# 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.

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 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).
Extended leica file | .xlef | Single file
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 DCIMG | .dcimg | 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 Object Format | .lof | 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
MetaXpress TIFF | .htd, .tif | One .htd file plus one or more .tif files
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
Mikroscan TIFF | .tif, .tiff | Single file
Minolta MRW | .mrw | Single file
Molecular Devices JDCE | .jdce | One .jdce (JSON) file with at least one .tif/.tiff 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, .jp2 | 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 .omp2info | .omp2info | One .omp2info file and at least one .oir or .vsi 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
RCPNL | .rcpnl | One .dv, .r3d, or .d3d file and up to two optional .log files
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 7 SLD (native) | .sldy, .sldyz | Single file
Slidebook TIFF | .tif, .tiff | Single file
Tagged Image File Format | .tif, .tiff, .tf2, .tf8, .btf | Single file
Tecan Spark Cyto | .db | SQLite database, TIFF files, optional analysis output
Text | .txt, .csv | Single file
TillVision | .vws, .pst, .inf | One .vws file and possibly one similarly-named directory
TissueFAXS | .aqproj, .tfcyto | An .aqproj file with one or more .tfcyto database files
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
Ventana .bif | .bif | 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
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
Zeiss XRM | .txm, .txrm | 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:

    …
    [FlexReaderServerMaps]
    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.