LSM datasets
pixelsRating = Outstanding
metadataRating = Very good
opennessRating = Good
presenceRating = Very good
utilityRating = Good
privateSpecification = true
reader = ZeissLSMReader
mif = true
notes = Bio-Formats uses the `OME MDB Tools Java port <https://github.com/ome/ome-mdbtools>`_. \n
This is a fork of the `mdbtools-java <https://github.com/mdbtools/mdbtools>`_ project. \n
\n
Commercial applications that support this format include: \n
\n
* `SVI Huygens <https://svi.nl/HomePage>`_ \n
* `Bitplane Imaris <http://www.bitplane.com/>`_ \n
* `Amira <https://www.fei.com/software/amira-avizo/>`_ \n
* `Image-Pro Plus <http://www.mediacy.com/>`_

[Zeiss XRM]
pagename = zeiss-xrm
extensions = .txm, .txrm
owner = `ZEISS International <https://www.zeiss.com>`_
developer = ZEISS X-Ray Microscopy division
bsd = no
software = XRM Data Explorer
weHave = * a few sample datasets
pixelsRating = Outstanding
metadataRating = Good
opennessRating = Good
presenceRating = Good
utilityRating = Good
reader = ZeissXRMReader
mif = false
