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 |
| 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 | 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 |
| 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 |
| 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, .tif, .tiff | One or more .stk or .tif/.tiff files plus an optional .nd 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 |
| 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 |
| 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 |
| 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:
…
[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.
