Class: ArgolightBInput

URI: microscopemetrics_schema:ArgolightBInput

classDiagram class ArgolightBInput MetricsInput <|-- ArgolightBInput ArgolightBInput : argolight_b_image ArgolightBInput --|> ImageAsNumpy : argolight_b_image ArgolightBInput : bit_depth ArgolightBInput : lower_threshold_correction_factors ArgolightBInput : remove_center_cross ArgolightBInput : saturation_threshold ArgolightBInput : sigma_x ArgolightBInput : sigma_y ArgolightBInput : sigma_z ArgolightBInput : spots_distance ArgolightBInput : upper_threshold_correction_factors

Inheritance

MetricsInput
- ArgolightBInput

Slots

Name	Cardinality and Range	Description	Inheritance
argolight_b_image	1..1 ImageAsNumpy	Input parameter: image of the argolight b pattern provided as a 5D numpy arra...	direct
bit_depth	0..1 Integer	Detector bit depth	direct
saturation_threshold	1..1 Float	Tolerated saturation threshold	direct
spots_distance	1..1 Float	Input parameter: distance between argolight spots	direct
sigma_z	1..1 Float	Input parameter: smoothing factor for objects detection in the Z axis	direct
sigma_y	1..1 Float	Input parameter: smoothing factor for objects detection in the Y axis	direct
sigma_x	1..1 Float	Input parameter: smoothing factor for objects detection in the X axis	direct
lower_threshold_correction_factors	0..* Float	Input parameter: correction factor for the lower thresholds	direct
upper_threshold_correction_factors	0..* Float	Input parameter: correction factor for the upper thresholds	direct
remove_center_cross	0..1 Boolean	Input parameter: remove the center cross found in some Argolight patterns	direct

Usages

used by	used in	type	used
ArgolightBDataset	input	range	ArgolightBInput

Identifier and Mapping Information

Schema Source

from schema: https://w3id.org/MontpellierRessourcesImagerie/microscopemetrics-schema

Mappings

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

LinkML Source

Direct

name: ArgolightBInput
from_schema: https://w3id.org/MontpellierRessourcesImagerie/microscopemetrics-schema
is_a: MetricsInput
slots:
- argolight_b_image
- bit_depth
- saturation_threshold
- spots_distance
- sigma_z
- sigma_y
- sigma_x
- lower_threshold_correction_factors
- upper_threshold_correction_factors
- remove_center_cross
slot_usage:
  saturation_threshold:
    name: saturation_threshold
    domain_of:
    - ArgolightBInput
    - ArgolightEInput
    - FieldIlluminationInput
    required: true

Induced

name: ArgolightBInput
from_schema: https://w3id.org/MontpellierRessourcesImagerie/microscopemetrics-schema
is_a: MetricsInput
slot_usage:
  saturation_threshold:
    name: saturation_threshold
    domain_of:
    - ArgolightBInput
    - ArgolightEInput
    - FieldIlluminationInput
    required: true
attributes:
  argolight_b_image:
    name: argolight_b_image
    description: 'Input parameter: image of the argolight b pattern provided as a
      5D numpy array in the order TZYXC'
    from_schema: https://w3id.org/MontpellierRessourcesImagerie/microscopemetrics-schema
    rank: 1000
    multivalued: false
    alias: argolight_b_image
    owner: ArgolightBInput
    domain_of:
    - ArgolightBInput
    range: ImageAsNumpy
    required: true
    inlined: true
  bit_depth:
    name: bit_depth
    description: Detector bit depth
    from_schema: https://w3id.org/MontpellierRessourcesImagerie/microscopemetrics-schema
    rank: 1000
    multivalued: false
    alias: bit_depth
    owner: ArgolightBInput
    domain_of:
    - ArgolightBInput
    - ArgolightEInput
    - FieldIlluminationInput
    range: integer
    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://w3id.org/MontpellierRessourcesImagerie/microscopemetrics-schema
    rank: 1000
    multivalued: false
    ifabsent: float(0.01)
    alias: saturation_threshold
    owner: ArgolightBInput
    domain_of:
    - ArgolightBInput
    - ArgolightEInput
    - FieldIlluminationInput
    range: float
    required: true
    minimum_value: 0
    maximum_value: 1
  spots_distance:
    name: spots_distance
    description: 'Input parameter: distance between argolight spots'
    from_schema: https://w3id.org/MontpellierRessourcesImagerie/microscopemetrics-schema
    rank: 1000
    multivalued: false
    alias: spots_distance
    owner: ArgolightBInput
    domain_of:
    - ArgolightBInput
    range: float
    required: true
  sigma_z:
    name: sigma_z
    description: 'Input parameter: smoothing factor for objects detection in the Z
      axis'
    from_schema: https://w3id.org/MontpellierRessourcesImagerie/microscopemetrics-schema
    rank: 1000
    multivalued: false
    ifabsent: float(1.0)
    alias: sigma_z
    owner: ArgolightBInput
    domain_of:
    - ArgolightBInput
    range: float
    required: true
    minimum_value: 0
    maximum_value: 5
  sigma_y:
    name: sigma_y
    description: 'Input parameter: smoothing factor for objects detection in the Y
      axis'
    from_schema: https://w3id.org/MontpellierRessourcesImagerie/microscopemetrics-schema
    rank: 1000
    multivalued: false
    ifabsent: float(3.0)
    alias: sigma_y
    owner: ArgolightBInput
    domain_of:
    - ArgolightBInput
    range: float
    required: true
    minimum_value: 0
    maximum_value: 10
  sigma_x:
    name: sigma_x
    description: 'Input parameter: smoothing factor for objects detection in the X
      axis'
    from_schema: https://w3id.org/MontpellierRessourcesImagerie/microscopemetrics-schema
    rank: 1000
    multivalued: false
    ifabsent: float(3.0)
    alias: sigma_x
    owner: ArgolightBInput
    domain_of:
    - ArgolightBInput
    range: float
    required: true
    minimum_value: 0
    maximum_value: 10
  lower_threshold_correction_factors:
    name: lower_threshold_correction_factors
    description: 'Input parameter: correction factor for the lower thresholds.  Must
      be a tuple with len = nr of channels or a float if all equal'
    from_schema: https://w3id.org/MontpellierRessourcesImagerie/microscopemetrics-schema
    rank: 1000
    multivalued: true
    alias: lower_threshold_correction_factors
    owner: ArgolightBInput
    domain_of:
    - ArgolightBInput
    range: float
    required: false
  upper_threshold_correction_factors:
    name: upper_threshold_correction_factors
    description: 'Input parameter: correction factor for the upper thresholds. Must
      be a tuple with len = nr of channels or a float if all equal'
    from_schema: https://w3id.org/MontpellierRessourcesImagerie/microscopemetrics-schema
    rank: 1000
    multivalued: true
    alias: upper_threshold_correction_factors
    owner: ArgolightBInput
    domain_of:
    - ArgolightBInput
    range: float
    required: false
  remove_center_cross:
    name: remove_center_cross
    description: 'Input parameter: remove the center cross found in some Argolight
      patterns'
    from_schema: https://w3id.org/MontpellierRessourcesImagerie/microscopemetrics-schema
    rank: 1000
    multivalued: false
    ifabsent: 'False'
    alias: remove_center_cross
    owner: ArgolightBInput
    domain_of:
    - ArgolightBInput
    range: boolean
    required: false