Class: PSFBeadsInputParameters

URI: microscopemetrics_schema:PSFBeadsInputParameters

classDiagram class PSFBeadsInputParameters click PSFBeadsInputParameters href "../PSFBeadsInputParameters" MetricsInputParameters <|-- PSFBeadsInputParameters click MetricsInputParameters href "../MetricsInputParameters" PSFBeadsInputParameters : bit_depth PSFBeadsInputParameters : fitting_r2_threshold PSFBeadsInputParameters : intensity_robust_z_score_threshold PSFBeadsInputParameters : min_lateral_distance_factor PSFBeadsInputParameters : saturation_threshold PSFBeadsInputParameters : sigma_x PSFBeadsInputParameters : sigma_y PSFBeadsInputParameters : sigma_z PSFBeadsInputParameters : snr_threshold

Inheritance

MetricsInputParameters
- PSFBeadsInputParameters

Slots

Name	Cardinality and Range	Description	Inheritance
bit_depth	0..1 Integer	Detector bit depth	direct
saturation_threshold	0..1 Float	Tolerated saturation threshold	direct
min_lateral_distance_factor	1 Float	Minimal distance that has to separate laterally the beads represented as the ...	direct
sigma_z	1 Float	Gaussian smoothing sigma to be applied to the image in the Z axis prior to be...	direct
sigma_y	1 Float	Gaussian smoothing sigma to be applied to the image in teh Y axis prior to be...	direct
sigma_x	1 Float	Gaussian smoothing sigma to be applied to the image in the X axis prior to be...	direct
snr_threshold	1 Float	Signal to noise ratio threshold to be used for bead detection	direct
fitting_r2_threshold	1 Float	Threshold for the coefficient of determination (R^2) of the fit to be conside...	direct
intensity_robust_z_score_threshold	1 Float	Threshold for the robust z-score of the intensity of the bead to be considere...	direct

Usages

used by	used in	type	used
PSFBeadsDataset	input_parameters	range	PSFBeadsInputParameters

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: PSFBeadsInputParameters
from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
is_a: MetricsInputParameters
slots:
- bit_depth
- saturation_threshold
- min_lateral_distance_factor
- sigma_z
- sigma_y
- sigma_x
- snr_threshold
- fitting_r2_threshold
- intensity_robust_z_score_threshold
slot_usage:
  sigma_z:
    name: sigma_z
    description: Gaussian smoothing sigma to be applied to the image in the Z axis
      prior to bead detection. Does not apply to resolution measurements
    ifabsent: float(1.0)
    required: true
  sigma_y:
    name: sigma_y
    description: Gaussian smoothing sigma to be applied to the image in teh Y axis
      prior to bead detection. Does not apply to resolution measurements
    ifabsent: float(1.0)
    required: true
  sigma_x:
    name: sigma_x
    description: Gaussian smoothing sigma to be applied to the image in the X axis
      prior to bead detection. Does not apply to resolution measurements
    ifabsent: float(1.0)
    required: true

Induced

name: PSFBeadsInputParameters
from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
is_a: MetricsInputParameters
slot_usage:
  sigma_z:
    name: sigma_z
    description: Gaussian smoothing sigma to be applied to the image in the Z axis
      prior to bead detection. Does not apply to resolution measurements
    ifabsent: float(1.0)
    required: true
  sigma_y:
    name: sigma_y
    description: Gaussian smoothing sigma to be applied to the image in teh Y axis
      prior to bead detection. Does not apply to resolution measurements
    ifabsent: float(1.0)
    required: true
  sigma_x:
    name: sigma_x
    description: Gaussian smoothing sigma to be applied to the image in the X axis
      prior to bead detection. Does not apply to resolution measurements
    ifabsent: float(1.0)
    required: true
attributes:
  bit_depth:
    name: bit_depth
    description: Detector bit depth
    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
    rank: 1000
    alias: bit_depth
    owner: PSFBeadsInputParameters
    domain_of:
    - FieldIlluminationInputParameters
    - PSFBeadsInputParameters
    range: integer
    multivalued: false
    minimum_value: 1
    maximum_value: 64
  saturation_threshold:
    name: saturation_threshold
    description: Tolerated saturation threshold. If the amount of saturated pixels
      is above this threshold,  the image is considered as saturated and the analysis
      is not performed.
    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
    rank: 1000
    ifabsent: float(0.01)
    alias: saturation_threshold
    owner: PSFBeadsInputParameters
    domain_of:
    - FieldIlluminationInputParameters
    - PSFBeadsInputParameters
    range: float
    multivalued: false
    minimum_value: 0.0
    maximum_value: 1.0
  min_lateral_distance_factor:
    name: min_lateral_distance_factor
    description: Minimal distance that has to separate laterally the beads represented
      as the  number of times the FWHM of the beads.
    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
    rank: 1000
    ifabsent: float(20)
    alias: min_lateral_distance_factor
    owner: PSFBeadsInputParameters
    domain_of:
    - PSFBeadsInputParameters
    range: float
    required: true
    minimum_value: 10.0
    maximum_value: 30.0
  sigma_z:
    name: sigma_z
    description: Gaussian smoothing sigma to be applied to the image in the Z axis
      prior to bead detection. Does not apply to resolution measurements
    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
    rank: 1000
    ifabsent: float(1.0)
    alias: sigma_z
    owner: PSFBeadsInputParameters
    domain_of:
    - PSFBeadsInputParameters
    range: float
    required: true
  sigma_y:
    name: sigma_y
    description: Gaussian smoothing sigma to be applied to the image in teh Y axis
      prior to bead detection. Does not apply to resolution measurements
    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
    rank: 1000
    ifabsent: float(1.0)
    alias: sigma_y
    owner: PSFBeadsInputParameters
    domain_of:
    - PSFBeadsInputParameters
    range: float
    required: true
  sigma_x:
    name: sigma_x
    description: Gaussian smoothing sigma to be applied to the image in the X axis
      prior to bead detection. Does not apply to resolution measurements
    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
    rank: 1000
    ifabsent: float(1.0)
    alias: sigma_x
    owner: PSFBeadsInputParameters
    domain_of:
    - PSFBeadsInputParameters
    range: float
    required: true
  snr_threshold:
    name: snr_threshold
    description: Signal to noise ratio threshold to be used for bead detection.
    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
    rank: 1000
    ifabsent: float(10.0)
    alias: snr_threshold
    owner: PSFBeadsInputParameters
    domain_of:
    - PSFBeadsInputParameters
    range: float
    required: true
  fitting_r2_threshold:
    name: fitting_r2_threshold
    description: Threshold for the coefficient of determination (R^2) of the fit to
      be considered good.
    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
    rank: 1000
    ifabsent: float(0.85)
    alias: fitting_r2_threshold
    owner: PSFBeadsInputParameters
    domain_of:
    - PSFBeadsInputParameters
    range: float
    required: true
  intensity_robust_z_score_threshold:
    name: intensity_robust_z_score_threshold
    description: Threshold for the robust z-score of the intensity of the bead to
      be considered good.
    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
    rank: 1000
    ifabsent: float(2.0)
    alias: intensity_robust_z_score_threshold
    owner: PSFBeadsInputParameters
    domain_of:
    - PSFBeadsInputParameters
    range: float
    required: true