ecl-logo Documentation

Object[Analysis, CellCount]

Image analysis of microscope data to count the number of cells in a given image, calculate the confluency, i.e., the total area that is covered by cells, and find different morphological properties of segmented cells.

Organizational Information

    Name

    Name of this Object.
    Format: Single
    Class: String
    Programmatic Pattern: _String
    Pattern Description: A string.

    ID

    ID of this Object.
    Format: Single
    Class: String
    Programmatic Pattern: _String
    Pattern Description: The ID of this object.

    Object

    Object of this Object.
    Format: Single
    Class: Expression
    Programmatic Pattern: Object[Analysis, CellCount, _String]
    Pattern Description: The object reference of this object.

    Type

    Type of this Object.
    Format: Single
    Class: Expression
    Programmatic Pattern: Object[Analysis, CellCount]
    Pattern Description: Object[Analysis, CellCount]

    Notebook

    Notebook this object belongs to.
    Format: Single
    Class: Link
    Programmatic Pattern: _Link
    Pattern Description: An object of that matches ObjectP[Object[LaboratoryNotebook]].
    Relation: Object[LaboratoryNotebook][Objects]

    Author

    The person who ran the analysis.
    Format: Single
    Class: Link
    Programmatic Pattern: _Link
    Relation: Object[User]

General

Output Image

    AdjustedImage

    For each member of ReferenceImage, the image after performing all the adjustment steps.
    Format: Multiple
    Class: Link
    Programmatic Pattern: EmeraldCloudFileP
    Relation: Object[EmeraldCloudFile]

    HighlightedCells

    For each member of ReferenceImage, the final image that contains the original image and epilogs that highlight all of the segmented components.
    Format: Multiple
    Class: Link
    Programmatic Pattern: EmeraldCloudFileP
    Relation: Object[EmeraldCloudFile]

Counting Properties

    ImageComponents

    For each member of ReferenceImage, an array in which the image's pixels have been replaced by integer indices indicating connected components.
    Format: Multiple
    Class: Compressed
    Programmatic Pattern: _?(MatrixQ[#1, IntegerQ] && Max[Flatten[#1]] >= 0 & )

    Confluency

    For each member of ReferenceImage, the calculated percentange of the image covered by cells. If the image is fluoresent an a threshold is specified, the confluency of fluoresent cells will be returned.
    Format: Multiple
    Class: Real
    Unit: 1 percent
    Programmatic Pattern: RangeP[0 Percent, 100 Percent]

    NumberOfCells

    For each member of ReferenceImage, the estimated number of cells in the image based on the NumberOfComponents, MinCellRadius, and MaxCellRadius.
    Format: Multiple
    Class: Expression
    Programmatic Pattern: _?DistributionParameterQ

    NumberOfComponents

    For each member of ReferenceImage, the calculated number of connected components in the image. If the image is fluoresent an a threshold is specified, the number of fluoresent components will be returned.
    Format: Multiple
    Class: Real
    Programmatic Pattern: GreaterEqualP[0]

    AverageSingleCellArea

    For each member of ReferenceImage, the average size of a single cell in square pixels that is obtained from the values of MinCellRadius and MaxCellRadius options.
    Format: Multiple
    Class: Real
    Unit: 1 Pixels squared
    Programmatic Pattern: 2 Hold[GreaterEqualP[0 Pixel ]]

    CellViability

    For each member of ReferenceImage, the percentage of the live components in the image, i.e. the number of live cells divided by the total number of components times 100.
    Format: Multiple
    Class: Real
    Unit: 1 percent
    Programmatic Pattern: RangeP[0 Percent, 100 Percent]

Analysis & Reports

    SampleCellDensity

    For each member of ReferenceImage, the calculated number of cells in the sample well per ml.
    Format: Multiple
    Class: Real
    Unit: 1 reciprocal milliliter
    Programmatic Pattern: GreaterEqualP[0]

    ImageDataLookup

    For each member of ReferenceImage, a comprehensive lookup that contains microscope detailed specifications and also analysis results.
    Format: Multiple

    [ProtocolBatchNumber]

      Header: ProtocolBatchNumber
      Class: Integer

    [DateAcquired]

      Header: DateAcquired
      Class: Date

    [Mode]

      Header: Mode
      Class: Expression

    [ObjectiveMagnification]

      Header: ObjectiveMagnification
      Class: Real

    [ObjectiveNumericalAperture]

      Header: ObjectiveNumericalAperture
      Class: Real

    [Objective]

    [ImageTimepoint]

      Header: ImageTimepoint
      Class: Integer

    [ImageZStep]

      Header: ImageZStep
      Class: Integer

    [ImagingSite]

      Header: ImagingSite
      Class: Integer

    [ExcitationWavelength]

      Header: ExcitationWavelength
      Class: Real
      Unit: 1 nanometer

    [EmissionWavelength]

      Header: EmissionWavelength
      Class: Real
      Unit: 1 nanometer

    [DichroicFilterWavelength]

      Header: DichroicFilterWavelength
      Class: Real
      Unit: 1 nanometer

    [EmissionFilter]

    [DichroicFilter]

    [ExcitationPower]

      Header: ExcitationPower
      Class: Real
      Unit: 1 percent

    [TransmittedLightPower]

      Header: TransmittedLightPower
      Class: Real
      Unit: 1 percent

    [ExposureTime]

      Header: ExposureTime
      Class: Real
      Unit: 1 millisecond

    [FocalHeight]

      Header: FocalHeight
      Class: Real
      Unit: 1 micrometer

    [ImageSizeX]

      Header: ImageSizeX
      Class: Real
      Unit: 1 Pixels

    [ImageSizeY]

      Header: ImageSizeY
      Class: Real
      Unit: 1 Pixels

    [ImageScaleX]

      Header: ImageScaleX
      Class: Real
      Unit: 1 micrometer per Pixels

    [ImageScaleY]

      Header: ImageScaleY
      Class: Real
      Unit: 1 micrometer per Pixels

    [ImageBitDepth]

      Header: ImageBitDepth
      Class: Integer

    [PixelBinning]

      Header: PixelBinning
      Class: Integer

    [ImageCorrection]

      Header: ImageCorrection
      Class: Expression

    [StagePositionX]

      Header: StagePositionX
      Class: Real
      Unit: 1 micrometer

    [StagePositionY]

      Header: StagePositionY
      Class: Real
      Unit: 1 micrometer

    [ImagingSiteRow]

      Header: ImagingSiteRow
      Class: Integer

    [ImagingSiteColumn]

      Header: ImagingSiteColumn
      Class: Integer

    [ImagingSiteRowSpacing]

      Header: ImagingSiteRowSpacing
      Class: Real
      Unit: 1 micrometer

    [ImagingSiteColumnSpacing]

      Header: ImagingSiteColumnSpacing
      Class: Real
      Unit: 1 micrometer

    [WellCenterOffsetX]

      Header: WellCenterOffsetX
      Class: Real
      Unit: 1 micrometer

    [WellCenterOffsetY]

      Header: WellCenterOffsetY
      Class: Real
      Unit: 1 micrometer

    [AdjustedImage]

    [HighlightedCells]

    [ImageComponents]

      Header: ImageComponents
      Class: Compressed

    [Confluency]

      Header: Confluency
      Class: Real

    [NumberOfComponents]

      Header: NumberOfComponents
      Class: Real

    [ComponentAreaDistribution]

      Header: ComponentAreaDistribution
      Class: Expression

    [ComponentArea]

      Header: ComponentArea
      Class: Compressed

    [ComponentDiameterDistribution]

      Header: ComponentDiameterDistribution
      Class: Expression

    [ComponentDiameter]

      Header: ComponentDiameter
      Class: Compressed

    [ComponentCircularityDistribution]

      Header: ComponentCircularityDistribution
      Class: Expression

    [ComponentCircularity]

      Header: ComponentCircularity
      Class: Compressed

    [AreaProperties]

      Header: AreaProperties
      Class: Expression

    [PerimeterProperties]

      Header: PerimeterProperties
      Class: Expression

    [CentroidProperties]

      Header: CentroidProperties
      Class: Expression

    [BestfitEllipse]

      Header: BestfitEllipse
      Class: Expression

    [ShapeMeasurements]

      Header: ShapeMeasurements
      Class: Expression

    [BoundingboxProperties]

      Header: BoundingboxProperties
      Class: Expression

    [TopologicalProperties]

      Header: TopologicalProperties
      Class: Expression

    [ImageIntensity]

      Header: ImageIntensity
      Class: Expression

Morphological Properties

    ComponentAreaDistribution

    For each member of ReferenceImage, the distribution of the area of each connected component in the image (in pixels squared or micrometer squared).
    Format: Multiple
    Class: Expression
    Programmatic Pattern: _?DistributionParameterQ

    ComponentArea

    For each member of ReferenceImage, the areas of each connected component in the image (in pixels squared or micrometer squared).
    Format: Multiple
    Class: Compressed
    Programmatic Pattern: 2 2 Hold[{(GreaterEqualP[0 Pixel ] | GreaterEqualP[0 Micrometer ])..}]

    ComponentCircularity Distribution

    For each member of ReferenceImage, the distribution of the circularity of the connected component in the image. A measure of how circular the cell is, with 1 being an ideal circle and 0 a line.
    Format: Multiple
    Class: Expression
    Programmatic Pattern: _?DistributionParameterQ

    ComponentCircularity

    For each member of ReferenceImage, the circularity of each connected component in the image. A measure of how circular the cell is, with 1 being an ideal circle and 0 a line.
    Format: Multiple
    Class: Compressed
    Programmatic Pattern: {GreaterEqualP[0]..}

    ComponentDiameterDistribution

    For each member of ReferenceImage, the distribution of the diameter of the connected component in the image (in pixelsor micrometer).
    Format: Multiple
    Class: Expression
    Programmatic Pattern: _?DistributionParameterQ

    ComponentDiameter

    For each member of ReferenceImage, the diameter for each connected component in the image (in pixels or micrometer).
    Format: Multiple
    Class: Compressed
    Programmatic Pattern: {(GreaterEqualP[0 Pixel] | GreaterEqualP[0 Micrometer])..}

    ComponentCentroid

    For each member of ReferenceImage, the centroid for each connected component in the image (in pixels).
    Format: Multiple
    Class: Compressed
    Programmatic Pattern: {{GreaterEqualP[0], GreaterEqualP[0]}..}

Component Properties

    AreaProperties

    For each member of ReferenceImage, the area measurement properties for all counted components, which includes PixelCount, Area, FilledPixelCount, EquivalentDiskRadius, and AreaRadiusCoverage.
    Format: Multiple
    Class: Expression
    Programmatic Pattern: {AreaMeasurementAssociationP..}

    PerimeterProperties

    For each member of ReferenceImage, the perimeter properties for all counted components, which includes AuthalicRadius, MaxPerimeterDistance, OuterPerimeterCount, PerimeterCount, PerimeterLength, PerimeterPositions, and PolygonalLength.
    Format: Multiple
    Class: Expression
    Programmatic Pattern: {PerimeterPropertiesAssociationP..}

    CentroidProperties

    For each member of ReferenceImage, the centroid properties for all counted components, which includes Centroid, Medoid, MeanCentroidDistance, MaxCentroidDistance, and MinCentroidDistance.
    Format: Multiple
    Class: Expression
    Programmatic Pattern: {CentroidPropertiesAssociationP..}

    BestfitEllipse

    For each member of ReferenceImage, the best-fit ellipse properties for all counted components, which includes Length, Width, SemiAxes, Orientation, Elongation, and Eccentricity.
    Format: Multiple
    Class: Expression
    Programmatic Pattern: {BestfitEllipseAssociationP..}

    ShapeMeasurements

    For each member of ReferenceImage, the shape measurements properties for all counted components, which includes Circularity, FilledCircularity, and Rectangularity.
    Format: Multiple
    Class: Expression
    Programmatic Pattern: {ShapeMeasurementsAssociationP..}

    BoundingboxProperties

    For each member of ReferenceImage, the bounding-box properties for all counted components, which includes Length, Width, SemiAxes, Orientation, Elongation, and Eccentricity.
    Format: Multiple
    Class: Expression
    Programmatic Pattern: {BoundingboxPropertiesAssociationP..}

    TopologicalProperties

    For each member of ReferenceImage, the topological properties for all counted components, which includes Fragmentation, Holes, Complexity, EulerNumber, EmbeddedComponents, EmbeddedComponentCount, EnclosingComponents, and EnclosingComponentCount.
    Format: Multiple
    Class: Expression
    Programmatic Pattern: {TopologicalPropertiesAssociationP..}

    ImageIntensity

    For each member of ReferenceImage, the image intensity properties for all counted components, which includes MinIntensity, MaxIntensity, MeanIntensity, MedianIntensity, StandardDeviationIntensity, TotalIntensity, Skew, and IntensityCentroid.
    Format: Multiple
    Class: Expression
    Programmatic Pattern: {ImageIntensityAssociationP..}
Last modified on Mon 26 Sep 2022 15:43:43
EMERALD CLOUD LAB
15500 Wells Port Drive
Austin, TX 78728
© 2023 Emerald Cloud Lab, Inc.