nexusLIMS.extractors.plugins.orion_HIM_tif#

Zeiss Orion/Fibics TIFF extractor plugin.

Module Contents#

Classes#

OrionTiffExtractor

Extractor for Zeiss Orion and Fibics helium ion microscope TIFF files.

Data#

ZEISS_TIFF_TAG

TIFF tag ID where Zeiss Orion stores XML metadata in TIFF files. The tag contains serialized XML with an root element that holds instrument configuration, beam parameters, stage position, detector settings, and other acquisition metadata.

FIBICS_TIFF_TAG

TIFF tag ID where Fibics helium ion microscope stores XML metadata in TIFF files. The tag contains serialized XML with a root element that holds application info, image data, scan parameters, stage position, beam info, and detector settings.

API#

nexusLIMS.extractors.plugins.orion_HIM_tif.ZEISS_TIFF_TAG#

65000

TIFF tag ID where Zeiss Orion stores XML metadata in TIFF files. The tag contains serialized XML with an root element that holds instrument configuration, beam parameters, stage position, detector settings, and other acquisition metadata.

nexusLIMS.extractors.plugins.orion_HIM_tif.FIBICS_TIFF_TAG#

51023

TIFF tag ID where Fibics helium ion microscope stores XML metadata in TIFF files. The tag contains serialized XML with a root element that holds application info, image data, scan parameters, stage position, beam info, and detector settings.

class nexusLIMS.extractors.plugins.orion_HIM_tif.OrionTiffExtractor[source]#

Extractor for Zeiss Orion and Fibics helium ion microscope TIFF files.

This extractor handles metadata extraction from .tif files saved by Zeiss Orion and Fibics helium ion microscopes (HIM). These files contain embedded XML metadata in custom TIFF tags:

  • Zeiss: TIFF tag 65000 with XML

  • Fibics: TIFF tag 51023 with XML

name#

‘orion_HIM_tif_extractor’

priority#

150

supported_extensions#

Type: typing.ClassVar

supports(context: ExtractionContext) → bool[source]#

Check if this extractor supports the given file.

Uses content sniffing to detect Zeiss/Fibics TIFF files by checking for the presence of custom TIFF tags containing XML metadata.

Parameters:

context – The extraction context containing file information

Returns:

True if file is a Zeiss Orion or Fibics TIFF file

Return type:

bool

extract(context: ExtractionContext) → list[dict[str, Any]][source]#

Extract metadata from a Zeiss Orion or Fibics TIFF file.

Parameters:

context – The extraction context containing file information

Returns:

List containing a single metadata dict with ‘nx_meta’ key

Return type:

list[dict]