(5) Gold Star = Excellent
(4) Silver Plus Sign = Very Good
(3) Green Check Mark = Good
(2) Gray Minus Sign = Fair
(1) Red X = Poor

Each format is rated according to five categories, which convey diverse information.

For further details, mouse over each individual heading (Pixels, Metadata, Openness, Presence and Utility).

1. A preliminary implementation created without a specification document, and few or no sample files.
2. Support based on little to no information, or missing one or more major features such as common compression types.
3. An implementation that works reasonably well with our sample data, but which has not been thoroughly exercised.
4. A solid implementation that performs well on a variety of samples, but potentially missing some lesser used features.
5. Thorough support based on an official specification document, tested on a wide variety of samples.

1. No metadata parsing.
2. A basic attempt to parse some subset of available metadata.
3. A good faith effort to handle known metadata, but with some gaps, or significant uncertainty that all fields are handled correctly.
4. A fairly thorough handling of nearly all metadata, but without complete certainty that every field is extracted and converted 100% correctly—perhaps a few rarely used fields are ignored, or some fields are not fully standardized into OME-XML.
5. Complete extraction and conversion of all metainformation.

1. A totally proprietary format with no information—perhaps intentionally obfuscated, incumbered by patents, or only officially accessible using an expensive closed-source software package.
2. Little official information is available from official sources. Perhaps the controlling interest is totally unresponsive to requests for details on the format, or there is no specification document even internally.
3. Some information is available, but the format is poorly documented with relatively few examples. Perhaps the controlling interest has released more detailed documentation to individual organizations—but with the stipulation that the information not be shared with the community at large.
4. A full specification document has been made available to the community (e.g., via an official web site), or multiple other sources of information are publically available, such as sample data and example source code.
5. The format has an up-to-date published specification document, the format's controlling interest promptly notifies the community of revisions, and ideally there is at least one officially sanctioned backing open source implementation.

1. A largely unknown or niche format.
2. The format is not very common. Perhaps it is limited to a particular subset of microscopy, or is rarely supported by third-party applications. Or it may be an largely unknown format but based on a popular specification such as TIFF.
3. The format is somewhat common, or becoming more so. If used in only some types of microscopy, it is popular or even a de facto standard in that niche. Or perhaps the format is new but gaining momentum.
4. The format is a successful and popular microscopy format, supported by many visualization and analysis packages in the field.
5. The format is ubiquitous and supported virtually everywhere, even outside of the microscopy community.

1. A pixels-only format with no ability to represent multidimensional image data nor the accompanying metadata.
2. A largely pixels-centric format with some associated metadata, but lacking key features.
3. Significant metadata storage capabilities, but without certain characteristics and types of information required to fully represent the experiment.
4. Encapsulates a wide variety of microscopy metadata relating to the experiment, but missing something that would allow the format to become an ideal interchange format—perhaps it is not fully extensible, or does not adequately address an important but oft-overlooked issue such as data provenance.
5. The format has been designed to effectively encapsulate the majority of microscopy-related metadata and is extensible enough to accommodate the community's emerging and future needs.

• a PSD specification document (v3.0.4, 16 July 1995)
• a few PSD files

• more PSD files

• an AL3D specification document (v1.0, from 2003, in PDF)
• only one AL3D dataset

• more AL3D datasets (Z series, T series, 16-bit)

• Support for 16-bit AL3D images is present, but has never been tested.
• Texture data is currently ignored.

• a GEL specification document (Revision 2, from 2001 Mar 15, in PDF)
• a few GEL datasets

• GEL technical overview

• an ABD-TIFF specification document (from 2005 Nov, in PDF)
• three ABD-TIFF datasets

• With a few minor exceptions, the ABD-TIFF format is identical to the Fluoview TIFF format.

• an Analyze 7.5 specification document
• several Analyze 7.5 datasets

• a specification document
• several APNG files

• Firefox 3
• Opera 9.5
• KSquirrel

• several SVS datasets
• an SVS specification document
• the ability to generate additional SVS datasets

• Aperio SVS reader

• one ARF dataset
• a specification document

• more ARF datasets

• several AVI datasets

• more AVI datasets:
  • files with audio tracks and/or multiple video tracks
  • files compressed with a common, unsupported codec
  • 2+ GB files

• AVI Reader plugin for ImageJ
• AVI Writer plugin for ImageJ

• AVI RIFF File Reference
• AVI on Wikipedia

• AVIReader
• AVIWriter

• Bio-Formats can save image stacks as AVI (uncompressed).
• The following codecs are supported for reading:
1. Microsoft Run-Length Encoding (MSRLE)
2. Microsoft Video (MSV1)
3. Raw (uncompressed)

• an SDT specification document (from 2006 Jun, in PDF)
• Becker & Hickl's SPCImage software
• a large number of SDT datasets
• the ability to produce new datasets

• a PIC specification document (v4.5, in PDF)
• an older PIC specification document (v4.2, from 1996 Dec 16, in DOC)
• a large number of PIC datasets
• the ability to produce new datasets

• Biorad PIC reader plugin for ImageJ

• Bitplane Imaris
• SVI Huygens

• sdub
• TAABA
• dub

• an Imaris (RAW) specification document (from no later than 1997 Nov 11, in HTML)
• an Imaris 5.5 (HDF) specification document
• Bitplane's bfFileReaderImaris3N code (from no later than 2005, in C++)
• several older Imaris (RAW) datasets
• only one Imaris 3 (TIFF) dataset
• several Imaris 5.5 (HDF) datasets

• an Imaris 3 (TIFF) specification document
• more Imaris 3 (TIFF) datasets

• Imaris software overview

• ImarisReader
• ImarisTiffReader
• ImarisHDFReader

• ImarisReader
• ImarisTiffReader
• ImarisHDFReader

• There are three distinct Imaris formats:
  1. the old binary format (introduced in Imaris version 2.7)
  2. Imaris 3, a TIFF variant (introduced in Imaris version 3.0)
  3. Imaris 5.5, an HDF variant (introduced in Imaris version 5.5)

• several BMP datasets

• BMP Writer plugin for ImageJ

• BMP technical overview
• Some BMP resources

• Compressed BMP files are currently not supported.

• a few Cellomics .c01 datasets

• a Cellomics .c01 specification document
• more Cellomics .c01 datasets

• DICOM specification documents (PS 3 - 2007, from 2006 Dec 28, in DOC and PDF)
• numerous DICOM datasets

• OsiriX Medical Imaging Software
• ezDICOM
• Chris Rorden's list of free DICOM viewers

• DICOM Homepage

• MRI Chest from FreeVol-3D web site
• Medical Image Samples from Sebastien Barre's Medical Imaging page
• DICOM sample image sets from OsiriX web site

• DICOM stands for "Digital Imaging and Communication in Medicine."
• Bio-Formats supports both compressed and uncompressed DICOM.

• a few EPS datasets
• the ability to produce new datasets

• EPS Writer plugin for ImageJ

• EPS technical overview

• EPSReader
• EPSWriter

• Bio-Formats can save individual planes as EPS.
• Certain types of compressed EPS files are not supported.

• a few Flex datasets

• a freely redistributable LuraWave LWF decoder

• LuraTech, developers of the proprietary LuraWave LWF compression used for Flex image planes

• FlexReader
• LuraWaveCodec

• The LuraWave LWF decoder library (e.g., lwf_jsdk2.6.jar) with license code is required to decode wavelet-compressed Flex files.

• a few FEI files

• a specification document
• more FEI files

• a FITS specification document (NOST 100-2.0, from 1999 Mar 29, in HTML)
• three FITS datasets

• MAST:FITS home page
• FITS Support Office

• Gatan's ImageReader2003 code (from 2003, in C++)
• numerous DM3 datasets
• some Bio-Formats developer notes for DM3

• a DM3 specification document

• DM3_Reader plugin for ImageJ
• EMAN

• Datasqueeze

• a GIF specification document (Version 89a, from 1990, in HTML)
• numerous GIF datasets
• the ability to produce new datasets

• Animated Gif Reader plugin for ImageJ
• Gif Stack Writer plugin for ImageJ

• a few NAF files

• a specification document
• more NAF files

• numerous ICS datasets

• libics, the ICS reference library
• Ics_Opener plugin for ImageJ
• IrfanView

• Bitplane Imaris
• SVI Huygens

• ICSReader
• ICSWriter

• ICS version 1.0 datasets have two files - an .ics file that contains
  all of the metadata in plain-text format, and an .ids file that contains all of the pixel data.
• ICS version 2.0 datasets are a single .ics file that contains both pixels and metadata.

• the Image-Pro Plus software
• a few SEQ datasets
• the ability to produce more datasets
• some Bio-Formats developer notes for SEQ

• an SEQ specification document

• the Image-Pro Plus software
• a few IPW datasets
• the ability to produce more datasets
• some Bio-Formats developer notes for IPW

• an IPW specification document
• more IPW datasets:
  • multiple datasets in one file
  • 2+ GB files

• Bio-Formats uses a modified version of the Apache Jakarta POI library to read IPW files.

• an Openlab specification document (from 2000 Feb 8, in DOC)
• Improvision's XLIFFFileImporter code for reading Openlab LIFF v5 files (from 2006, in C++)
• several Openlab datasets

• more Openlab datasets (32-bit integer data)

• Openlab software overview

• an Openlab Raw specification document (from 2004 Nov 09, in HTML)
• a few Openlab Raw datasets

• Openlab software overview

• an Improvision TIFF specification document
• a few Improvision TIFF datasets

• Openlab software overview

• a few InCell 1000 datasets

• an InCell 1000 specification document
• more InCell 1000 datasets

• an IPLab specification document (v3.6.5, from 2004 Dec 1 in PDF)
• several IPLab datasets

• more IPLab datasets (32-bit integer or floating point data)

• IPLab Reader plugin for ImageJ

• Bitplane Imaris
• SVI Huygens

• IPLab software overview

• a few IPLab-Mac datasets
• a specification document

• more IPLab-Mac datasets

• a JPEG specification document (v1.02, from 1992 Sep 1, in PDF)
• numerous JPEG datasets
• the ability to produce more datasets

• JPEG Homepage

• JPEGReader
• JPEGWriter

• Bio-Formats can save individual planes as JPEG.
• Bio-Formats uses the Java Image I/O API to read and write JPEG files.
• JPEG stands for "Joint Photographic Experts Group."

• a JPEG 2000 specification document (final draft, from 2000, in PDF)
• a few JP2 datasets

• JJ2000, a JPEG2000 library for Java

• JPEG 2000 home page

• Bio-Formats uses the JAI Image I/O Tools library to read JP2 files.
• JPEG stands for "Joint Photographic Experts Group."

• several VIFF datasets

• VisiQuest software overview (formerly known as KhorosPro)

• one L2D dataset

• more L2D datasets
• an L2D specification document

• L2D datasets cannot be imported into OME using server-side import. They can, however, be imported from ImageJ, or using the omeul utility.

• a LIF specification document (Version 2, from no later than 2007 July 26, in PDF)
• a LIF specification document (Version 1, from no later than 2006 Apr 3, in PDF)
• numerous LIF datasets

• Leica LAS AF Lite

• Bitplane Imaris
• SVI Huygens
• Amira

• LAS stands for "Leica Application Suite."
• AF stands for "Advanced Fluorescence."

• an LEI specification document (beta 2.000, from no later than 2004 Feb 17, in PDF)
• several LEI datasets

• Leica LCS Lite

• Bitplane Imaris
• SVI Huygens
• Image-Pro Plus

• LCS stands for "Leica Confocal Software."
• LEI presumably stands for "Leica Experimental Information."

• several LIM files
• the ability to produce more LIM files

• a LIM specification document

• NIS Elements

• Bio-Formats supports only uncompressed LIM.

• one Metamorph 7.5 TIFF dataset

• more Metamorph 7.5 TIFF datasets

• an STK specification document (from 2006 Nov 21, in DOC)
• an older STK specification document (from 2005 Mar 25, in DOC)
• an ND specification document (from 2002 Jan 24, in PDF)
• a large number of STK datasets

• Bitplane Imaris
• SVI Huygens
• DIMIN

• MetaMorph imaging system overview

• a few μmanager datasets

• μManager

• a few MINC files

• MINC.

• the libmng-testsuites package (from 2003 Mar 05, in C)
• a large number of MNG datasets

• libmng, the MNG reference library

• MNG sample files

• MNG specification
• MNG home page

• an MRC specification document (in HTML)
• another MRC specification document (in TXT)
• only one MRC dataset

• Bitplane Imaris

• MRC on Wikipedia

• several .mrw files

• dcraw

• Description of MRW format

• a NEF specification document (v0.1, from 2003, in PDF)
• several NEF datasets

• neffile1.zip from a page on NEF Conversion
• sample NEF images from nikondigital.org

• NIfTI specification documents
• several NIfTI datasets

• official test data

• several ND2 datasets
• some Bio-Formats developer notes for ND2

• an ND2 specification document
• more ND2 datasets:
  • files acquired with most recent NIS-Elements

• NIS-Elements software overview

• NativeND2Reader
• LegacyND2Reader

• There are two distinct versions of ND2: an old version, which uses JPEG-2000 compression, and a new version which is either uncompressed or Zip-compressed. We are not aware of the version number or release date for either format.
• Bio-Formats uses the JAI Image I/O Tools library to read ND2 files compressed with JPEG-2000.
• There is also an ND2 reader that uses Nikon's native libraries. To use it, you must be using Windows and have Nikon's ND2 reader plugin for ImageJ installed. Additionally, you will need to download LegacyND2Reader.dll and place it in your ImageJ folder.

• a nrrd specification document (v1.9, from 2005 Dec 24, in HTML)
• a few nrrd datasets

• nrrd, the nrrd reference library

• numerous SlideBook datasets
• some Bio-Formats developer notes for SlideBook

• a SlideBook specification document
• more SlideBook datasets (preferably acquired with the most recent SlideBook software)

• SlideBook software overview

• a few CellR datasets

• more CellR datasets
• a CellR specification document

• an OIF specification document (v2.0.0.0, from 2008, in PDF)
• an FV1000 specification document (v1.0.0.0, from 2004 Jun 22, in PDF)
• older FV1000 specification documents (Draft, in DOC and XLS)
• numerous FV1000 datasets

• more OIB datasets (2+ GB files)
• more FV1000 version 2 datasets

• Bitplane Imaris
• SVI Huygens

• Olympus FluoView Resource Center

• Bio-Formats uses a modified version of the Apache Jakarta POI library to read OIB files.
• OIF stands for "Original Imaging Format."
• OIB stands for "Olympus Image Binary."
• OIF is a multi-file format that includes a .oif file and a directory of .tif, .roi, .pty, .lut, and .bmp files.
• OIB is a single file format.

• a FluoView specification document (from 2002 Nov 14, in DOC)
• Olympus's FluoView Image File Reference Suite (from 2002 Mar 1, in DOC)
• several FluoView datasets

• DIMIN

• Bitplane Imaris
• SVI Huygens

• Olympus FluoView Resource Center

• an OME-TIFF specification document (from 2006 Oct 19, in HTML)
• numerous OME-TIFF datasets
• the ability to produce additional datasets

• Bitplane Imaris
• SVI Huygens

• OME-TIFF technical overview

• OMETiffReader
• OMETiffWriter

• Bio-Formats can save image stacks as OME-TIFF.

• OME-XML specification documents (FC, from 2004, in XSD and HTML)
• several OME-XML datasets

• Bitplane Imaris
• SVI Huygens

• Bio-Formats uses the OME-XML Java library to read OME-XML files.

• several .pcx files
• the ability to generate additional .pcx files

• Zeiss LSM Image Browser

• several PerkinElmer datasets
• some Bio-Formats developer notes for PerkinElmer

• Bitplane Imaris
• Image-Pro Plus

• PerkinElmer UltraView system overview

• numerous PICT datasets

• PICT technical overview
• another PICT technical overview

• PictReader
• LegacyPictReader

• QuickTime for Java is required for reading vector files, and some compressed files.

• a PGM specification document (from 2003 Oct 3, in HTML)

• Netbpm graphics package

• PGM technical overview

• a PNG specification document (W3C/ISO/IEC version, from 2003 Nov 10, in HTML)
• several PNG datasets

• PNG Writer plugin for ImageJ

• PNG technical overview

• Bio-Formats can save individual planes as PNG.
• Bio-Formats uses the Java Image I/O API to read and write PNG files.

• several Prairie datasets

• a QuickTime specification document (from 2001 Mar 1, in HTML)
• several QuickTime datasets
• the ability to produce more datasets

• more QuickTime datasets:
  • files compressed with a common, unsupported codec
  • files with audio tracks and/or multiple video tracks

• QuickTime Player

• QuickTime software overview

• NativeQTReader
• QTWriter
• LegacyQTReader
• LegacyQTWriter

• Bio-Formats has two modes of operation for QuickTime:
  • QTJava mode requires QuickTime to be installed.
  • Native mode works on systems with no QuickTime (e.g., Linux).
• Bio-Formats can save image stacks as QuickTime movies.
• The following table shows supported codecs:

• several SimplePCI files

• SimplePCI software overview

• Bio-Formats uses a modified version of the Apache Jakarta POI library to read CXD files.

• a TIFF specification document (v6.0, from 1992 Jun 3, in PDF)
• a large number of TIFF datasets
• a few BigTIFF datasets

• more TIFF datasets:
  • anything unusual—preferably rare/unsupported compression or photometric interpretation type

• TIFF technical overview
• BigTIFF technical overview

• Bio-Formats can also read BigTIFF files (TIFF files larger than 4 GB).
• Bio-Formats can save image stacks as TIFF or BigTIFF.

• NESb
• LZW TIFF Data Gallery
• BigTIFF

• TiffReader
• TiffWriter

• several TillVision datasets

• a TillVision specification document

• several VisiTech datasets

• a VisiTech XYS specification document

• a ZVI specification document (v2.0.2, from 2006 Aug 23, in PDF)
• an older ZVI specification document (v2.0.1, from 2005 Apr 21, in PDF)
• an older ZVI specification document (v1.0.26.01.01, from 2001 Jan 29, in DOC)
• Zeiss's ZvImageRead code (v1.0, from 2001 Jan 25, in C++)
• numerous ZVI datasets

• more ZVI datasets:
  • with JPEG-compressed image planes
  • with lossless compression
  • tiled
  • 2+ GB files

• Zeiss Axiovision LE

• Bitplane Imaris

• AxioVision software overview

• Bio-Formats uses a modified version of the Apache Jakarta POI library to read ZVI files.

• an LSM specification document (v3.2, from 2003 Mar 12, in PDF)
• numerous LSM datasets

• Zeiss LSM Image Browser
• LSM Toolbox plugin for ImageJ
• LSM Reader plugin for ImageJ
• DIMIN

• SVI Huygens
• Bitplane Imaris
• Amira
• Image-Pro Plus

• Bio-Formats uses the MDB Tools Java port to read MDB files.

• ZeissLSMReader
• MDBParser