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Class: PSFBeadsOutput

URI: microscopemetrics_schema:PSFBeadsOutput

classDiagram class PSFBeadsOutput click PSFBeadsOutput href "../PSFBeadsOutput" MetricsOutput <|-- PSFBeadsOutput click MetricsOutput href "../MetricsOutput" PSFBeadsOutput : analyzed_bead_centers PSFBeadsOutput --> "*" Roi : analyzed_bead_centers click Roi href "../Roi" PSFBeadsOutput : average_bead PSFBeadsOutput --> "0..1" Image : average_bead click Image href "../Image" PSFBeadsOutput : bead_profiles_x PSFBeadsOutput --> "0..1" Table : bead_profiles_x click Table href "../Table" PSFBeadsOutput : bead_profiles_y PSFBeadsOutput --> "0..1" Table : bead_profiles_y click Table href "../Table" PSFBeadsOutput : bead_profiles_z PSFBeadsOutput --> "0..1" Table : bead_profiles_z click Table href "../Table" PSFBeadsOutput : bead_properties PSFBeadsOutput --> "0..1" Table : bead_properties click Table href "../Table" PSFBeadsOutput : comment PSFBeadsOutput --> "0..1" Comment : comment click Comment href "../Comment" PSFBeadsOutput : considered_bead_centers_axial_edge PSFBeadsOutput --> "*" Roi : considered_bead_centers_axial_edge click Roi href "../Roi" PSFBeadsOutput : considered_bead_centers_intensity_outlier PSFBeadsOutput --> "*" Roi : considered_bead_centers_intensity_outlier click Roi href "../Roi" PSFBeadsOutput : considered_bead_centers_lateral_edge PSFBeadsOutput --> "*" Roi : considered_bead_centers_lateral_edge click Roi href "../Roi" PSFBeadsOutput : considered_bead_centers_self_proximity PSFBeadsOutput --> "*" Roi : considered_bead_centers_self_proximity click Roi href "../Roi" PSFBeadsOutput : considered_bead_centers_x_fit_quality PSFBeadsOutput --> "*" Roi : considered_bead_centers_x_fit_quality click Roi href "../Roi" PSFBeadsOutput : considered_bead_centers_y_fit_quality PSFBeadsOutput --> "*" Roi : considered_bead_centers_y_fit_quality click Roi href "../Roi" PSFBeadsOutput : considered_bead_centers_z_fit_quality PSFBeadsOutput --> "*" Roi : considered_bead_centers_z_fit_quality click Roi href "../Roi" PSFBeadsOutput : errors PSFBeadsOutput : key_measurements PSFBeadsOutput --> "0..1" PSFBeadsKeyMeasurements : key_measurements click PSFBeadsKeyMeasurements href "../PSFBeadsKeyMeasurements" PSFBeadsOutput : processing_application PSFBeadsOutput : processing_datetime PSFBeadsOutput : processing_entity PSFBeadsOutput : processing_log PSFBeadsOutput : processing_version PSFBeadsOutput : validated PSFBeadsOutput : validation_datetime PSFBeadsOutput : warnings

Inheritance

Slots

Name Cardinality and Range Description Inheritance
analyzed_bead_centers *
Roi		 The centers of the beads that have been analyzed direct
considered_bead_centers_lateral_edge *
Roi		 The centers of the beads detected but considered as too close to the edge of ... direct
considered_bead_centers_self_proximity *
Roi		 The centers of the beads detected but considered as too close to another bead direct
considered_bead_centers_axial_edge *
Roi		 The centers of the beads detected but considered as too close to the top and ... direct
considered_bead_centers_intensity_outlier *
Roi		 The centers of the beads detected but considered as being too intense and pot... direct
considered_bead_centers_z_fit_quality *
Roi		 The centers of the beads detected but considered as the fit quality in z was ... direct
considered_bead_centers_y_fit_quality *
Roi		 The centers of the beads detected but considered as the fit quality in y was ... direct
considered_bead_centers_x_fit_quality *
Roi		 The centers of the beads detected but considered as the fit quality in x was ... direct
key_measurements 0..1
PSFBeadsKeyMeasurements		 The key measurements of the PSF beads analysis direct
bead_properties 0..1
Table		 Properties associated with the analysis of the beads direct
bead_profiles_z 0..1
Table		 The intensity profiles along the z axis of the analyzed beads as well as the ... direct
bead_profiles_y 0..1
Table		 The intensity profiles along the y axis of the analyzed beads as well as the ... direct
bead_profiles_x 0..1
Table		 The intensity profiles along the x axis of the analyzed beads as well as the ... direct
average_bead 0..1
Image		 The average bead image created from all the beads considered valid direct
comment 0..1
Comment		 A human readable comment MetricsOutput
processing_application 1..*
String		 The application used to process the dataset MetricsOutput
processing_version 1..*
String		 The version of the application used to process the dataset MetricsOutput
processing_entity *
String		 The entity that processed the dataset MetricsOutput
processing_datetime 1
datetime		 The datetime of the processing by microscope-metrics MetricsOutput
processing_log 0..1
String		 The log of the processing by microscope-metrics MetricsOutput
warnings *
String		 The warnings of the processing by microscope-metrics MetricsOutput
errors *
String		 The errors of the processing by microscope-metrics MetricsOutput
validated 1
Boolean		 Has the dataset been validated by a human MetricsOutput
validation_datetime 0..1
datetime		 The datetime of the validation MetricsOutput

Usages

used by used in type used
PSFBeadsDataset output range PSFBeadsOutput

Identifier and Mapping Information

Schema Source

  • from schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema

Mappings

Mapping Type Mapped Value
self microscopemetrics_schema:PSFBeadsOutput
native microscopemetrics_schema:PSFBeadsOutput

LinkML Source

Direct

name: PSFBeadsOutput
from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
is_a: MetricsOutput
attributes:
  analyzed_bead_centers:
    name: analyzed_bead_centers
    description: The centers of the beads that have been analyzed. One point shape
      will be provided per bead correctly detected. One ROI per channel.
    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/psf_beads
    rank: 1000
    domain_of:
    - PSFBeadsOutput
    range: Roi
    multivalued: true
    inlined: true
    inlined_as_list: true
  considered_bead_centers_lateral_edge:
    name: considered_bead_centers_lateral_edge
    description: The centers of the beads detected but considered as too close to
      the edge of the image. Measurements on these bead not considered for the dataset
      analysis. One point will be provided per bead. One ROI per channel.
    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/psf_beads
    rank: 1000
    domain_of:
    - PSFBeadsOutput
    range: Roi
    multivalued: true
    inlined: true
    inlined_as_list: true
  considered_bead_centers_self_proximity:
    name: considered_bead_centers_self_proximity
    description: The centers of the beads detected but considered as too close to
      another bead. Measurements on these bead not considered for the dataset analysis.
      One point will be provided per bead. One ROI per channel.
    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/psf_beads
    rank: 1000
    domain_of:
    - PSFBeadsOutput
    range: Roi
    multivalued: true
    inlined: true
    inlined_as_list: true
  considered_bead_centers_axial_edge:
    name: considered_bead_centers_axial_edge
    description: The centers of the beads detected but considered as too close to
      the top and or bottom of the image. Measurements on these bead not considered
      for the dataset analysis. One point will be provided per bead. One ROI per channel.
    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/psf_beads
    rank: 1000
    domain_of:
    - PSFBeadsOutput
    range: Roi
    multivalued: true
    inlined: true
    inlined_as_list: true
  considered_bead_centers_intensity_outlier:
    name: considered_bead_centers_intensity_outlier
    description: The centers of the beads detected but considered as being too intense
      and potentially represent a cluster of beads. Intensity robust z-score over
      requested threshold. Measurements on these bead not considered for the dataset
      analysis. One point will be provided per bead. One ROI per channel.
    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/psf_beads
    rank: 1000
    domain_of:
    - PSFBeadsOutput
    range: Roi
    multivalued: true
    inlined: true
    inlined_as_list: true
  considered_bead_centers_z_fit_quality:
    name: considered_bead_centers_z_fit_quality
    description: The centers of the beads detected but considered as the fit quality
      in z was not good enough.  coefficient of determination (R^2) (R^2) over requested
      threshold. Measurements in z for this bead not considered for the dataset analysis.
      One point will be provided per bead. One ROI per channel.
    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/psf_beads
    rank: 1000
    domain_of:
    - PSFBeadsOutput
    range: Roi
    multivalued: true
    inlined: true
    inlined_as_list: true
  considered_bead_centers_y_fit_quality:
    name: considered_bead_centers_y_fit_quality
    description: The centers of the beads detected but considered as the fit quality
      in y was not good enough.  coefficient of determination (R^2) (R^2) over requested
      threshold. Measurements in y for this bead not considered for the dataset analysis.
      One point will be provided per bead. One ROI per channel.
    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/psf_beads
    rank: 1000
    domain_of:
    - PSFBeadsOutput
    range: Roi
    multivalued: true
    inlined: true
    inlined_as_list: true
  considered_bead_centers_x_fit_quality:
    name: considered_bead_centers_x_fit_quality
    description: The centers of the beads detected but considered as the fit quality
      in x was not good enough.  coefficient of determination (R^2) (R^2) over requested
      threshold. Measurements in x for this bead not considered for the dataset analysis.
      One point will be provided per bead. One ROI per channel.
    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/psf_beads
    rank: 1000
    domain_of:
    - PSFBeadsOutput
    range: Roi
    multivalued: true
    inlined: true
    inlined_as_list: true
  key_measurements:
    name: key_measurements
    description: The key measurements of the PSF beads analysis.
    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/psf_beads
    domain_of:
    - MetricsOutput
    - FieldIlluminationOutput
    - PSFBeadsOutput
    - LightSourcePowerOutput
    range: PSFBeadsKeyMeasurements
    multivalued: false
    inlined: true
    inlined_as_list: true
  bead_properties:
    name: bead_properties
    description: Properties associated with the analysis of the beads.
    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/psf_beads
    rank: 1000
    domain_of:
    - PSFBeadsOutput
    range: Table
    multivalued: false
    inlined: true
    inlined_as_list: true
  bead_profiles_z:
    name: bead_profiles_z
    description: The intensity profiles along the z axis of the analyzed beads as
      well as the fits.
    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/psf_beads
    rank: 1000
    domain_of:
    - PSFBeadsOutput
    range: Table
    multivalued: false
    inlined: true
    inlined_as_list: true
  bead_profiles_y:
    name: bead_profiles_y
    description: The intensity profiles along the y axis of the analyzed beads as
      well as the fits.
    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/psf_beads
    rank: 1000
    domain_of:
    - PSFBeadsOutput
    range: Table
    multivalued: false
    inlined: true
    inlined_as_list: true
  bead_profiles_x:
    name: bead_profiles_x
    description: The intensity profiles along the x axis of the analyzed beads as
      well as the fits.
    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/psf_beads
    rank: 1000
    domain_of:
    - PSFBeadsOutput
    range: Table
    multivalued: false
    inlined: true
    inlined_as_list: true
  average_bead:
    name: average_bead
    description: The average bead image created from all the beads considered valid.
      The average bead is calculated after aligning the beads in all three axes. This
      one image contains all the channels. If the analysis does not detect at least
      two beads in a channel, the average bead for this channel is not calculated.
    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/psf_beads
    rank: 1000
    domain_of:
    - PSFBeadsOutput
    range: Image
    required: false
    multivalued: false
    inlined: true
    inlined_as_list: true

Induced

name: PSFBeadsOutput
from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
is_a: MetricsOutput
attributes:
  analyzed_bead_centers:
    name: analyzed_bead_centers
    description: The centers of the beads that have been analyzed. One point shape
      will be provided per bead correctly detected. One ROI per channel.
    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/psf_beads
    rank: 1000
    alias: analyzed_bead_centers
    owner: PSFBeadsOutput
    domain_of:
    - PSFBeadsOutput
    range: Roi
    multivalued: true
    inlined: true
    inlined_as_list: true
  considered_bead_centers_lateral_edge:
    name: considered_bead_centers_lateral_edge
    description: The centers of the beads detected but considered as too close to
      the edge of the image. Measurements on these bead not considered for the dataset
      analysis. One point will be provided per bead. One ROI per channel.
    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/psf_beads
    rank: 1000
    alias: considered_bead_centers_lateral_edge
    owner: PSFBeadsOutput
    domain_of:
    - PSFBeadsOutput
    range: Roi
    multivalued: true
    inlined: true
    inlined_as_list: true
  considered_bead_centers_self_proximity:
    name: considered_bead_centers_self_proximity
    description: The centers of the beads detected but considered as too close to
      another bead. Measurements on these bead not considered for the dataset analysis.
      One point will be provided per bead. One ROI per channel.
    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/psf_beads
    rank: 1000
    alias: considered_bead_centers_self_proximity
    owner: PSFBeadsOutput
    domain_of:
    - PSFBeadsOutput
    range: Roi
    multivalued: true
    inlined: true
    inlined_as_list: true
  considered_bead_centers_axial_edge:
    name: considered_bead_centers_axial_edge
    description: The centers of the beads detected but considered as too close to
      the top and or bottom of the image. Measurements on these bead not considered
      for the dataset analysis. One point will be provided per bead. One ROI per channel.
    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/psf_beads
    rank: 1000
    alias: considered_bead_centers_axial_edge
    owner: PSFBeadsOutput
    domain_of:
    - PSFBeadsOutput
    range: Roi
    multivalued: true
    inlined: true
    inlined_as_list: true
  considered_bead_centers_intensity_outlier:
    name: considered_bead_centers_intensity_outlier
    description: The centers of the beads detected but considered as being too intense
      and potentially represent a cluster of beads. Intensity robust z-score over
      requested threshold. Measurements on these bead not considered for the dataset
      analysis. One point will be provided per bead. One ROI per channel.
    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/psf_beads
    rank: 1000
    alias: considered_bead_centers_intensity_outlier
    owner: PSFBeadsOutput
    domain_of:
    - PSFBeadsOutput
    range: Roi
    multivalued: true
    inlined: true
    inlined_as_list: true
  considered_bead_centers_z_fit_quality:
    name: considered_bead_centers_z_fit_quality
    description: The centers of the beads detected but considered as the fit quality
      in z was not good enough.  coefficient of determination (R^2) (R^2) over requested
      threshold. Measurements in z for this bead not considered for the dataset analysis.
      One point will be provided per bead. One ROI per channel.
    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/psf_beads
    rank: 1000
    alias: considered_bead_centers_z_fit_quality
    owner: PSFBeadsOutput
    domain_of:
    - PSFBeadsOutput
    range: Roi
    multivalued: true
    inlined: true
    inlined_as_list: true
  considered_bead_centers_y_fit_quality:
    name: considered_bead_centers_y_fit_quality
    description: The centers of the beads detected but considered as the fit quality
      in y was not good enough.  coefficient of determination (R^2) (R^2) over requested
      threshold. Measurements in y for this bead not considered for the dataset analysis.
      One point will be provided per bead. One ROI per channel.
    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/psf_beads
    rank: 1000
    alias: considered_bead_centers_y_fit_quality
    owner: PSFBeadsOutput
    domain_of:
    - PSFBeadsOutput
    range: Roi
    multivalued: true
    inlined: true
    inlined_as_list: true
  considered_bead_centers_x_fit_quality:
    name: considered_bead_centers_x_fit_quality
    description: The centers of the beads detected but considered as the fit quality
      in x was not good enough.  coefficient of determination (R^2) (R^2) over requested
      threshold. Measurements in x for this bead not considered for the dataset analysis.
      One point will be provided per bead. One ROI per channel.
    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/psf_beads
    rank: 1000
    alias: considered_bead_centers_x_fit_quality
    owner: PSFBeadsOutput
    domain_of:
    - PSFBeadsOutput
    range: Roi
    multivalued: true
    inlined: true
    inlined_as_list: true
  key_measurements:
    name: key_measurements
    description: The key measurements of the PSF beads analysis.
    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/psf_beads
    alias: key_measurements
    owner: PSFBeadsOutput
    domain_of:
    - MetricsOutput
    - FieldIlluminationOutput
    - PSFBeadsOutput
    - LightSourcePowerOutput
    range: PSFBeadsKeyMeasurements
    multivalued: false
    inlined: true
    inlined_as_list: true
  bead_properties:
    name: bead_properties
    description: Properties associated with the analysis of the beads.
    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/psf_beads
    rank: 1000
    alias: bead_properties
    owner: PSFBeadsOutput
    domain_of:
    - PSFBeadsOutput
    range: Table
    multivalued: false
    inlined: true
    inlined_as_list: true
  bead_profiles_z:
    name: bead_profiles_z
    description: The intensity profiles along the z axis of the analyzed beads as
      well as the fits.
    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/psf_beads
    rank: 1000
    alias: bead_profiles_z
    owner: PSFBeadsOutput
    domain_of:
    - PSFBeadsOutput
    range: Table
    multivalued: false
    inlined: true
    inlined_as_list: true
  bead_profiles_y:
    name: bead_profiles_y
    description: The intensity profiles along the y axis of the analyzed beads as
      well as the fits.
    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/psf_beads
    rank: 1000
    alias: bead_profiles_y
    owner: PSFBeadsOutput
    domain_of:
    - PSFBeadsOutput
    range: Table
    multivalued: false
    inlined: true
    inlined_as_list: true
  bead_profiles_x:
    name: bead_profiles_x
    description: The intensity profiles along the x axis of the analyzed beads as
      well as the fits.
    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/psf_beads
    rank: 1000
    alias: bead_profiles_x
    owner: PSFBeadsOutput
    domain_of:
    - PSFBeadsOutput
    range: Table
    multivalued: false
    inlined: true
    inlined_as_list: true
  average_bead:
    name: average_bead
    description: The average bead image created from all the beads considered valid.
      The average bead is calculated after aligning the beads in all three axes. This
      one image contains all the channels. If the analysis does not detect at least
      two beads in a channel, the average bead for this channel is not calculated.
    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/psf_beads
    rank: 1000
    alias: average_bead
    owner: PSFBeadsOutput
    domain_of:
    - PSFBeadsOutput
    range: Image
    required: false
    multivalued: false
    inlined: true
    inlined_as_list: true
  comment:
    name: comment
    description: A human readable comment
    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
    rank: 1000
    alias: comment
    owner: PSFBeadsOutput
    domain_of:
    - MetricsOutput
    range: Comment
    required: false
    multivalued: false
  processing_application:
    name: processing_application
    description: The application used to process the dataset
    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core
    rank: 1000
    alias: processing_application
    owner: PSFBeadsOutput
    domain_of:
    - MetricsOutput
    range: string
    required: true
    multivalued: true
  processing_version:
    name: processing_version
    description: The version of the application used to process the dataset
    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core
    rank: 1000
    alias: processing_version
    owner: PSFBeadsOutput
    domain_of:
    - MetricsOutput
    range: string
    required: true
    multivalued: true
  processing_entity:
    name: processing_entity
    description: The entity that processed the dataset
    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core
    rank: 1000
    alias: processing_entity
    owner: PSFBeadsOutput
    domain_of:
    - MetricsOutput
    range: string
    required: false
    multivalued: true
  processing_datetime:
    name: processing_datetime
    description: The datetime of the processing by microscope-metrics
    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core
    rank: 1000
    alias: processing_datetime
    owner: PSFBeadsOutput
    domain_of:
    - MetricsOutput
    range: datetime
    required: true
    multivalued: false
  processing_log:
    name: processing_log
    description: The log of the processing by microscope-metrics
    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core
    rank: 1000
    alias: processing_log
    owner: PSFBeadsOutput
    domain_of:
    - MetricsOutput
    range: string
    required: false
    multivalued: false
  warnings:
    name: warnings
    description: The warnings of the processing by microscope-metrics
    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core
    rank: 1000
    alias: warnings
    owner: PSFBeadsOutput
    domain_of:
    - MetricsOutput
    range: string
    required: false
    multivalued: true
  errors:
    name: errors
    description: The errors of the processing by microscope-metrics
    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core
    rank: 1000
    alias: errors
    owner: PSFBeadsOutput
    domain_of:
    - MetricsOutput
    range: string
    required: false
    multivalued: true
  validated:
    name: validated
    description: Has the dataset been validated by a human
    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core
    rank: 1000
    ifabsent: 'False'
    alias: validated
    owner: PSFBeadsOutput
    domain_of:
    - MetricsOutput
    range: boolean
    required: true
    multivalued: false
  validation_datetime:
    name: validation_datetime
    description: The datetime of the validation
    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core
    rank: 1000
    alias: validation_datetime
    owner: PSFBeadsOutput
    domain_of:
    - MetricsOutput
    range: datetime
    required: false
    multivalued: false