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SEM/FIB Tomography Acquisition to JSON

Description

The SEM/FIB Tomography Acquisition to JSON component was developed to handle with a specific acquisition file structure. It accepts either a zipped input archive or an input data folder containing one or more datasets of research images in Tagged Image File Format (TIFF), or PNG format with associated header .hdr metadata files. From this input, it generates a single summary metadata document in JSON format conforming to a publicly-available schema created in collaboration with materials research experts working on SEM/FIB Tomography acquisitions.

The component extracts metadata from a generic XML or HDR metadata file present in the acquisition directory, as well as from each individual image within the datasets. All metadata is then compiled into one JSON metadata document. Because acquisition files typically contain dozens to hundreds of images, the resulting JSON is expected to be very large (often > 10,000 lines).

Due to the size of the input, this functionality is only provided as a standalone executable available for download, rather than a plugin button within the mapping service. The executable is available in the release Assets and is compatible with Windows, macOS, and Ubuntu. The documentation on how to use it can be found here.

Input

  • Compressed directory containing the project files in .zip format or the direct input data folder.
  • The input must contain one or more project metadata files in .xml, .emxml or .hdr format, and directories containing the corresponding image datasets.
  • The images must be in .tiff format. In the special case of Tescan instruments, PNG images must be provided together with their corresponding .hdr metadata files.

Supported Vendors

  • Zeiss
  • Thermo Fisher Scientific
  • Tescan

Output

  • Structured metadata document in .json format