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 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 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

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

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

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.