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.