BioImageFormat (.nii, .img, .lif, .ome.tiff, ...)

Background

    • 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 (this may have to be in the agreement dialog).

Import & Export

  • 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
    "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)

Download a NIfTI file:

Import the NIfTI file:

Scope  (1)

Download a Leica LIF file:

Import the number of series:

By default, images from all series are imported:

Check series dimensions:

Import the second series:

Import Elements  (1)

Download a NIfTI file:

Import original metadata:

Import OME-XML metadata: