WOLFRAM

  • Import tries to import images and metadata from files with the following extensions: .1sc, .2fl, .acff, .afi, .afm, .aiix, .aim, .aisf, .al3d, .ali, .am, .amiramesh, .ano, .apl, .arf, .atsf, .bif, .bin, .bip, .btf, .c01, .cfg, .ch5, .companion.ome, .cxd, .czi, .db, .df3, .dm2, .dm3, .dm4, .dti, .dv.log, .env, .ets, .fake, .fdf, .ffr, .flex, .fli, .frm, .gel, .grey, .hed, .his, .htd, .hx, .i2i, .ids, .im3, .ima, .img, .ims, .inf, .inr, .ipl, .ipm, .ips, .ipw, .j2ki, .j2kr, .jpk, .jpx, .klb, .l2d, .labels, .lei, .lif, .liff, .lim, .lms, .lsm, .lut, .map, .mea, .mnc, .mng, .mrc, .mrcs, .msr, .mtb, .mvd2, .naf, .nd, .nd2, .ndpi, .ndpis, .nhdr, .nii, .nrrd, .obf, .oib, .oif, .oir, .ome, .ome.btf, .ome.tf2, .ome.tf8, .ome.tif, .ome.tiff, .ome.xml, .omp2info, .par, .pcoraw, .pct, .pict, .pnl, .pr3, .psd, .pst, .pty, .qptiff, .r3d, .r3d_d3d, .r3d.log, .rcpnl, .rec, .res, .scan, .scn, .sdt, .seq, .set, .sif, .sld, .sm2, .sm3, .spc, .spe, .spi, .spl, .st, .stk, .stp, .svs, .sxm, .tf2, .tf8, .tfr, .thm, .tim, .tnb, .top, .v, .vff, .vms, .vsi, .vws, .wat, .wlz, .wpi, .xdce, .xlog, .xqd, .xqf, .xv, .xys, .zfp, .zfr, .zpo, .zvi.

Background & Context

    • Supports reading proprietary microscopy image data and metadata.
    • Supports more than 160 file formats.
    • Developed by the Open Microscopy Environment consortium, including development teams at LOCI at the University of Wisconsin-Madison, University of Dundee and Glencoe Software.
    • Licensing and citing information is on the OME licensing page.

Import

  • Import["file.nii"] imports, for example, a NIfTI file and returns a list of images.
  • Import["file",elem] imports the specified element.
  • The import format can be specified with Import["file"," BioImageFormat"] or Import["file",{" BioImageFormat",elem,}].
  • See the following reference pages for full general information:
  • Importimport from a file
    CloudImportimport from a cloud object
    ImportStringimport from a string
    ImportByteArrayimport from a byte array

Import Elements

  • General Import elements:
  • "Elements" list of elements and options available in this file
    "Summary"summary of the file
    "Rules"list of rules for all available elements
  • Data representation elements:
  • {"ImageList",series}a list of images (default series=All)
  • Advanced Import elements:
  • "SeriesCount"number of data series in the file
  • Metadata elements:
  • "OriginalMetaInformation"original metadata
    "OMEXMLMetaInformation"metadata in the OME-XML format
  • The default Import element is "ImageList".

Examples

open allclose all

Basic Examples  (1)Summary of the most common use cases

Download a NIfTI file:

Out[1]=1

Import the NIfTI file:

Out[2]=2
Out[3]=3

Scope  (1)Survey of the scope of standard use cases

Download a Leica LIF file:

Out[1]=1

Import the number of series:

Out[2]=2

By default, images from all series are imported:

Out[4]=4

Check series dimensions:

Out[5]=5

Import the second series:

Out[6]=6

Import Elements  (1)

Download a NIfTI file:

Out[1]=1

Import original metadata:

Out[2]=2

Import OME-XML metadata: