XML Schema Reference#

This page provides automatically-generated documentation for the NexusLIMS XML schema used to represent experimental records.

Introduction#

NexusLIMS generates output experimental records as XML documents that conform to the Nexus Experiment Schema (XSD). These records can then be curated in the NexusLIMS CDCS frontend application, and capture comprehensive metadata about microscopy sessions, including:

Session information: Who performed the experiment, when, and why
Instrument details: Which microscope(s) were used and their configurations
Acquisition activities: Temporal grouping of related data files
Dataset metadata: Comprehensive technical parameters for each file

From Internal to Output XML Representations#

Added in version 2.2.0: Starting with v2.2.0, NexusLIMS uses a two-stage metadata pipeline. This validation and standardization system is still evolving as EM Glossary coverage expands and community standards develop.

Extraction & Validation (Internal): NexusLIMS extractors produce metadata dictionaries validated against internal Pydantic schemas (NexusMetadata, ImageMetadata, SpectrumMetadata, etc.) with:
- EM Glossary standardized fields (where available - the vocabulary is still developing)
- Physical quantities with units (via Pint)
- Basic validation and unit normalization
Serialization to XML: Validated metadata is transformed into XML following the Nexus Experiment Schema with:
- Quantity fields → XML elements with unit attributes
- Extension fields → <summary> elements in <nx:extensions> blocks
- EM Glossary metadata → emg:display_name and emg:id attributes on quantity elements (where EMG terms are available)

Example Transformation#

# Pydantic metadata (Python objects)
{
    "acceleration_voltage": Quantity(200, "kV"),
    "magnification": Quantity(50, "kiloX"),
    "extensions": {
        "detector_brightness": 50.0,
    }
}

Metadata Serialized to XML (within a Dataset element)#

<nx:dataset type="Image" role="Experimental">
    <nx:name>micrograph_001.tif</nx:name>
    <nx:location>/path/to/data/micrograph_001.tif</nx:location>
    <nx:format>image/tiff</nx:format>
    <nx:meta name="Acceleration Voltage" unit="kV">200.0</nx:meta>
    <nx:meta name="Magnification" unit="kX">50</nx:meta>
    <nx:meta name="detector_brightness">50.0</nx:meta>
</nx:dataset>

This two-stage approach provides:

Basic type safety during extraction (Pydantic validation)
Emerging standardization via EM Glossary (where terms are available)
Interoperability through standard XML format
Semantic enrichment with EMG metadata attributes (where EMG IDs are available)

See Internal Metadata Schema System for complete details on the Pydantic schema system and EM Glossary Field Reference for EM Glossary integration.

Nexus Experiment Schema#

The Nexus Experiment schema defines the final output structure of XML records generated by NexusLIMS. Each record describes a microscopy session, including metadata about the experiment, instruments used, and data files acquired.

A metadata schema for describing an experiment utilizing equipment from the Nexus Microscopy Lab.

Schema Structure (Interactive)

The diagram below shows the hierarchical structure of the schema. Pan by clicking and dragging, zoom with the mouse wheel, and click on any type node to jump to its detailed documentation below. You can also hover over nodes to see more information about that element.

Legend

Root Element

Complex Type

Required Element

Optional Element

Schema Information

Target Namespace: https://data.nist.gov/od/dm/nexus/experiment/v1.0

Version: 1.03-10-2022

Root Elements

Element Path	Purpose	Required
`Experiment/summary/title`	Session title	Yes
`Experiment/summary/experimenter`	User information	Yes
`Experiment/instrument`	Microscope used	Yes
`Experiment/AcquisitionActivity`	File grouping	Yes (1+)
`AcquisitionActivity/dataset`	Individual file	Yes (1+)
`dataset/acquisition`	Technical metadata	No
`dataset/acquisition/extensions`	Vendor-specific data	No

XML Schema Reference#

Introduction#

From Internal to Output XML Representations#

Example Transformation#

Metadata Serialized to XML (within a Dataset element)#

Nexus Experiment Schema#

Example Record#

Navigating the XSD Documentation#

Schema Structure#

Finding Specific Information#

Common Elements Reference#

Physical Quantities with Units#

See Also#

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