FAQ: Which file formats are supported by ImageJ

One of ImageJ's strength lies in its ability to recognize many different file formats, from exotic scientific data files to well-known quicktime movies.

A known image file format is either:

  • natively supported by ImageJ. No additional plugin installation is required. To fully profit from ImageJ's ability to open many types of images, please install or upgrade to the most recent version of ImageJ.
  • or requires a format specific reader plugin. You will need to install a plugin that enables ImageJ to recognize your file type. Plugins are extensions to ImageJ that add functionality. Plugins are written by ImageJ aficionados all around the world and are available at the ImageJ web site's Plugins page.

The aim of this FAQ is to compile a list of supported file types, indicating the type of support (native or by plugin) as well as some additional information.

Many of the plugins listed in the table are supported directly through the HandleExtraFileTypes plugin (bundled with ImageJ). When opening a file, ImageJ first checks whether it can natively handle the format. If not, it looks to see if the proper standalone file reader plugin is installed. If that fails, it lastly tries the Bio-Formats plugin if it is present.


List in progress. Last updated 20 Jun 2007
most "export only" plugins have not been included yet
R = read; W = write; RW = both read and write


Format (extension) Full format name
Native?
Plugins
TIFF (.tiff, .tif)
Tagged Image File Format RW
RW: JIMI
W: JIMI Writer
RW: Bio-Formats
JPEG (.jpeg, .jpg)
Joint Photographic Experts Group
RW
RW: JIMI
W: JIMI Writer
RW: Bio-Formats
BMP (.bmp)
BitMap RW
RW: JIMI
W: JIMI Writer
W: BMP Writer
R: Bio-Formats
FITS (.fits)
Flexible Image Transport System
R
-
PGM (.pgm)
PPM (.ppm)
PBM (.pbm)
Portable Gray Map
Portable Pixmap
Portable Bitmap
RW
W: PGM/PPM/PNM_Writer
R: Bio-Formats
GIF (.gif)
Graphics Interchange Format
RW
R: Bio-Formats
Animated GIF (.gif)
Animated GIF
no W: Gif Stack Writer
R: Animated GIF Reader
R: Bio-Formats
PNG (.png)
Portable Networks Graphics
RW
RW: JIMI
W: JIMI Writer
W: PNG Writer
RW: Bio-Formats
DICOM (.dic, .dcm, .dicom)
Digital Imaging and Communications in Medecine
R
RW: Tudor DICOM Toolkit
R: Import Dicom Sequence
RW: Dicom Rewriter
RW: Dicom Sort
R: Query Dicom Header
R: Dicom Directory Analyzer
RW: Dicom Import/Export
R: Bio-Formats
PICT (.pict, .pic, .pct)
Apple PICTure
no RW: JIMI
W: JIMI Writer
R: Bio-Formats
PSD (.psd)
Photoshop Document no RW: JIMI
W: JIMI Writer
TGA (.tga)
TrueVision Targa File Format
no RW: JIMI
W: JIMI Writer
ICO (.ico)
Windows icon no
RW: JIMI
CUR (.cur)
Windows cursor no
RW: JIMI
Sunraster (.sun)
Sun Microsystems SunRaster
no RW: JIMI
XBM (.xbm)
X Bitmap Format
no RW: JIMI
W: JIMI Writer
XPM (.xpm)
X PixMap
no RW: JIMI
W: JIMI Writer
PCX (.pcx) ZSoft PC Paintbrush File Format
no RW: JIMI
W: JIMI Writer
ANALYZE
Mayo Clinic Analyze File Format
no RW: ANALYZE
RW: Nifti_io
NIfTi NIfTi - 1 File Format
no RW: Nifti_io
AHF (.ahf)
ASCII Header Format no RW: AHF
SPE (.spe)
WinView SPE File Format
no
RW: SPE
PIC (.pic)
Bio-Rad PIC Format
no R: Biorad Reader
R: Bio-Formats
Leica TIFF (.tiff, .lei)
Leica Multichannel SP
no R: Leica SP
R: Leica SP SPlitter
R: Leica_TIFF_Sequence
R: Bio-Formats
Quicktime (.pic, .mov)
Quicktime Movie no R: Quicktime Opener
R: JMF Movie Reader
W: Quicktime Writer
RW: Bio-Formats
AVI (.avi)
uncompressed AVI movie files RW
R: AVI Reader
R: JMF Movie Reader
R: AVI Splitter
W: AVI Writer
RW: Bio-Formats
PDS (.pds)
Planetary Data Systems Image Format no PDS Reader
LSM (.lsm)
Zeiss Laser Scanning Microscope Image Format R R: LSM_Reader (native)
R: LSMToolbox (LSM_Reader extension)
R: Bio-Formats
RAW Guess Raw from Fuji Bas 1000 Phosphor imager no R: Guess Raw Reader
ISAC Fuji Bas Scanner
no R: ISAC Manager
FluoView TIFF (.tiff)
Olympus Fluoview tiff no R: Image Viewer
R: Bio-Formats
Fluoview FV1000 OIB (.oib) Olympus Fluoview FV1000 OIB
no R: Bio-Formats
Fluoview FV1000 OIF (.oif, .tif, -ro.pty, .lut, .bmp)
Olympus Fluoview FV1000 OIF
no R: Bio-Formats
IPLAB (.ipl)
IPLab/Windows Scanalytics BD Science
no R: IPLab Reader
R: Bio-Formats
Bruker NMR (.fid, .ser, .2dseq, .2rr, .2ii, .3rrr, .3iii)
Bruker NMR Sprectrometer File Format
no
R: Bruker Opener
FDF (.fdf)
Varian MRI Imaging System
no
R: Multi FDF_Opener
VFF (.vff) EVS 900 micro-CT system no R: Multi_VFF_Opener
SIF (.sif)
Andor SIF File Format
no R: OpenSIF
AxioVision ZVI (.zvi)
Zeiss ZVI File Format no R: Zeiss ZVI Reader
R: Bio-Formats
DM3 (.dm3)
Gatan Digital Micrograph File Format
no R: DM3_Reader
R: Bio-Formats
Deltavision (.dv, .r3d)
Applied Precision Deltavision Systems File Format
no R: DeltaVision_Opener
R: Bio-Formats
MI, NII, NIII
Molecular Imaging and Nanoscope AFM File Format
no R: Open_MI
IMG (.img)
Packard InstantImager
no R: InstantImager_Reader
UNC UNC File Format
no RW: UNC
PerkinElmer (.tif, .tim, .zpo, .csv, .htm, .ano, .rec, .cfg, .2, .3, .4, .5, .6, .7, .8, …)
PerkinElmer UltraView
no R: PE_Plugins
R: Bio-Formats
EPS (.eps, .epsi) Encapsulated PostScript no W: EPS_Writer
RW: Bio-Formats
SEQ (.seq) Image-Pro Sequence
no
R: Bio-Formats
IPW (.ipw) Image-Pro Workspace
no R: Bio-Formats
OpenLab LIFF (.liff)
Improvision Openlab LIFF
no R: Bio-Formats
OpenLab RAW (.raw)
Improvision Openlab RAW
no R: Bio-Formats
Metamorph (.stk)
Universal Imaging (Molecular Devices)
no R: Bio-Formats
ICS (.ics, .ids)
Image Cytometry Standard no R: Bio-Formats
Leica Lif (.lif)
Leica Image File Format
no R: Bio-Formats
Imaris (.ims)
BitPlane Imaris
no R: Bio-Formats
OME-XML (.ome)
Open Microscopy Environment XML
no R: Bio-Formats
OME-TIFF (.tiff)
Open Microscopy Environment TIFF
no R: Bio-Formats
ABD-TIFF (.tiff)
Andor Biotechnology Division TIFF
no
R: Bio-Formats
GEL (.gel)
Amersham Biosciences GEL Image Format
no R: Bio-Formats
Nikon (.nef, .tiff)
Nikon Electronic Format
no R: Bio-Formats
Slidebook (.sld)
Olympus SlideBook
no
R: Bio-Formats
SPCImage (.sdt)
Becker & Hickl SPCImage
no
R: Bio-Formats
AL3D (.al3d)
Alicona 3D
no
R: Bio-Formats
ND2 (.nd2)
Nikon NIS-Elements ND2 no R: Bio-Formats
μManager (.tif, .txt)
μManager
no
R: Bio-Formats
MRC (.mrc) Medical Research Council
no
R: Bio-Formats
JPEG2000 (.jp2)
JPEG2000 Format
no
R: Bio-Formats
MNG (.mng)
Multiple-image Network Graphics no
R: Bio-Formats
Flex (.flex)
Evotec Flex no
R: Bio-Formats
(LuraWave license code required)
NRRD (.nrrd, .nhdr)
Nearly Raw Raster Data no R: Bio-Formats
VIFF bitmap image (.xv)
Khoros Visualization Image File no R: Bio-Formats
ROI (.roi)
Region of Interest
yes -
ERS (.ers), RS (.rs)
PerkinElmer UltraView(E)RS no R: PE_Plugins, requires Image5D
HPGL
Hewlett Packs Graphics Language no R: HPGL_Reader

About this table:

  • Extensions are purely informative; on several operating systems, file extensions are rare (e.g., MacOS).
  • Several very different file formats have the same extensions (see Biorad pic versus Apple quicktime pic, Leica tiff versus standard tiff).

Bugs, comments? mail me

faq/general/which_file_formats_are_supported_by_imagej.txt · Last modified: 2010/01/26 11:07 (external edit)
Back to top
CC Attribution-Noncommercial-Share Alike 3.0 Unported
chimeric.de = chi`s home Valid CSS Driven by DokuWiki do yourself a favour and use a real browser - get firefox!! Recent changes RSS feed Valid XHTML 1.0