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Class: Microscopy_Acquisition (MicroscopyAcquisition)

Metadata describing a microscopy acquisition experiment

URI: microbial_experiment_schema:MicroscopyAcquisition

classDiagram class MicroscopyAcquisition click MicroscopyAcquisition href "../MicroscopyAcquisition" ExperimentWithInstrument <|-- MicroscopyAcquisition click ExperimentWithInstrument href "../ExperimentWithInstrument" MicroscopyAcquisition : core_data_path MicroscopyAcquisition --> "1" StringValue : core_data_path click StringValue href "../StringValue" MicroscopyAcquisition : data_acquisition_date MicroscopyAcquisition --> "1" DateValue : data_acquisition_date click DateValue href "../DateValue" MicroscopyAcquisition : elab_experiment MicroscopyAcquisition --> "1" ELabExperiment : elab_experiment click ELabExperiment href "../ELabExperiment" MicroscopyAcquisition : fixation_method MicroscopyAcquisition --> "0..1" FixationMethodValue : fixation_method click FixationMethodValue href "../FixationMethodValue" MicroscopyAcquisition : fluorescent_probe MicroscopyAcquisition --> "0..1" FluorescentProbeValue : fluorescent_probe click FluorescentProbeValue href "../FluorescentProbeValue" MicroscopyAcquisition : incubation_agitation MicroscopyAcquisition --> "0..1" AgitationValue : incubation_agitation click AgitationValue href "../AgitationValue" MicroscopyAcquisition : incubation_atmosphere MicroscopyAcquisition --> "0..1" IncubationAtmosphereValue : incubation_atmosphere click IncubationAtmosphereValue href "../IncubationAtmosphereValue" MicroscopyAcquisition : incubation_duration MicroscopyAcquisition --> "0..1" DurationValue : incubation_duration click DurationValue href "../DurationValue" MicroscopyAcquisition : incubation_temperature MicroscopyAcquisition --> "0..1" TemperatureValue : incubation_temperature click TemperatureValue href "../TemperatureValue" MicroscopyAcquisition : instrument_id MicroscopyAcquisition --> "1" ELabItemValue : instrument_id click ELabItemValue href "../ELabItemValue" MicroscopyAcquisition : microbial_material_id MicroscopyAcquisition --> "0..1" MicrobialMaterialIDValue : microbial_material_id click MicrobialMaterialIDValue href "../MicrobialMaterialIDValue" MicroscopyAcquisition : modalities MicroscopyAcquisition --> "0..1" ModalitiesValue : modalities click ModalitiesValue href "../ModalitiesValue" MicroscopyAcquisition : objective MicroscopyAcquisition --> "0..1" ObjectivesValue : objective click ObjectivesValue href "../ObjectivesValue" MicroscopyAcquisition : operator_id MicroscopyAcquisition --> "1" OperatorIDValue : operator_id click OperatorIDValue href "../OperatorIDValue" MicroscopyAcquisition : project_id MicroscopyAcquisition --> "1" ELabItemValue : project_id click ELabItemValue href "../ELabItemValue" MicroscopyAcquisition : sample_purpose_codes MicroscopyAcquisition --> "0..1" SamplePurposeCodesValue : sample_purpose_codes click SamplePurposeCodesValue href "../SamplePurposeCodesValue" MicroscopyAcquisition : series_image_types MicroscopyAcquisition --> "0..1" SeriesImageTypesValue : series_image_types click SeriesImageTypesValue href "../SeriesImageTypesValue" MicroscopyAcquisition : series_images MicroscopyAcquisition --> "0..1" BooleanValue : series_images click BooleanValue href "../BooleanValue" MicroscopyAcquisition : single_images MicroscopyAcquisition --> "0..1" BooleanValue : single_images click BooleanValue href "../BooleanValue" MicroscopyAcquisition : specific_data_path MicroscopyAcquisition --> "1" StringValue : specific_data_path click StringValue href "../StringValue" MicroscopyAcquisition : template_name MicroscopyAcquisition --> "1" MicroscopyAcquisitionTemplateNameValue : template_name click MicroscopyAcquisitionTemplateNameValue href "../MicroscopyAcquisitionTemplateNameValue"

Inheritance

Slots

Name Cardinality and Range Description Inheritance
fixation_method 0..1
FixationMethodValue		 Specific treatment applied to cells to prevent future changes direct
fluorescent_probe 0..1
FluorescentProbeValue		 Fluorescent probe(s) used in the experiment, as linked item(s) from ELabFTW direct
incubation_agitation 0..1
AgitationValue		 Speed of agitation that cells were incubated during an experiment direct
incubation_atmosphere 0..1
IncubationAtmosphereValue		 Atmosphere that cells were incubated in to encourage growth direct
incubation_duration 0..1
DurationValue		 Length of time that cells were incubated during an experiment direct
incubation_temperature 0..1
TemperatureValue		 Temperature at which cells were incubated during an experiment or culture direct
microbial_material_id 0..1
MicrobialMaterialIDValue		 Cell material(s) used in experiment as named in the eLabFTW database (linked ... direct
modalities 0..1
ModalitiesValue		 The type (modality) of a microscopy acquisition experiment direct
objective 0..1
ObjectivesValue		 The microscope objectives used in a microscopy acquisition experiment direct
sample_purpose_codes 0..1
SamplePurposeCodesValue		 The types of samples acquired in an experiment (from a controlled list) direct
series_image_types 0..1
SeriesImageTypesValue		 The types of series images acquired in an experiment direct
series_images 0..1
BooleanValue		 Whether series images were acquired in an experiment direct
single_images 0..1
BooleanValue		 Whether single images were acquired in an experiment direct
instrument_id 1
ELabItemValue		 The instrument used to acquire the data in an experiment (linked item from EL... ExperimentWithInstrument
core_data_path 1
StringValue		 Portion of the data pathway that will not change as the template is used to g... ExperimentWithData
specific_data_path 1
StringValue		 Portion of the data pathway specific to data from a given experimental record... ExperimentWithData
data_acquisition_date 1
DateValue		 Date on which data were acquired according to eLabFTW record Experiment
elab_experiment 1
ELabExperiment		 A self-reference to this experiment record Experiment
operator_id 1
OperatorIDValue		 Instrument operator during an experiment (a linked item from ELabFTW) Experiment
project_id 1
ELabItemValue		 The project that an experiment supports (link to an ELabFTW item) Experiment
template_name 1
MicroscopyAcquisitionTemplateNameValue		 The name of the template used to collect metadata for an experiment in ELabFT... Experiment

Identifier and Mapping Information

Annotations

property value
elabftw_template True

Schema Source

  • from schema: https://w3id.org/usnistgov/microbial-experiment-schema

Mappings

Mapping Type Mapped Value
self microbial_experiment_schema:MicroscopyAcquisition
native microbial_experiment_schema:MicroscopyAcquisition

LinkML Source

Direct

name: MicroscopyAcquisition
annotations:
  elabftw_template:
    tag: elabftw_template
    value: true
description: Metadata describing a microscopy acquisition experiment
title: Microscopy_Acquisition
from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
is_a: ExperimentWithInstrument
slots:
- fixation_method
- fluorescent_probe
- incubation_agitation
- incubation_atmosphere
- incubation_duration
- incubation_temperature
- microbial_material_id
- modalities
- objective
- sample_purpose_codes
- series_image_types
- series_images
- single_images
slot_usage:
  template_name:
    name: template_name
    range: MicroscopyAcquisitionTemplateNameValue

Induced

name: MicroscopyAcquisition
annotations:
  elabftw_template:
    tag: elabftw_template
    value: true
description: Metadata describing a microscopy acquisition experiment
title: Microscopy_Acquisition
from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
is_a: ExperimentWithInstrument
slot_usage:
  template_name:
    name: template_name
    range: MicroscopyAcquisitionTemplateNameValue
attributes:
  fixation_method:
    name: fixation_method
    annotations:
      elabftw_group:
        tag: elabftw_group
        value: Generic Microbial
      elabftw_user_input:
        tag: elabftw_user_input
        value: true
    description: Specific treatment applied to cells to prevent future changes
    title: FixationMethod
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    ifabsent: None
    alias: fixation_method
    owner: MicroscopyAcquisition
    domain_of:
    - CytoFLEXAcquisition
    - GenericTemplateDeprecated
    - FormaldehydeFixation
    - MicroscopyAcquisition
    - GenericTemplate
    - CoulterAcquisition
    - BactoBoxAcquisition
    - LogCOMETSamplePrep
    - CFU
    range: FixationMethodValue
    required: false
  fluorescent_probe:
    name: fluorescent_probe
    annotations:
      elabftw_group:
        tag: elabftw_group
        value: Generic Microbial
      elabftw_user_input:
        tag: elabftw_user_input
        value: true
    description: Fluorescent probe(s) used in the experiment, as linked item(s) from
      ELabFTW
    title: FluorescentProbe
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    alias: fluorescent_probe
    owner: MicroscopyAcquisition
    domain_of:
    - CytoFLEXAcquisition
    - GenericTemplateDeprecated
    - MicroscopyAcquisition
    - GenericTemplate
    range: FluorescentProbeValue
    required: false
  incubation_agitation:
    name: incubation_agitation
    annotations:
      elabftw_group:
        tag: elabftw_group
        value: Generic Microbial
      elabftw_user_input:
        tag: elabftw_user_input
        value: true
      elabftw_default_unit:
        tag: elabftw_default_unit
        value: rpm
    description: Speed of agitation that cells were incubated during an experiment
    title: IncubationAgitation
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    alias: incubation_agitation
    owner: MicroscopyAcquisition
    domain_of:
    - CytoFLEXAcquisition
    - CellCultureInBroth
    - GenericTemplateDeprecated
    - FormaldehydeFixation
    - MicroscopyAcquisition
    - GenericTemplate
    - InitiateGrowthOfBSpizizenii
    range: AgitationValue
    required: false
  incubation_atmosphere:
    name: incubation_atmosphere
    annotations:
      elabftw_group:
        tag: elabftw_group
        value: Generic Microbial
      elabftw_user_input:
        tag: elabftw_user_input
        value: true
    description: Atmosphere that cells were incubated in to encourage growth
    title: IncubationAtmosphere
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    alias: incubation_atmosphere
    owner: MicroscopyAcquisition
    domain_of:
    - CytoFLEXAcquisition
    - CellCultureInBroth
    - GenericTemplateDeprecated
    - FormaldehydeFixation
    - MicroscopyAcquisition
    - GenericTemplate
    - CFU
    - InitiateGrowthOfBSpizizenii
    range: IncubationAtmosphereValue
    required: false
  incubation_duration:
    name: incubation_duration
    annotations:
      elabftw_group:
        tag: elabftw_group
        value: Generic Microbial
      elabftw_user_input:
        tag: elabftw_user_input
        value: true
      elabftw_default_unit:
        tag: elabftw_default_unit
        value: hr
    description: Length of time that cells were incubated during an experiment
    title: IncubationDuration
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    alias: incubation_duration
    owner: MicroscopyAcquisition
    domain_of:
    - CytoFLEXAcquisition
    - CellCultureInBroth
    - GenericTemplateDeprecated
    - FormaldehydeFixation
    - MicroscopyAcquisition
    - GenericTemplate
    - CFU
    - InitiateGrowthOfBSpizizenii
    range: DurationValue
    required: false
  incubation_temperature:
    name: incubation_temperature
    annotations:
      elabftw_group:
        tag: elabftw_group
        value: Generic Microbial
      elabftw_user_input:
        tag: elabftw_user_input
        value: true
      elabftw_default_unit:
        tag: elabftw_default_unit
        value: oC
    description: Temperature at which cells were incubated during an experiment or
      culture
    title: IncubationTemperature
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    alias: incubation_temperature
    owner: MicroscopyAcquisition
    domain_of:
    - CytoFLEXAcquisition
    - CellCultureInBroth
    - GenericTemplateDeprecated
    - FormaldehydeFixation
    - MicroscopyAcquisition
    - GenericTemplate
    - CFU
    - InitiateGrowthOfBSpizizenii
    range: TemperatureValue
    required: false
  microbial_material_id:
    name: microbial_material_id
    annotations:
      elabftw_group:
        tag: elabftw_group
        value: LabCAS
      elabftw_user_input:
        tag: elabftw_user_input
        value: true
    description: Cell material(s) used in experiment as named in the eLabFTW database
      (linked items)
    title: MicrobialMaterialID
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    alias: microbial_material_id
    owner: MicroscopyAcquisition
    domain_of:
    - CytoFLEXAcquisition
    - NucleicAcidExtraction
    - CellCultureInBroth
    - GenericTemplateDeprecated
    - FormaldehydeFixation
    - MicroscopyAcquisition
    - GenericTemplate
    - CoulterAcquisition
    - BactoBoxAcquisition
    - LogCOMETSamplePrep
    - CFU
    - InitiateGrowthOfBSpizizenii
    range: MicrobialMaterialIDValue
    required: false
  modalities:
    name: modalities
    description: The type (modality) of a microscopy acquisition experiment
    title: Modalities
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    alias: modalities
    owner: MicroscopyAcquisition
    domain_of:
    - MicroscopyAcquisition
    - GenericTemplate
    range: ModalitiesValue
    required: false
  objective:
    name: objective
    description: The microscope objectives used in a microscopy acquisition experiment
    title: Objective
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    alias: objective
    owner: MicroscopyAcquisition
    domain_of:
    - GenericTemplateDeprecated
    - MicroscopyAcquisition
    - GenericTemplate
    range: ObjectivesValue
    required: false
  sample_purpose_codes:
    name: sample_purpose_codes
    annotations:
      elabftw_group:
        tag: elabftw_group
        value: Generic Microbial
      elabftw_user_input:
        tag: elabftw_user_input
        value: true
    description: The types of samples acquired in an experiment (from a controlled
      list)
    title: SamplePurposeCodes
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    ifabsent: Positive control
    alias: sample_purpose_codes
    owner: MicroscopyAcquisition
    domain_of:
    - CytoFLEXAcquisition
    - NucleicAcidExtraction
    - CellCultureInBroth
    - GenericTemplateDeprecated
    - FormaldehydeFixation
    - MicroscopyAcquisition
    - GenericTemplate
    - CoulterAcquisition
    - BactoBoxAcquisition
    - LogCOMETSamplePrep
    - CFU
    - InitiateGrowthOfBSpizizenii
    range: SamplePurposeCodesValue
    required: false
  series_image_types:
    name: series_image_types
    description: The types of series images acquired in an experiment
    title: SeriesImageTypes
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    alias: series_image_types
    owner: MicroscopyAcquisition
    domain_of:
    - MicroscopyAcquisition
    - GenericTemplate
    range: SeriesImageTypesValue
    required: false
  series_images:
    name: series_images
    description: Whether series images were acquired in an experiment
    title: SeriesImages
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    alias: series_images
    owner: MicroscopyAcquisition
    domain_of:
    - MicroscopyAcquisition
    - GenericTemplate
    range: BooleanValue
    required: false
  single_images:
    name: single_images
    description: Whether single images were acquired in an experiment
    title: SingleImages
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    alias: single_images
    owner: MicroscopyAcquisition
    domain_of:
    - MicroscopyAcquisition
    - GenericTemplate
    range: BooleanValue
    required: false
  instrument_id:
    name: instrument_id
    annotations:
      elabftw_group:
        tag: elabftw_group
        value: LabCAS
      elabftw_user_input:
        tag: elabftw_user_input
        value: true
    description: The instrument used to acquire the data in an experiment (linked
      item from ELabFTW)
    title: InstrumentID
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    alias: instrument_id
    owner: MicroscopyAcquisition
    domain_of:
    - ExperimentWithInstrument
    - ExperimentWithInstrumentNoData
    range: ELabItemValue
    required: true
  core_data_path:
    name: core_data_path
    annotations:
      elabftw_group:
        tag: elabftw_group
        value: LabCAS
      elabftw_user_input:
        tag: elabftw_user_input
        value: true
      read_only:
        tag: read_only
        value: true
    description: Portion of the data pathway that will not change as the template
      is used to generate experimental records (should be network-resolvable)
    title: CoreDataPath
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    alias: core_data_path
    owner: MicroscopyAcquisition
    domain_of:
    - ExperimentWithData
    range: StringValue
    required: true
  specific_data_path:
    name: specific_data_path
    annotations:
      elabftw_group:
        tag: elabftw_group
        value: LabCAS
      elabftw_user_input:
        tag: elabftw_user_input
        value: true
    description: Portion of the data pathway specific to data from a given experimental
      record  (should be a sub-path of the location specified by `CoreDataPath`)
    title: SpecificDataPath
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    alias: specific_data_path
    owner: MicroscopyAcquisition
    domain_of:
    - ExperimentWithData
    range: StringValue
    required: true
  data_acquisition_date:
    name: data_acquisition_date
    annotations:
      elabftw_group:
        tag: elabftw_group
        value: LabCAS
      elabftw_user_input:
        tag: elabftw_user_input
        value: true
    description: Date on which data were acquired according to eLabFTW record
    title: DataAcquisitionDate
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    alias: data_acquisition_date
    owner: MicroscopyAcquisition
    domain_of:
    - Experiment
    range: DateValue
    required: true
  elab_experiment:
    name: elab_experiment
    annotations:
      elabftw_user_input:
        tag: elabftw_user_input
        value: false
    description: A self-reference to this experiment record
    title: ELabFTW Experiment
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    alias: elab_experiment
    owner: MicroscopyAcquisition
    domain_of:
    - Experiment
    range: ELabExperiment
    required: true
    inlined: true
    inlined_as_list: true
  operator_id:
    name: operator_id
    annotations:
      elabftw_group:
        tag: elabftw_group
        value: LabCAS
      elabftw_user_input:
        tag: elabftw_user_input
        value: true
    description: Instrument operator during an experiment (a linked item from ELabFTW)
    title: OperatorID
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    alias: operator_id
    owner: MicroscopyAcquisition
    domain_of:
    - Experiment
    range: OperatorIDValue
    required: true
  project_id:
    name: project_id
    annotations:
      elabftw_group:
        tag: elabftw_group
        value: LabCAS
      elabftw_user_input:
        tag: elabftw_user_input
        value: true
    description: The project that an experiment supports (link to an ELabFTW item)
    title: ProjectID
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    alias: project_id
    owner: MicroscopyAcquisition
    domain_of:
    - Experiment
    range: ELabItemValue
    required: true
  template_name:
    name: template_name
    annotations:
      elabftw_group:
        tag: elabftw_group
        value: LabCAS
      read_only:
        tag: read_only
        value: true
      elabftw_user_input:
        tag: elabftw_user_input
        value: true
    description: The name of the template used to collect metadata for an experiment
      in ELabFTW. This value controls what specific metadata fields are allowed.
    title: TemplateName
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    alias: template_name
    owner: MicroscopyAcquisition
    domain_of:
    - Experiment
    range: MicroscopyAcquisitionTemplateNameValue
    required: true