📖 Vocabulary dictionary

Use the Canonical ID when authoring controlled fields. Synonyms are rewrite-safe lexical aliases. Classified values are more specific scientific descriptions that map to a broader category but are preserved verbatim and never automatically rewritten.

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Capabilities & workflows: Adaptive Illumination Methods · Assay Operations · Contrast Methods · Imaging Modes · Measurement Readouts · Modalities · Modules · Non Optical Capabilities · Optical Routes · Workflow Tags

Light paths & optics: Autofocus Types · Branch Modes · Detector Kinds · Endpoint Types · Light Sheet Types · Light Source Kinds · Light Source Roles · Light Source Technologies · Light Source Timing Modes · Ocular Availability · Optical Component Types · Optical Modulator Types · Optical Path Element Types · Optical Path Stage Roles · Phase Mask Types · Scanner Types · Selection Modes · Stage Types · Stand Orientations · Triggering Modes

Objectives: Objective Corrections · Objective Immersion · Objective Specialties

Software: Software Roles

Quality control: Metric Unit · QC Artifact Roles · QC Evaluation Status · QC Measurement Positions · QC Metric Classes · QC Setpoint Units · QC Type

Maintenance: Maintenance Action · Maintenance Reason · Maintenance Status · Service Provider

Record semantics: Identity Semantics

Capabilities & workflows

Adaptive Illumination Methods

Canonical source: vocab/adaptive_illumination_methods.yaml
Used by namespaces: adaptive_illumination_methods

Label	Canonical ID	Synonyms (rewrite-safe)	Classified values (preserved)	Description
Confocal/STED switching	confocal_sted_switching	-	-	Instrument logic for alternating confocal and STED illumination modes.
Patterned depletion control	patterned_depletion_control	-	-	Adaptive control over depletion beam pattern generation.
RESCue STED	rescue_sted	-	-	Adaptive STED strategy suppressing depletion in low-signal regions.
ROI-adaptive illumination	roi_adaptive_illumination	-	-	Enables adaptive illumination based on selected regions of interest.

Assay Operations

Canonical source: vocab/assay_operations.yaml
Used by namespaces: assay_operations

Label	Canonical ID	Synonyms (rewrite-safe)	Classified values (preserved)	Description
FRAP	frap	-	-	Fluorescence Recovery After Photobleaching. Photobleaches a region and measures fluorescence recovery over time. Used to quantify mobility, exchange, and binding dynamics.
Optogenetics	optogenetics	-	-	Provides patterned or wavelength-specific light stimulation for genetically encoded light-sensitive actuators. Used to control signaling, neural activity, or cellular behavior during imaging.
Photoactivation	photoactivation	-	-	Activates photoactivatable fluorophores in selected regions or times. Supports pulse-chase imaging, sparse labeling, and dynamic experiments.
Photobleaching	photobleaching	-	-	Selectively bleaches fluorophores in defined regions using high-intensity illumination. Used as a perturbation step in FRAP and related assays, or to reduce background from unwanted signal.
Uncaging	uncaging	-	-	Releases biologically active molecules from a photo-labile cage compound using targeted illumination. Enables spatiotemporally controlled delivery of ligands, signaling molecules, or probes.

Contrast Methods

Canonical source: vocab/contrast_methods.yaml
Used by namespaces: contrast_methods

Label	Canonical ID	Synonyms (rewrite-safe)	Classified values (preserved)	Description
Darkfield	darkfield	-	-	Collects only scattered light while excluding directly transmitted illumination. Highlights small structures and edges on a dark background.
DIC	dic	-	-	Differential Interference Contrast. Uses polarized beam shearing to create relief-like contrast from optical path gradients. Useful for high-contrast imaging of unstained live samples.
Differential Phase Contrast (DPC)	differential_phase_contrast	-	-	Computational transmitted-light contrast from asymmetric illumination in opposing directions; does not require a phase annulus or phase-contrast objective.
Optical sectioning	optical_sectioning	-	-	Uses patterned illumination and computational processing to suppress out-of-focus signal. Common examples include ApoTome or grid-projection approaches.
Phase contrast	phase_contrast	-	-	Converts phase shifts from transparent specimens into intensity differences. Useful for live, unlabeled cells on standard culture plastic.
Polarized light	polarized_light	-	-	Uses crossed polarizers to generate contrast from birefringent materials like crystals, amyloid fibrils, or muscle fibers.
Reflected brightfield	reflected_brightfield	-	-	Uses incident reflected light rather than transmitted illumination to visualize opaque or thick specimens in brightfield mode.
Transmitted brightfield	transmitted_brightfield	-	-	Uses transmitted white light to image absorption and scattering contrast in unstained specimens. Common for routine morphology and context imaging.

Imaging Modes

Canonical source: vocab/imaging_modes.yaml
Used by namespaces: imaging_modes

Label	Canonical ID	Synonyms (rewrite-safe)	Classified values (preserved)	Description
Confocal point scanning	confocal_point	-	-	Scans a focused laser spot with a pinhole to reject out-of-focus light. Provides optical sectioning and improved contrast in thick specimens.
Confocal spinning disk	confocal_spinning_disk	-	-	Uses a rotating pinhole disk to image many points in parallel. Enables fast, lower-phototoxicity 3D optical sectioning in live samples.
ISM (AiryScan)	ism	-	-	Image Scanning Microscopy. Uses detector array information in scanning microscopy to improve resolution and signal usage. Airyscan is a common commercial implementation.
Light sheet	light_sheet	-	-	Illuminates samples with a thin sheet orthogonal to detection. Supports gentle, rapid volumetric imaging with reduced out-of-focus exposure.
Multiphoton	multiphoton	-	-	Uses nonlinear excitation, typically with pulsed near-infrared lasers, to excite fluorophores only at the focal volume. Improves deep-tissue imaging and reduces out-of-plane photodamage.
RESOLFT	resolft	-	-	Reversibly Saturable Optical Linear Fluorescence Transitions. Achieves super-resolution using reversibly switchable fluorophores and targeted on/off control. Often allows lower light intensities than depletion-based methods.
SIM	sim	-	-	Structured Illumination Microscopy. Uses shifted illumination patterns and reconstruction to increase resolution and sectioning performance. Suitable for super-resolution with moderate light dose.
SMLM	smlm	-	-	Single-Molecule Localization Microscopy. Builds super-resolved images by localizing sparse single emitters over many frames. Includes methods such as PALM and STORM.
STED	sted	-	-	Stimulated Emission Depletion. Shrinks the effective fluorescence spot using a depletion beam around the excitation focus. Enables sub-diffraction super-resolution imaging.
TIRF	tirf	-	-	Total Internal Reflection Fluorescence. Excites fluorophores with an evanescent field near the coverslip interface. Ideal for membrane-proximal events within roughly the first 100–200 nm.
Widefield fluorescence	widefield_fluorescence	-	-	Illuminates and captures fluorescence from the full field of view without optical sectioning. Best for fast imaging of bright samples and thin specimens.

Measurement Readouts

Canonical source: vocab/measurement_readouts.yaml
Used by namespaces: measurement_readouts

Label	Canonical ID	Synonyms (rewrite-safe)	Classified values (preserved)	Description
FCS	fcs	-	-	Fluorescence Correlation Spectroscopy. Analyzes fluorescence intensity fluctuations in a tiny observation volume. Used to estimate concentration, diffusion, and molecular kinetics.
FLIM	flim	-	-	Fluorescence Lifetime Imaging Microscopy. Measures fluorescence decay timing rather than only intensity. Useful for environmental sensing and interaction readouts such as FRET changes.
FRET	fret	-	-	Förster Resonance Energy Transfer. Measures non-radiative energy transfer between donor and acceptor fluorophores at nanometer distances. Used as a readout of molecular proximity or conformational change.
Spectral Imaging	spectral_imaging	-	-	Records fluorescence across wavelength bands rather than fixed channels. Enables unmixing of overlapping fluorophores and autofluorescence separation.

Modalities

Canonical source: vocab/modalities.yaml
Used by namespaces: modalities

Label	Canonical ID	Synonyms (rewrite-safe)	Classified values (preserved)	Description
Atomic Force Microscopy	afm	AFM	-	Uses a nanoscale cantilever probe to measure topography and mechanical properties at high spatial resolution. Can be combined with optical microscopy workflows.
Confocal (Legacy Route Alias)	confocal	-	-	Legacy compatibility route alias used in older modality hints.
Darkfield	darkfield	dark field	-	Collects only scattered light while excluding directly transmitted illumination. Highlights small structures and edges on a dark background.
Differential Interference Contrast	dic	DIC, nomarski	-	Uses polarized beam shearing to create relief-like contrast from optical path gradients. Useful for high-contrast imaging of unstained live samples.
Differential Phase Contrast (DPC)	differential_phase_contrast	DPC, differential phase contrast	-	Computational transmitted-light contrast generated from asymmetric illumination in opposing directions.
Epi (Legacy Route Alias)	epi	-	-	Legacy compatibility route alias used in older source/element modality hints.
Fluorescence Correlation Spectroscopy	fcs	FCS	-	Analyzes fluorescence intensity fluctuations in a tiny observation volume. Used to estimate concentration, diffusion, and molecular kinetics.
Fluorescence Lifetime Imaging	flim	FLIM	-	Measures fluorescence decay timing rather than only intensity. Useful for environmental sensing and interaction readouts such as FRET changes.
Fluorescence Recovery After Photobleaching	frap	FRAP	-	Photobleaches a region and measures fluorescence recovery over time. Used to quantify mobility, exchange, and binding dynamics.
Förster Resonance Energy Transfer	fret	FRET	-	Measures non-radiative energy transfer between donor and acceptor fluorophores at nanometer distances. Used as a readout of molecular proximity or conformational change.
Image Scanning Microscopy	ism	ISM, airyscan	-	Uses detector array information in scanning microscopy to improve resolution and signal usage. Airyscan implementations are a common form.
Impedance Cytometry	impedance_cytometry	electrical cytometry	-	Measures electrical impedance changes as cells pass sensing regions to infer size and biophysical properties. Often used for label-free cell phenotyping.
Light Sheet	light_sheet	SPIM, LSFM	-	Illuminates samples with a thin sheet orthogonal to detection. Supports gentle, rapid volumetric imaging with reduced out-of-focus exposure.
Live Cell Imaging	live_cell_imaging	live imaging, time-lapse live imaging	-	Refers to imaging workflows optimized for viable cells over time with controlled environment and low phototoxicity. Can be combined with multiple optical modalities.
Multiphoton	multiphoton	two-photon, 2p	-	Uses nonlinear excitation, typically with pulsed near-infrared lasers, to excite fluorophores only at the focal volume. Improves deep-tissue imaging and reduces out-of-plane photodamage.
Phase Contrast	phase_contrast	phase, ph	-	Converts phase shifts from transparent specimens into intensity differences. Useful for live, unlabeled cells on standard culture plastic.
Photoactivation	photoactivation	pa, photo-activation	-	Activates photoactivatable fluorophores in selected regions or times. Supports pulse-chase imaging, sparse labeling, and dynamic experiments.
Point-Scanning Confocal	confocal_point	laser scanning confocal, lsm	-	Scans a focused laser spot with a pinhole to reject out-of-focus light. Provides optical sectioning and improved contrast in thick specimens.
Polarized Light	polarized_light	polarization	-	Uses crossed polarizers to generate contrast from birefringent materials like crystals, amyloid fibrils, or muscle fibers.
Reflected Brightfield	reflected_brightfield	epi brightfield, reflected light brightfield	-	Uses incident reflected light rather than transmitted illumination to visualize opaque or thick specimens in brightfield mode.
RESOLFT	resolft	RESOLFT	-	Achieves super-resolution using reversibly switchable fluorophores and targeted on/off control. Often allows lower light intensities than depletion-based methods.
Second Harmonic Generation	shg	SHG	-	Label-free nonlinear imaging modality generating signal at half the excitation wavelength from non-centrosymmetric structures such as collagen.
Single-Molecule Localization Microscopy	smlm	SMLM, PALM/STORM	-	Builds super-resolved images by localizing sparse single emitters over many frames. Includes methods such as PALM and STORM.
Single-Particle Tracking	spt	SPT, single molecule tracking	-	Tracks individual particles or molecules over time to quantify motion and dynamics. Used for diffusion, transport, and interaction studies.
Spectral Imaging	spectral_imaging	lambda imaging, spectral detection	-	Records fluorescence across wavelength bands rather than fixed channels. Enables unmixing of overlapping fluorophores and autofluorescence separation.
Spinning-Disk Confocal	confocal_spinning_disk	SDC, spinning disk	-	Uses a rotating pinhole disk to image many points in parallel. Enables fast, lower-phototoxicity 3D optical sectioning in live samples.
Stimulated Emission Depletion	sted	STED	-	Shrinks the effective fluorescence spot using a depletion beam around the excitation focus. Enables sub-diffraction super-resolution imaging.
Structured Illumination Microscopy	sim	SIM, structured illumination	-	Uses shifted illumination patterns and reconstruction to increase resolution and sectioning performance. Suitable for super-resolution with moderate light dose.
Structured Optical Sectioning	optical_sectioning	apotome, grid projection	-	Uses patterned illumination and computational processing to suppress out-of-focus signal. Common examples include ApoTome or grid-projection approaches.
Third Harmonic Generation	thg	THG	-	Label-free nonlinear imaging modality generating signal at one-third the excitation wavelength, often sensitive to refractive-index discontinuities.
TIRF-SIM	tirf_sim	TIRF-SIM, 2D TIRF-SIM	-	Combines Total Internal Reflection with Structured Illumination for high-speed, high-contrast, super-resolved surface imaging.
Total Internal Reflection Fluorescence	tirf	TIRF	-	Excites fluorophores with an evanescent field near the coverslip interface. Ideal for membrane-proximal events within roughly the first 100–200 nm.
Transmitted (Legacy Route Alias)	transmitted	-	-	Legacy compatibility transmitted-route alias used in older modality hints.
Transmitted Brightfield	transmitted_brightfield	brightfield, bf	-	Uses transmitted white light to image absorption and scattering contrast in unstained specimens. Common for routine morphology and context imaging.
Widefield Fluorescence	widefield_fluorescence	epifluorescence, widefield epi	-	Illuminates and captures fluorescence from the full field of view without optical sectioning. Best for fast imaging of bright samples and thin specimens.

Modules

Canonical source: vocab/modules.yaml
Used by namespaces: modules

Label	Canonical ID	Synonyms (rewrite-safe)	Classified values (preserved)	Description
3D-SIM Module	3d_sim	Blaze R2 3D-SIM	-	Structured illumination module for three-dimensional super-resolution imaging with enhanced axial and lateral detail.
Acousto-Optical Beam Splitter (AOBS)	aobs	AOBS	-	Acousto-optic beam splitting component for dynamic wavelength selection and flexible excitation-emission routing.
Adaptive Optics	adaptive_optics	ao	-	Corrects sample- or system-induced aberrations using deformable elements and feedback. Improves resolution and signal quality, especially in deep or heterogeneous samples.
AFM Module	afm_module	AFM	-	Atomic force microscopy integration module for combining topographical or mechanical probing with optical imaging.
AiryScan Detector/Module	airyscan	AiryScan	-	Detector and reconstruction module that improves confocal sensitivity and resolution via multi-element signal collection.
Easy3D STED	easy3d_sted	Easy3D_STED	-	STED imaging enhancement for simplified three-dimensional super-resolution acquisition with optimized 3D depletion beam handling.
Environmental Enclosure	environmental_enclosure	Environmental Enclosure, Temperature Control, environmental_tolerance, Live Cell Option	-	Enclosure and control accessories that stabilize temperature and related conditions for live-cell compatibility.
External Camera Port	camera_port	trinocular head, c-mount port, photo port	-	An available optical port (e.g., trinocular head or side port) and c-mount adapter allowing users to attach external or third-party imaging devices.
FCS Module	fcs	correlation module, FCS	-	Instrumentation support for fluorescence fluctuation measurements and autocorrelation analysis. Enables diffusion and concentration quantification in tiny volumes.
FLIM Module	flim	lifetime module, FLIM	-	Adds lifetime-resolved detection and analysis to fluorescence imaging. Enables contrast based on fluorophore decay kinetics.
FRAP Module	frap	photobleach module, FRAP	-	Hardware or software capability to perform targeted photobleaching for recovery measurements. Typically controls ROI bleaching power and timing.
Hardware Autofocus	hardware_autofocus	focus lock, z-drift compensation	-	Active focus stabilization that compensates focus drift during acquisition. Common implementations include reflected-light focus locks such as Definite Focus or PFS.
Hardware Triggering	hardware_triggering	triggering kit, device synchronization, ttl triggering	-	Hardware-level synchronization module for deterministic timing between cameras, scanners, lasers, shutters, and other devices during fast or complex acquisitions.
High-Performance Workstation	workstation	workstation	-	Dedicated compute workstation for acquisition control, rapid image processing, and handling large microscopy datasets.
Impedance Module	impedance_module	impedance_module	-	Module supporting impedance-based measurement workflows alongside optical imaging for complementary sample characterization.
Incubation	incubation	environmental chamber, temp/co2 control	-	Environmental control module for temperature, CO2, and often humidity around the specimen. Supports physiologic conditions during long-term live imaging.
Microfluidics / Perfusion	microfluidics	perfusion pump	-	Hardware for controlled delivery of media or drugs to the sample during live imaging.
Motorized Stage	motorized_stage	multiposition, xy stage	-	Automated XY stage enabling multi-position imaging, large-area tiling, and multi-well plate screening.
Optogenetics	optogenetics	photo-stimulation	-	Provides patterned or wavelength-specific stimulation for light-controlled biological perturbations. Used to control signaling or neural activity during imaging.
Photoactivation Module	photoactivation	photo-manipulation, pa module	-	Capability to activate or uncage photoresponsive probes in defined regions. Used for selective labeling and dynamic tracking experiments.
Piezo Z-Stage	piezo_z_stage	piezo_z_stage	-	High-precision piezoelectric Z positioning module for rapid and repeatable axial movement during fine focus control and volume imaging.
RESCue STED	rescue_sted	RESCue_STED	-	Adaptive STED mode that limits depletion exposure to signal-bearing regions to reduce photobleaching and phototoxicity.
Ring TIRF Module	ring_tirf	Ring TIRF	-	TIRF implementation using ring illumination to improve field uniformity near the coverslip interface.
SIM Module	sim_module	SIM	-	Structured illumination imaging module enabling resolution enhancement beyond diffraction-limited widefield microscopy.
TIRF Module	tirf	TIRF	-	Dedicated total internal reflection fluorescence illumination path for near-membrane imaging.
Universal Vessel Holder	universal_vessel_holder	Universal vessel holder	-	Adaptable sample holder supporting multiple dish, slide, or plate formats within a single imaging setup.

Non Optical Capabilities

Canonical source: vocab/non_optical_capabilities.yaml
Used by namespaces: non_optical_capabilities

Label	Canonical ID	Synonyms (rewrite-safe)	Classified values (preserved)	Description
AFM	afm	-	-	Atomic Force Microscopy. Uses a nanoscale cantilever probe to measure topography and mechanical properties at high spatial resolution. Can be combined with optical microscopy workflows.
Impedance cytometry	impedance_cytometry	-	-	Measures electrical impedance changes as cells pass sensing regions to infer size and biophysical properties. Often used for label-free cell phenotyping.

Optical Routes

Canonical source: vocab/optical_routes.yaml
Used by namespaces: optical_routes

Label	Canonical ID	Synonyms (rewrite-safe)	Classified values (preserved)	Description
Light sheet	light_sheet	SPIM, LSFM, light sheet fluorescence microscopy	-	Light-sheet illumination and detection route family, including SPIM variants.
Multiphoton	multiphoton	two-photon, 2p, nonlinear microscopy, non-linear microscopy	-	Multiphoton excitation route family.
Point-scanning confocal	confocal_point	LSM, laser scanning confocal, CLSM, point scanning confocal	-	Broad point-scanning confocal route family, including point-scanning super-resolution or readout workflows implemented on the confocal scanner path.
Reflected light	reflected_light	incident light, epi brightfield, reflected illumination	-	Reflected or incident-light route family used to illuminate opaque or thick specimens from above the sample.
Spinning-disk confocal	confocal_spinning_disk	SDC, spinning disk confocal, Nipkow disk confocal	-	Broad spinning-disk confocal route family, including CSU-W1 and Borealis spinning disk implementations.
Transmitted light	transmitted_light	transmitted, brightfield, diascopic, transmitted illumination	-	Broad transmitted-light route family covering brightfield and transmitted contrast methods.
Widefield fluorescence	widefield_fluorescence	widefield, epifluorescence, epi fluorescence, widefield epi	-	Broad widefield/epi fluorescence route family, including TIRF and widefield-based localization or structured illumination acquisitions when implemented through the widefield fluorescence path.

Workflow Tags

Canonical source: vocab/workflow_tags.yaml
Used by namespaces: workflow_tags

Label	Canonical ID	Synonyms (rewrite-safe)	Classified values (preserved)	Description
High-content screening	high_content_screening	-	-	Automated acquisition and analysis across many samples, fields, or conditions. Typically involves motorized stages, plate formats, and quantitative readout pipelines.
Live cell imaging	live_cell_imaging	-	-	Imaging workflows optimized for viable cells over time with controlled environment and low phototoxicity. Can be combined with multiple optical modalities.
Single-molecule imaging	single_molecule	-	-	Workflows that detect and analyze individual fluorescent molecules. Requires low labeling densities and sensitive detection conditions.
Single-particle tracking	single_particle_tracking	spt	-	Tracks individual particles or molecules over time to quantify motion and dynamics. Used for diffusion, transport, and interaction studies.
Super-resolution	super_resolution	-	-	Workflows that achieve spatial resolution beyond the classical diffraction limit. Encompasses techniques including STED, RESOLFT, SIM, and SMLM.

Light paths & optics

Autofocus Types

Canonical source: vocab/autofocus_types.yaml
Used by namespaces: autofocus_types

Label	Canonical ID	Synonyms (rewrite-safe)	Classified values (preserved)	Description
Capacitance-Based Autofocus	capacitance_based	capacitive autofocus	-	Autofocus using capacitive sensing to track objective-to-sample distance and stabilize focus.
Contrast-Based Autofocus	contrast_based	image-based autofocus, software autofocus, focus metric	-	Autofocus that optimizes image sharpness or contrast directly from the captured image signal.
Infrared Reflection Autofocus	infrared_reflection	PFS, perfect focus, Nikon Perfect Focus, Nikon Perfect Focus System, Definite Focus, Zeiss Definite Focus, Leica AFC, Olympus ZDC	-	Hardware autofocus based on infrared reflection from the coverslip or sample interface to compensate focus drift.
Laser Reflection Autofocus	laser_reflection	reflection autofocus, hardware focus lock	-	Hardware autofocus that uses reflected laser light to maintain focal position during imaging.
Other	other	custom, misc	-	Hardware autofocus implementation not covered by the predefined terms.

Branch Modes

Canonical source: vocab/branch_modes.yaml
Used by namespaces: branch_modes

Label	Canonical ID	Synonyms (rewrite-safe)	Classified values (preserved)	Description
Passthrough	passthrough	-	-	Branch does not materially alter routing beyond target selection.
Reflected	reflected	-	-	Branch follows the reflected path of a selector or splitter.
Selected	selected	-	-	Branch is selected by state rather than by transmitted/reflected optics.
Transmitted	transmitted	-	-	Branch follows the transmitted path of a selector or splitter.

Detector Kinds

Canonical source: vocab/detector_kinds.yaml
Used by namespaces: detector_kinds

Label	Canonical ID	Synonyms (rewrite-safe)	Classified values (preserved)	Description
Avalanche Photodiode	apd	APD	-	Semiconductor point detector with internal gain and fast timing response. Used in photon counting and correlation-based measurements.
Charge-Coupled Device	ccd	CCD	-	Area detector technology with historically strong image quality and uniformity. Still used in some fluorescence and brightfield setups.
Electron-Multiplying CCD	emccd	EMCCD	-	CCD detector with on-chip gain for very low-light imaging. Useful for single-molecule and fast, dim signal applications.
GaAsP Photomultiplier Tube	gaasp_pmt	GaAsP_PMT, gaasp detector	-	PMT using gallium arsenide phosphide photocathodes with improved quantum efficiency over conventional PMTs. Useful for low-light confocal imaging.
Hybrid Detector	hyd	HyD, hybrid pmt	-	Combines features of PMTs and avalanche gain to provide high sensitivity and fast response. Frequently used in modern confocal systems.
Photomultiplier Tube	pmt	PMT	-	Highly sensitive point detector that amplifies photoelectrons through a dynode chain. Common in confocal detection paths.
Scientific CMOS	scmos	sCMOS	-	Low-noise, high-speed area detector with large field of view and high dynamic range. Common for widefield, spinning-disk, and fast live imaging.
SPAD Array	spad	-	-	Single-Photon Avalanche Diode array. Provides exceptional timing resolution and single-photon sensitivity, crucial for advanced FLIM.
Standard CMOS	cmos	CMOS	-	Standard digital camera sensor. Commonly used in routine brightfield, color histology, or basic fluorescence.

Endpoint Types

Canonical source: vocab/endpoint_types.yaml
Used by namespaces: endpoint_types

Label	Canonical ID	Synonyms (rewrite-safe)	Classified values (preserved)	Description
Camera port	camera_port	camera port, cameraport	-	Passive camera port endpoint.
Detector	detector	camera, pmt, hyd, apd, spad	-	Detection endpoint represented by an electronic detector channel.
Eyepiece	eyepiece	ocular, eyepieces, binocular, trinocular	-	Ocular/eyepiece endpoint for visual observation.

Light Sheet Types

Canonical source: vocab/light_sheet_types.yaml
Used by namespaces: light_sheet_types

Label	Canonical ID	Synonyms (rewrite-safe)	Classified values (preserved)	Description
Airy Beam Light Sheet	airy_beam	-	-	Airy-beam light sheet implementation.
diSPIM	di_spim	-	-	Dual-view inverted selective-plane illumination microscopy.
Lattice Light Sheet	lattice	-	-	Structured lattice light-sheet implementation.
Other	other	-	-	Light-sheet architecture not covered by the predefined terms.
SCAPE	scape	-	-	Swept confocally aligned planar excitation.
Single-Objective Light Sheet	single_objective	-	-	Single-objective light-sheet architecture.
Standard SPIM	standard_spim	-	-	Conventional selective-plane illumination geometry.

Light Source Kinds

Canonical source: vocab/light_source_kinds.yaml
Used by namespaces: light_source_kinds

Label	Canonical ID	Synonyms (rewrite-safe)	Classified values (preserved)	Description
Arc Lamp	arc_lamp	mercury lamp, xenon lamp	-	Broad-spectrum lamp, such as mercury or xenon, used with filter sets for fluorescence excitation. Historically common on epifluorescence microscopes.
Halogen Lamp	halogen_lamp	tungsten-halogen, quartz halogen	-	Continuous-spectrum tungsten-halogen illumination, primarily for transmitted light imaging. Common for brightfield and contrast techniques.
Laser	laser	single-line laser, laser_diode, laser_dpss, laser (diode), laser (DPSS), dpss	-	Provides coherent, narrowband excitation at specific wavelengths. Common for fluorescence imaging requiring high irradiance and precise line selection.
LED	led	light-emitting diode	-	Solid-state light source with stable output and fast switching. Widely used for widefield fluorescence and transmitted illumination.
Metal Halide Lamp	metal_halide	hxp	-	Broad-spectrum lamp coupled via a liquid light guide. Provides intense, stable excitation for standard widefield fluorescence.
Pulsed Near-IR Laser	multiphoton_laser	-	ti_sapphire, ti:sapphire	Femtosecond pulsed laser tunable in the near-infrared. Used for deep-tissue multiphoton excitation.
Supercontinuum Source	supercontinuum	white supercontinuum laser	-	Broadband laser-like source generated by nonlinear spectral broadening. Provides highly flexible, selectable excitation bands.
White Light Laser	white_light_laser	WLL	-	Broadband laser source with tunable output wavelengths selected by software or optics. Supports flexible excitation across many fluorophores.

Light Source Roles

Canonical source: vocab/light_source_roles.yaml
Used by namespaces: light_source_roles

Label	Canonical ID	Synonyms (rewrite-safe)	Classified values (preserved)	Description
Activation	activation	-	-	Photoactivation or photoswitching source.
Alignment	alignment	-	-	Alignment or service beam not used as primary excitation/depletion.
Depletion	depletion	sted_depletion, sted	-	Source that depletes or switches off fluorescence outside the effective focus. The mechanism belongs to the technique: stimulated emission under STED, reversible photoswitching under RESOLFT.
Excitation	excitation	excitation_laser	-	Primary fluorophore excitation source.
Reflected Illumination	reflected_illumination	epi illumination, incident illumination	-	Source provides reflected-light illumination onto the sample from the objective or an epi/top-light path.
Transmitted Illumination	transmitted_illumination	transmitted, brightfield, diascopic, dia	-	Diascopic or transmitted-light illumination source used for brightfield, phase contrast, darkfield, or DIC.

Light Source Technologies

Canonical source: vocab/light_source_technologies.yaml
Used by namespaces: light_source_technologies

Label	Canonical ID	Synonyms (rewrite-safe)	Classified values (preserved)	Description
Diode	diode	-	-	Diode laser or diode-driven light source.
DPSS	dpss	-	-	Diode-pumped solid-state laser.
LED Array	led_array	-	-	Multi-channel LED engine or array.
Other	other	-	-	Technology subtype not covered by the predefined terms.
Supercontinuum	supercontinuum	-	-	Supercontinuum broadband source.
Ti:Sapphire	ti_sapphire	-	-	Tunable femtosecond Ti:Sapphire source.

Light Source Timing Modes

Canonical source: vocab/light_source_timing_modes.yaml
Used by namespaces: light_source_timing_modes

Label	Canonical ID	Synonyms (rewrite-safe)	Classified values (preserved)	Description
Continuous Wave	cw	continuous, continuous_wave	-	Continuous-wave operation without pulse train timing metadata.
Pulsed	pulsed	pulse, pulse_train	-	Pulsed operation with pulse width and repetition rate metadata.

Ocular Availability

Canonical source: vocab/ocular_availability.yaml
Used by namespaces: ocular_availability

Label	Canonical ID	Synonyms (rewrite-safe)	Classified values (preserved)	Description
Binocular	binocular	2 eyepiece, two eyepiece, biocular	-	Microscope stand provides two-eyepiece direct viewing.
Camera-only	camera_only	camera only, digital only, no eyepieces	-	No direct visual eyepiece path; observation is camera-mediated only.
Trinocular	trinocular	3 port, trinoc, trinocular head	-	Microscope stand provides binocular viewing plus a camera port.
Unknown	unknown	unspecified, not documented	-	Eyepiece availability is not yet documented.

Optical Component Types

Canonical source: vocab/optical_component_types.yaml
Used by namespaces: optical_component_types

Label	Canonical ID	Synonyms (rewrite-safe)	Classified values (preserved)	Description
Analyzer	analyzer	-	-	Polarization analyzer element used in DIC or polarized-light detection paths.
Bandpass	bandpass	-	-	Requires center_nm and width_nm.
Block	block	-	-	A 100% blocking/shutter position.
Dichroic	dichroic	-	-	Requires cutoffs_nm array.
Empty	empty	-	-	An explicitly empty slot.
Filter Cube	filter_cube	-	-	Linked excitation/dichroic/emission cube or filter-set assembly installed as a single selectable position. Supports explicit excitation_filter, dichroic, and emission_filter sub-component objects for authoritative spectral authoring.
Longpass	longpass	-	-	Requires cut_on_nm.
Mirror	mirror	-	-	A 100% reflective surface.
Multiband Bandpass	multiband_bandpass	-	-	Bandpass component containing multiple pass bands.
Multiband Dichroic	multiband_dichroic	-	-	Requires cutoffs_nm array.
Neutral Density	neutral_density	-	-	Broadband neutral-density attenuator. Spectral shape is preserved even if total intensity is reduced.
Notch	notch	-	-	Requires center_nm and width_nm.
Passthrough	passthrough	-	-	Explicit slot that does not materially alter spectral routing.
Polychroic	polychroic	-	-	Synonym for multiband.
Shortpass	shortpass	-	-	Requires cut_off_nm.

Optical Modulator Types

Canonical source: vocab/optical_modulator_types.yaml
Used by namespaces: optical_modulator_types

Label	Canonical ID	Synonyms (rewrite-safe)	Classified values (preserved)	Description
Acousto-Optic Deflector	aod	-	-	AOD-based beam steering or modulation device.
Deformable Mirror	deformable_mirror	-	-	Adaptive mirror with controllable surface profile.
Electro-Optic Modulator	eom	-	-	Electro-optic phase or amplitude modulator.
Other	other	-	-	Other optical modulator type not covered above.
Phase Plate	phase_plate	-	-	Static phase plate for beam shaping.
Spatial Light Modulator	slm	-	-	Programmable spatial light modulator used for phase shaping.
Vortex Plate	vortex_plate	-	-	Vortex phase element used for donut beam generation.

Optical Path Element Types

Canonical source: vocab/optical_path_element_types.yaml
Used by namespaces: optical_path_element_types

Label	Canonical ID	Synonyms (rewrite-safe)	Classified values (preserved)	Description
Dual View	dual_view	-	-	Two-way image splitter with explicit branch targets.
Emission Splitter	emission_splitter	-	-	Emission-path splitter that routes detected light into explicit branches.
Filter Wheel	filter_wheel	-	-	Discrete wheel or carousel that selects one optical position at a time.
Fixed	fixed	-	-	Fixed optical element with no active selection mechanism.
Image Splitter	image_splitter	-	-	Image-splitting element such as a dual-view or quad-view splitter.
Quad View	quad_view	-	-	Four-way image splitter with explicit branch targets.
Selector	selector	-	-	Selection element that routes light into one or more explicit branches.
Slider	slider	-	-	Linear slider with one active position at a time.
Spectral Array	spectral_array	-	-	Multi-band or array-based spectral selection element.
Spectral Slider	spectral_slider	-	-	Spectral slit/slider mechanism used to define wavelength windows.
Splitter	splitter	-	-	Optical splitter with explicit branch definitions and endpoint targets.
Tunable	tunable	-	-	Continuously tunable optical element such as an AOTF or spectral selector.
Turret	turret	-	-	Rotary turret or cube carousel.

Optical Path Stage Roles

Canonical source: vocab/optical_path_stage_roles.yaml
Used by namespaces: optical_path_stage_roles

Label	Canonical ID	Synonyms (rewrite-safe)	Classified values (preserved)	Description
Analyzer	analyzer	-	-	Element represents a DIC/polarization analyzer stage in the detection path.
Cube	cube	-	-	Element represents a linked cube/filter-set assembly.
Dichroic	dichroic	-	-	Element participates in dichroic routing around the sample plane.
Emission	emission	-	-	Element participates in the detection path after the sample plane.
Excitation	excitation	-	-	Element participates in the illumination path before the sample plane.
Splitter	splitter	-	-	Element explicitly branches or selects downstream routes/endpoints.

Phase Mask Types

Canonical source: vocab/phase_mask_types.yaml
Used by namespaces: phase_mask_types

Label	Canonical ID	Synonyms (rewrite-safe)	Classified values (preserved)	Description
3D-STED	3d_sted	-	-	Combined mask strategy for three-dimensional STED depletion.
Bottle	bottle	-	-	Bottle-beam phase mask for axial confinement.
Top-Hat	top_hat	-	-	Top-hat phase profile for beam shaping.
Vortex	vortex	-	-	Azimuthal vortex phase mask for donut-shaped depletion beam.
Z-STED	z_sted	-	-	Phase mask optimized for axial STED depletion.

Scanner Types

Canonical source: vocab/scanner_types.yaml
Used by namespaces: scanner_types

Label	Canonical ID	Synonyms (rewrite-safe)	Classified values (preserved)	Description
Acousto-Optic Scanner	acousto_optic	AOD, acousto-optic deflector	-	Deflects beams using acousto-optic elements for rapid, inertia-free positioning. Useful for fast random-access scanning patterns.
Galvanometric Scanner	galvo	galvanometer, galvo mirrors, point_scanning	-	Uses galvanometer mirrors to steer the excitation beam across the sample. Common in point-scanning confocal systems with flexible scan control.
No Scanner	none	camera-based	-	No dedicated beam scanner is used for image formation. Typical of camera-based widefield modalities.
Polygon Scanner	polygon	polygon mirror	-	Uses a rotating polygon mirror for rapid beam deflection. Often used in high-speed scanning implementations.
Resonant Scanner	resonant	resonant galvo	-	Uses a resonant oscillating mirror for very high line rates. Enables faster imaging than standard galvo scanning, often with reduced dwell time.
Spinning Disk Scanner	spinning_disk	nipkow disk, sdc scanner	-	Uses rotating pinhole disks to scan multiple points in parallel. Supports high-speed confocal imaging with lower phototoxicity.
Stage Scanning	stage_scanning	sample scanning	-	Forms images by moving the sample stage relative to fixed optics or beam position. Common in slide scanning and some large-area acquisitions.
Tandem Scanner (Galvo/Resonant)	tandem	galvanometric_and_resonant	-	Dual-mode scanning configuration that supports switching between galvanometric and resonant scanning behavior.

Selection Modes

Canonical source: vocab/selection_modes.yaml
Used by namespaces: selection_modes

Label	Canonical ID	Synonyms (rewrite-safe)	Classified values (preserved)	Description
Exclusive	exclusive	-	-	Exactly one branch should be selected at a time.
Fixed	fixed	-	-	No user branch selection is required; the branch state is fixed.
Multiple	multiple	-	-	More than one branch may be active simultaneously.

Stage Types

Canonical source: vocab/stage_types.yaml
Used by namespaces: stage_types

Label	Canonical ID	Synonyms (rewrite-safe)	Classified values (preserved)	Description
Manual Stage	manual	manual focus, manual drive	-	Manual stage or focus drive without motorized control.
Motorized XY Stage	xy_motorized	motorized_xy, xy stage, xy motorized	-	Motorized translational stage for automated X/Y movement across the sample plane.
Other	other	custom, misc	-	Stage or focus-drive type not covered by the predefined terms.
Z Piezo Stage	z_piezo	piezo, piezo stage, piezo z	-	Piezo-driven stage or objective positioner used for rapid, precise axial stepping.

Stand Orientations

Canonical source: vocab/stand_orientations.yaml
Used by namespaces: stand_orientations

Label	Canonical ID	Synonyms (rewrite-safe)	Classified values (preserved)	Description
Benchtop	benchtop	-	-	Compact benchtop imaging instrument.
Inverted	inverted	-	-	Inverted microscope stand.
Other	other	-	-	Stand orientation not covered by the predefined terms.
Stereo	stereo	-	-	Stereo / dissecting microscope stand.
Upright	upright	-	-	Conventional upright microscope stand.

Triggering Modes

Canonical source: vocab/triggering_modes.yaml
Used by namespaces: triggering_modes

Label	Canonical ID	Synonyms (rewrite-safe)	Classified values (preserved)	Description
Hardware Triggering	hardware	ttl, external trigger	-	Synchronization is driven primarily by hardware timing signals such as TTL triggers.
Mixed Triggering	mixed	hybrid	-	Synchronization uses a combination of hardware triggers and software orchestration.
Software Triggering	software	computer controlled	-	Synchronization is driven primarily through software control rather than dedicated timing signals.

Objectives

Objective Corrections

Canonical source: vocab/objective_corrections.yaml
Used by namespaces: objective_corrections

Label	Canonical ID	Synonyms (rewrite-safe)	Classified values (preserved)	Description
Achromat	achromat	achro	-	Basic objective correction class with limited chromatic and spherical correction. Often used for standard, non-demanding imaging tasks.
Apochromat	apochromat	apo	-	Objective with strong chromatic and spherical aberration correction, typically over multiple colors. May not guarantee full field flatness.
Fluorite	fluorite	semi-apo, fluor	-	Objective class with improved color correction and transmission relative to basic achromats. Common compromise between performance and cost.
Plan Achromat	plan_achromat	plan achro	-	Objective with flat field correction and basic chromatic correction for two wavelengths. Suitable for routine brightfield and general imaging.
Plan Apochromat	plan_apochromat	plan-apo, plan apo, super apochromat, super_apochromat, uplsapo	-	High-end objective with flat field correction and strong chromatic/spherical correction across wavelengths. Preferred for quantitative, multicolor imaging.
Plan Fluorite	plan_fluorite	plan fluor, plan fluorite	-	Objective with flat field correction and moderate-to-high aberration correction, typically between achromat and apochromat classes.

Objective Immersion

Canonical source: vocab/objective_immersion.yaml
Used by namespaces: objective_immersion

Label	Canonical ID	Synonyms (rewrite-safe)	Classified values (preserved)	Description
Air	air	dry	-	Objective is used without immersion liquid, with air between front lens and coverslip. Common for lower magnification or long working distance imaging.
Dipping	dipping	water dipping, dipping objective	-	Front lens is dipped directly into sample medium without coverslip contact. Common in electrophysiology and in vivo preparations.
Glycerol	glycerol	glycerin	-	Uses glycerol immersion to better match intermediate refractive indices. Useful for some cleared or thick biological specimens.
Multi-Immersion	multi	multi immersion	-	Objective is designed to operate with multiple immersion media, often with correction adjustments. Provides flexibility across sample types.
Oil	oil	oil immersion	-	Uses immersion oil to better match refractive index and increase numerical aperture. Common for high-resolution fluorescence objectives.
Silicone	silicone	silicone oil	-	Uses silicone oil immersion with refractive index close to tissue, improving deep imaging stability. Often used in live or thick sample imaging.
Water	water	water immersion	-	Uses water as immersion medium for improved index matching in aqueous samples. Useful for live-cell and deeper tissue imaging.

Objective Specialties

Canonical source: vocab/objective_specialties.yaml
Used by namespaces: objective_specialties

Label	Canonical ID	Synonyms (rewrite-safe)	Classified values (preserved)	Description
Cleared Tissue Imaging	cleared_tissue_imaging	-	Cleared Tissue Imaging (CLARITY and TDE)	Objective suitable for imaging optically cleared tissue samples.
Correction Collar	correction_collar	Correction Ring, Correction Ring (CORR), correction collar	correction collar for 0-1.5mm glass, correction ring for 0.17 mm cover glass	Objective is explicitly described as having an adjustable correction collar or correction ring.
Cover Glass Specification	cover_glass_specification	-	cover glass 0.17, cover glass 0.75	Objective has an explicit cover-glass thickness or specification; this does not imply an adjustable correction collar.
Coverslip Correction	coverslip_correction	-	-	Objective is explicitly described as supporting coverslip correction.
DIC	dic	DIC	DIC (Suitable), DIC (Recommended), dic compatible, DIC N1, DIC N1 (Suitable), DIC N2, DIC N2 (Suitable), DIC N2 (Recommended), DIC Prism A, DIC Prism B, DIC Prism C, DIC Prism D, DIC Prism E	Objective supports differential interference contrast.
IR Transmission	ir_transmission	-	UV-VIS-IR, (UV)VIS-IR, VISIR, IR-compatible to 1300 nm	Objective optimized for IR / multiphoton transmission.
Long Working Distance	long_working_distance	LWD, ELWD	ELWD ADM	Objective designed for increased working distance.
Multi-immersion	multi_immersion	-	Multi-immersion, Multi-immersion (BABB/W/Glyc/Sil-Oil)	Objective is explicitly described as supporting multiple immersion media; this does not imply a correction collar.
Other	other	-	-	Specialty not covered by the predefined terms.
Phase	phase	-	Ph1, phase contrast (ph), phase contrast (ph 0), phase contrast (ph 1), phase contrast (ph1 dl), phase contrast (ph2), phase contrast (ext ph4), phase contrast (ph1), phase compatible	Objective supports phase-contrast use.
Polarization	polarization	-	Polarization (Possible), Polarization (Suitable)	Objective supports polarization imaging workflows.
SIM	sim	SIM	-	Objective suitable for structured illumination microscopy workflows.
STED	sted	STED	-	Objective suitable for stimulated emission depletion microscopy workflows.
TIRF	tirf	TIRF	-	Objective optimized for total internal reflection fluorescence imaging.
UV Transmission	uv_transmission	-	UV ≥340 nm, UV ≥365 nm	Objective optimized for UV transmission.
Water Dipping	water_dipping	-	-	Objective designed for direct immersion into sample medium.

Software

Software Roles

Canonical source: vocab/software_roles.yaml
Used by namespaces: software_roles

Label	Canonical ID	Synonyms (rewrite-safe)	Classified values (preserved)	Description
Acquisition	acquisition	capture	-	Software used for instrument control and image acquisition.
Analysis	analysis	quantification	-	Software used for quantitative analysis, fitting, and measurement.
Hardware Control	hardware_control	control	-	Software used to control ancillary hardware subsystems.
Other	other	-	-	Software that does not fit acquisition, processing, analysis, or hardware control roles.
Processing	processing	reconstruction, deconvolution, post_processing	-	Software used for post-acquisition image processing and reconstruction workflows.

Quality control

Metric Unit

Canonical source: vocab/metric_unit.yaml
Used by namespaces: metric_unit

Label	Canonical ID	Synonyms (rewrite-safe)	Classified values (preserved)	Description
Ampere	A	amp, amps, ampere	-	Electrical current expressed in amperes.
Degrees Celsius	celsius	C, °C	-	Temperature expressed in degrees Celsius.
Hour	h	hour, hours	-	Elapsed time expressed in hours.
Micrometer	um	-	-	Length expressed in micrometers.
Milliwatt	mW	-	-	Optical power expressed in milliwatts.
Nanometer	nm	-	-	Length expressed in nanometers.
Percent	percent	-	-	Percentage value represented in %.
Pixel	px	pixel, pixels	-	Image-space distance or count expressed in pixels.
Unitless	unitless	-	-	Dimensionless value with no physical unit.

QC Artifact Roles

Canonical source: vocab/qc_artifact_roles.yaml
Used by namespaces: artifact_role, qc_artifact_roles

Label	Canonical ID	Synonyms (rewrite-safe)	Classified values (preserved)	Description
Other	other	-	-	Artifact role not captured by existing categories; describe in details.
Preview	preview	-	-	Rendered quick-look artifact intended for visual inspection.
Raw Image	raw_image	-	-	Original unprocessed image data artifact produced by the QC run.
Report	report	-	-	Human-readable summary report such as PDF or HTML output.
Table	table	-	-	Tabular artifact such as CSV, TSV, or spreadsheet-like export.

QC Evaluation Status

Canonical source: vocab/qc_evaluation_status.yaml
Used by namespaces: evaluation_status, qc_evaluation_status

Label	Canonical ID	Synonyms (rewrite-safe)	Classified values (preserved)	Description
Fail	fail	-	-	Measured value is out of acceptable range and requires follow-up action.
Pass	pass	-	-	Measured value meets expected criteria or threshold.
Warn	warn	-	-	Measured value is borderline or drifting and should be monitored.

QC Measurement Positions

Canonical source: vocab/qc_measurement_positions.yaml
Used by namespaces: measurement_positions, qc_measurement_positions

Label	Canonical ID	Synonyms (rewrite-safe)	Classified values (preserved)	Description
At Objective	at_objective	-	-	Measured at or near the objective/sample plane where illumination reaches the specimen.
Fiber Output	fiber_output	-	-	Measured at the optical fiber output before downstream beam delivery optics.
Pre-objective	pre_objective	-	-	Measured in the optical path before the objective lens.

QC Metric Classes

Canonical source: vocab/qc_metric_classes.yaml
Used by namespaces: qc_metric_classes

Label	Canonical ID	Synonyms (rewrite-safe)	Classified values (preserved)	Description
Absolute or relative illumination intensity	laser_power	-	-	Class of illumination metrics describing measured excitation intensity or power output.
Axial (Z) Full Width at Half Maximum	fwhm_axial	-	-	Class of resolution metrics describing axial point-spread width along the optical axis.
Baseline noise of the camera/detector	detector_dark_noise	-	-	Class of detector metrics describing dark signal and baseline electronic noise without illumination.
Error or variance in stage repositioning	stage_repeatability	-	-	Class of positioning metrics describing precision and repeatability of stage return to target coordinates.
Flatness of the field of view	illumination_uniformity	-	-	Class of illumination metrics describing spatial uniformity of intensity across the field.
Lateral (XY) Full Width at Half Maximum	fwhm_lateral	-	-	Class of resolution metrics describing lateral point-spread width in the imaging plane.
Signal-to-noise or contrast ratio	signal_to_noise	-	-	Class of image quality metrics describing signal strength relative to background noise or contrast.
Spatial offset between color channels	chromatic_shift	-	-	Class of alignment metrics describing chromatic displacement between channels in multicolor imaging.

QC Setpoint Units

Canonical source: vocab/qc_setpoint_units.yaml
Used by namespaces: qc_setpoint_units, setpoint_units

Label	Canonical ID	Synonyms (rewrite-safe)	Classified values (preserved)	Description
mW Setpoint	mW_setpoint	-	-	Device setpoint expressed in milliwatts as configured in acquisition software. This is a commanded drive value, not a measured optical power; use metric_unit.mW for measured power values.
Percent	percent	-	-	Setpoint expressed as a percentage of configured maximum or reference output.

QC Type

Canonical source: vocab/qc_type.yaml
Used by namespaces: qc_type

Label	Canonical ID	Synonyms (rewrite-safe)	Classified values (preserved)	Description
Alignment	alignment	-	-	Optical alignment checks such as channel registration and beam path consistency.
Laser Power	laser_power	-	-	Laser output and stability checks against expected setpoints.
Other	other	-	-	QC activity that does not fit the predefined categories; document details in free text.
PSF	psf	-	-	Point spread function measurements for optical performance and resolution tracking.
Stage	stage	-	-	Mechanical stage repeatability and positioning accuracy checks.

Maintenance

Maintenance Action

Canonical source: vocab/maintenance_action.yaml
Used by namespaces: action, maintenance_action

Label	Canonical ID	Synonyms (rewrite-safe)	Classified values (preserved)	Description
Align	align	realignment, alignment	-	Adjusts optical or mechanical alignment to restore expected performance. Typical examples include beam path or stage alignment.
Calibrate	calibrate	calibration	-	Performs calibration against known references to ensure accurate measurement or positioning. Use for intensity, stage, focus, or scaling calibration events.
Clean	clean	cleaning	-	Removes contamination from optics, mechanics, or enclosures to recover performance and reliability. Includes routine cleaning of lenses and filters.
Install	install	installation	-	Installs a new component, module, or subsystem as part of maintenance or upgrade work.
Other	other	misc	-	Action does not match the predefined categories. Provide specific context in free-text details.
Repair	repair	fix	-	Fixes a confirmed fault or malfunction by restoring or replacing failing parts. Use when resolving a broken or degraded subsystem.
Replace	replace	part replacement, part_replacement	-	Substitutes a component with a new or refurbished part. Use when parts are worn, failed, or upgraded directly.
Service	service	maintenance, calibration_and_alignment	-	General maintenance intervention including inspection and routine adjustments. Used when work does not fit a more specific action type.
Update	update	upgrade software, firmware update, software_update	-	Applies software, firmware, or configuration updates to the instrument ecosystem. Use for non-hardware-change version or settings updates.

Maintenance Reason

Canonical source: vocab/maintenance_reason.yaml
Used by namespaces: maintenance_reason, reason

Label	Canonical ID	Synonyms (rewrite-safe)	Classified values (preserved)	Description
Check	check	inspection, diagnostic	-	Focused verification or inspection to confirm system status without major intervention. Includes diagnostic visits and quick health checks.
Cleaning	cleaning	clean	-	Triggered specifically by planned or corrective cleaning activity.
Install	install	commissioning, setup	-	Triggered by initial installation of a system, add-on module, or newly delivered component. Use for setup and commissioning events.
Issue Reported	issue_reported	incident, fault reported	-	Triggered by an issue report indicating degraded or failed operation, often before root cause is confirmed.
Other	other	misc	-	Reason does not fit the predefined categories. Document the rationale in free-text details.
Problem	problem	issue, breakdown, repair	-	Triggered by a reported fault, performance issue, or unexpected behavior. Use when intervention is reactive to a defect.
Scheduled	scheduled	preventive maintenance, preventative_maintenance, preventive_maintenance, pm	-	Planned preventive maintenance performed at regular intervals. Includes routine service contracts and periodic inspections.
Upgrade	upgrade	enhancement	-	Initiated to improve capability, performance, or feature set beyond baseline operation. Can include hardware or software enhancement projects.

Maintenance Status

Canonical source: vocab/maintenance_status.yaml
Used by namespaces: maintenance_status

Label	Canonical ID	Synonyms (rewrite-safe)	Classified values (preserved)	Description
In Service	in_service	operational, available, fully functional	-	Instrument is fully available for use.
Limited Service	limited	restricted, degraded, remaining issue	-	Instrument is partially available with restrictions.
Out of Service	out_of_service	offline, down	-	Instrument is unavailable for use.

Service Provider

Canonical source: vocab/service_provider.yaml
Used by namespaces: service_provider

Label	Canonical ID	Synonyms (rewrite-safe)	Classified values (preserved)	Description
Distributor	distributor	-	-	Service performed by an authorized distributor or reseller partner.
Internal	internal	-	-	Service performed by in-house staff within the facility or institution.
Third Party	third_party	-	-	Service performed by an independent external provider not classified as vendor or distributor.
Unknown	unknown	-	-	Service provider type is not known or not documented.
Vendor	vendor	-	-	Service performed directly by the original equipment manufacturer or official vendor organization.

Record semantics

Identity Semantics

Canonical source: vocab/identity_semantics.yaml
Used by namespaces: identity_semantics

Label	Canonical ID	Synonyms (rewrite-safe)	Classified values (preserved)	Description
Manufacturer	manufacturer	-	-	Company/vendor/brand that makes the component or module.
Model	model	-	-	Vendor-facing model name/designation; primary structured identity field.
Name	name	-	-	Local/display/instance label only; not equivalent to model or product_code. Use only when it differs from model.
Product code	product_code	-	-	Explicit catalogue/order/SKU/reference code only; optional and never inferred from model or name.