Dataset Structure Table

This table shows the extension of the file that you should choose if you want to open/import a dataset in a particular format.

You can sort this table by clicking on any of the headings.

Format name File to choose Structure of files
AIM .aim Single file
ARF .arf Single file
Adobe Photoshop .psd Single file
Adobe Photoshop TIFF .tif, .tiff Single file
Alicona AL3D .al3d Single file
Amersham Biosciences GEL .gel Single file
Amira .am, .amiramesh, .grey, .hx, .labels Single file
Analyze 7.5 .img, .hdr One .img file and one similarly-named .hdr file
Andor SIF .sif Single file
Animated PNG .png Single file
Aperio AFI .afi One .afi file and several similarly-named .svs files
Aperio SVS .svs Single file
Audio Video Interleave .avi Single file
BD Pathway .exp, .tif Multiple files (.exp, .dye, .ltp, …) plus one or more directories containing .tif and .bmp files
BDV .xml, .h5 Single file
Bio-Rad GEL .1sc Single file
Bio-Rad PIC .pic, .xml, .raw One or more .pic files and an optional lse.xml file
Bio-Rad SCN .scn Single file
Bitplane Imaris .ims Single file
Bitplane Imaris 3 (TIFF) .ims Single file
Bitplane Imaris 5.5 (HDF) .ims Single file
Bruker (no extension) One ‘fid’ and one ‘acqp’ plus several other metadata files and a ‘pdata’ directory
Burleigh .img Single file
Canon RAW .cr2, .crw, .jpg, .thm, .wav Single file
CellH5 (HDF) .ch5 Single file
CellSens VSI .vsi, .ets One .vsi file and an optional directory with a similar name that contains at least one subdirectory with .ets files
CellVoyager .tif, .xml Directory with 2 master files ‘MeasurementResult.xml’ and ‘MeasurementResult.ome.xml’, used to stitch together several TIF files.
CellWorx .pnl, .htd, .log One .htd file plus one or more .pnl or .tif files and optionally one or more .log files
Cellomics C01 .c01, .dib One or more .c01 files
Compix Simple-PCI .cxd Single file
DICOM .dic, .dcm, .dicom, .jp2, .j2ki, .j2kr, .raw, .ima One or more .dcm or .dicom files
DNG .cr2, .crw, .jpg, .thm, .wav, .tif, .tiff Single file
Deltavision .dv, .r3d, .r3d_d3d, .dv.log, .r3d.log One .dv, .r3d, or .d3d file and up to two optional .log files
ECAT7 .v Single file
Encapsulated PostScript .eps, .epsi, .ps Single file
Evotec Flex .flex, .mea, .res One directory containing one or more .flex files, and an optional directory containing an .mea and .res file. The .mea and .res files may also be in the same directory as the .flex file(s).
FEI TIFF .tif, .tiff Single file
FEI/Philips .img Single file
Flexible Image Transport System .fits, .fts Single file
FlowSight .cif Single file
Fuji LAS 3000 .img, .inf Single file
Gatan DM2 .dm2 Single file
Gatan Digital Micrograph .dm3, .dm4 Single file
Graphics Interchange Format .gif Single file
Hamamatsu Aquacosmos .naf Single file
Hamamatsu HIS .his Single file
Hamamatsu NDPI .ndpi Single file
Hamamatsu NDPIS .ndpis One .ndpis file and at least one .ndpi file
Hamamatsu VMS .vms One .vms file plus several .jpg files
Hitachi .txt One .txt file plus one similarly-named .tif, .bmp, or .jpg file
I2I .i2i Single file
IMAGIC .hed, .img One .hed file plus one similarly-named .img file
IMOD .mod Single file
INR .inr Single file
IPLab .ipl Single file
IVision .ipm Single file
Imacon .fff Single file
Image Cytometry Standard .ics, .ids One .ics and possibly one .ids with a similar name
Image-Pro Sequence .seq, .ips Single file
Image-Pro Workspace .ipw Single file
Improvision TIFF .tif, .tiff Single file
InCell 1000/2000 .xdce, .xml, .tiff, .tif, .xlog One .xdce file with at least one .tif/.tiff or .im file
InCell 3000 .frm Single file
Inveon .hdr One .hdr file plus one similarly-named file
Ionpath MIBI .tif, tiff Single file
JEOL .dat, .img, .par A single .dat file or an .img file with a similarly-named .par file
JPEG .jpg, .jpeg, .jpe Single file
JPEG-2000 .jp2, .j2k, .jpf Single file
JPK Instruments .jpk Single file
JPX .jpx Single file
KLB .klb Single file
Khoros XV .xv Single file
Kodak Molecular Imaging .bip Single file
LEO .sxm, .tif, .tiff Single file
LI-FLIM .fli Single file
Laboratory Imaging .lim Single file
Lavision Imspector .msr Single file
Leica .lei, .tif, .tiff, .raw One .lei file with at least one .tif/.tiff file and an optional .txt file
Leica Image File Format .lif Single file
Leica SCN .scn Single file
Leica TCS TIFF .tif, .tiff, .xml Single file
Li-Cor L2D .l2d, .scn, .tif One .l2d file with one or more directories containing .tif/.tiff files
MIAS .tif, .tiff, .txt One directory per plate containing one directory per well, each with one or more .tif/.tiff files
MINC MRI .mnc Single file
Medical Research Council .mrc, .st, .ali, .map, .rec, .mrcs Single file
Metamorph STK .stk, .nd, .scan, .tif, .tiff One or more .stk or .tif/.tiff files plus an optional .nd or .scan file
Metamorph TIFF .tif, .tiff One or more .tif/.tiff files
Micro-Manager .tif, .tiff, .txt, .xml A file ending in ‘metadata.txt’ plus one or more .tif files
MicroCT .vff Directory with XML file and one .tif/.tiff file per plane
Minolta MRW .mrw Single file
Molecular Imaging .stp Single file
Multiple-image Network Graphics .mng Single file
NIfTI .nii, .img, .hdr, .nii.gz A single .nii file or a single .nii.gz file or one .img file and a similarly-named .hdr file
NOAA-HRD Gridded Data Format (no extension) Single file
NRRD .nrrd, .nhdr A single .nrrd file or one .nhdr file and one other file containing the pixels
Nikon Elements TIFF .tif, .tiff Single file
Nikon ND2 .nd2 Single file
Nikon NEF .nef, .tif, .tiff Single file
Nikon TIFF .tif, .tiff Single file
OBF .obf, .msr OBF file
OME-TIFF .ome.tiff, .ome.tif, .ome.tf2, .ome.tf8, .ome.btf, .companion.ome One or more .ome.tiff files
OME-XML .ome, .ome.xml Single file
Olympus APL .apl, .tnb, .mtb, .tif One .apl file, one .mtb file, one .tnb file, and a directory containing one or more .tif files
Olympus FV1000 .oib, .oif, .pty, .lut Single .oib file or one .oif file and a similarly-named directory containing .tif/.tiff files
Olympus Fluoview/ABD TIFF .tif, .tiff One or more .tif/.tiff files, and an optional .txt file
Olympus OIR .oir Single file
Olympus SIS TIFF .tif, .tiff Single file
Olympus ScanR .dat, .xml, .tif One .xml file, one ‘data’ directory containing .tif/.tiff files, and optionally two .dat files
Olympus Slidebook .sld, .spl Single file
Openlab LIFF .liff Single file
Openlab RAW .raw Single file
Oxford Instruments .top Single file
PCO-RAW .pcoraw, .rec A single .pcoraw file with a similarly-named .rec file
PCX .pcx Single file
PICT .pict, .pct Single file
POV-Ray .df3 Single file
Perkin Elmer Densitometer .hdr, .img One .hdr file and a similarly-named .img file
Perkin-Elmer Nuance IM3 .im3 Single file
PerkinElmer .ano, .cfg, .csv, .htm, .rec, .tim, .zpo, .tif One .htm file, several other metadata files (.tim, .ano, .csv, …) and either .tif files or .2, .3, .4, etc. files
PerkinElmer Columbus .xml Directory with XML file and one .tif/.tiff file per plane
PerkinElmer Operetta .tif, .tiff, .xml Directory with XML file and one .tif/.tiff file per plane
PerkinElmer Vectra/QPTIFF .tiff, .tif, .qptiff Single file
PicoQuant Bin .bin Single file
Portable Any Map .pbm, .pgm, .ppm Single file
Prairie TIFF .tif, .tiff, .cfg, .env, .xml One .xml file, one .cfg file, and one or more .tif/.tiff files
Princeton Instruments SPE .spe Single file
Pyramid TIFF .tif, .tiff Single file
Quesant AFM .afm Single file
QuickTime .mov Single file
RHK Technologies .sm2, .sm3 Single file
SBIG (no extension) Single file
SM Camera (no extension) Single file
SPC FIFO Data .spc, .set One .spc file and similarly named .set file
SPCImage Data .sdt Single file
SPIDER .spi Single file
Seiko .xqd, .xqf Single file
SimplePCI TIFF .tif, .tiff Single file
Simulated data .fake Single file
Slidebook TIFF .tif, .tiff Single file
Tagged Image File Format .tif, .tiff, .tf2, .tf8, .btf Single file
Text .txt, .csv Single file
TillVision .vws, .pst, .inf One .vws file and possibly one similarly-named directory
TopoMetrix .tfr, .ffr, .zfr, .zfp, .2fl Single file
Trestle .tif One .tif file plus several other similarly-named files (e.g. .FocalPlane-, .sld, .slx, .ROI)
Truevision Targa .tga Single file
UBM .pr3 Single file
Unisoku STM .hdr, .dat One .HDR file plus one similarly-named .DAT file
VG SAM .dti Single file
Varian FDF .fdf Single file
Veeco .hdf Single file
Visitech XYS .xys, .html One .html file plus one or more .xys files
Volocity Library .mvd2, .aisf, .aiix, .dat, .atsf One .mvd2 file plus a ‘Data’ directory
Volocity Library Clipping .acff Single file
WA Technology TOP .wat Single file
Windows Bitmap .bmp Single file
Woolz .wlz Single file
Yokogawa CV7000 .wpi Directory with XML files and one .tif/.tiff file per plane
Zeiss AxioVision TIFF .tif, .xml Single file
Zeiss CZI .czi Single file
Zeiss LMS .lms Single file
Zeiss Laser-Scanning Microscopy .lsm, .mdb One or more .lsm files; if multiple .lsm files are present, an .mdb file should also be present
Zeiss Vision Image (ZVI) .zvi Single file
Zip .zip Single file

Flex Support

OMERO.importer supports importing analyzed Flex files from an Opera system.

Basic configuration is done via the importer.ini. Once the user has run the Importer once, this file will be in the following location:

  • C:\Documents and Settings\<username>\omero\importer.ini

The user will need to modify or add the [FlexReaderServerMaps] section of the INI file as follows:

CIA-1 = \\\\hostname1\\mount;\\\\archivehost1\\mount
CIA-2 = \\\\hostname2\\mount;\\\\archivehost2\\mount

where the key of the INI file line is the value of the “Host” tag in the .mea measurement XML file (here: <Host name="CIA-1">) and the value is a semicolon-separated list of escaped UNC path names to the Opera workstations where the Flex files reside.

Once this resolution has been encoded in the configuration file and you have restarted the importer, you will be able to select the .mea measurement XML file from the Importer user interface as the import target.