Wolfram Language

Import and Utilize Microscope Metadata

Image metainformation such as the modality, the recording device, exposure time, etc. is usually stored in the metadata of an image file. BioFormatsLink is a package for interacting with the Bio-Formats library to import image data and metadata into the Wolfram Language.

Download and unpack a ZIP-archived Leica LIF file of a mouse kidney section as provided by Jean-Yves Tinevez of the PFID Imagopôle at the Institut Pasteur, Paris.

Import the first series of images as a 3D volume.

View the stack of images.

Extract the plain metainformation as a list of rules.

Import the OME metainformation as an XML structure.

Extract voxel-related information of the first image series as a list of replacement rules.

Construct the voxel size in the , and directions as a list of quantities.

The first image series was acquired by stimulated emission depletion (STED). Here, the laser wavelengths used in this modality are extracted.

Construct the a list of applied laser wavelengths.

A lot more information can be extracted, e.g. microscope and filter specifications, acquisition dates, data and channel encodings, etc.

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