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ExperimentPickColonies

ExperimentPickColonies[Objects]⟹Protocol

creates a Protocol to pick colonies from the provided sample or container Objects and deposit them into a destination container.

    
Pick Colonies allows for the isolation of microbial colonies growing on top of a solid medium to duplicate them for further use. The colonies are picked with a thin needle and then transferred to a desired media. The picked colonies can either be placed onto solid or liquid media and then grown and use for further analysis.
    

Experimental Principles

    Figure 1.1: Procedural Overview of a PickColonies experiment using a QPix 420 HT Colony Picker. Step 1: Samples are imaged using the CCD camera on the instrument. Step 2: The images are analyzed by the function AnalyzeColonies in order to find the locations of the colonies on the plates. Step 3: The selected colonies are picked by the QPix 420 HT colony picking tool. Step 4: The picked colonies are placed on the desired media. Step 5: The colony picking tool is washed in sanitization solution. Step 6: The colony picking tool is dried by a fan.
    Figure 1.2: Overview of the preferred inputs and outputs of a PickColonies experiment.

Instrumentation

    QPix 420 HT

    Figure 2.1.1: Overview of the ColonyHandler WorkCell. This figure provides a comprehensive view of the ColonyHandler, showcasing its layout and main components. The QPix instrument is designed to perform multiple tasks including imaging solid media plates, picking colonies from solid media, and plating suspended colonies onto solid media. Its bed features a deck with designated positions for multi-well and single-well SBS plates, a light table, and wash baths for cleaning the pins before and during the process. Above the deck, a robotic gantry moves and is equipped with several components: a pipette nozzle, an LED-based light source, preset filter pairs for fluorescence excitation and emission wavelengths, a monochrome CCD camera, and a position to accept a ColonyHandlerHeadCassette. The robotic gantry moves seamlessly between tasks, and have the capacity to capture multiple types of images.

Diameter

    diameterRules

    Key/value pairs that define a set of colonies into a population based on their diameter.
    Pattern: {_Rule..}

    Characterization

    Select

    The method used to group colonies into a population. Colonies are first ordered by their Diameter, defined as the diameter of a colony is the diameter of a disk with the same area as the colony. If the Select option is Min or Max, the ordered colonies are divided into partitions based on the NumberOfDivisions. From there, the smallest or largest partition is grouped into a population depending on if the Select option is Min or Max. For example, if the Select option is set to Max and the NumberOfDivisions is 10, the colonies will be divided into 10 partitions sorted from smallest to largest and the partition with the largest colonies will be selected as the population. Alternatively, if the Select option is AboveThreshold or BelowThreshold, an absolute cutoff is used to group ordered colonies into a population. The threshold is set by the ThresholdDiameter option. For example, if the Select option is BelowThreshold and the ThresholdDiameter is 0.8 Millimeter, all colonies smaller than 0.8 Millimeter in Diameter are grouped into a population.
    Default Value: Automatic
    Default Calculation: If the Threshold is specified, set to AboveThreshold, otherwise set to Max.
    Pattern Description: Min, Max, AboveThreshold, or BelowThreshold.
    Programmatic Pattern: (Min | Max | AboveThreshold | BelowThreshold) | Automatic

    ThresholdDiameter

    The min or max possible diameter for a colony to be included in the population. When the Select option is AboveThreshold or BelowThreshold, all colonies with a diameter larger or smaller than the ThresholdDiameter, respectively, are grouped into a population. The colony diameter is defined as the diameter of a disk with the same area as the colony.
    Default Value: Null
    Pattern Description: Greater than or equal to 0.2 millimeters and less than or equal to 10 millimeters or Null.
    Programmatic Pattern: RangeP[$QPixMinDiameter, 10*Millimeter] | Null

    NumberOfColonies

    The upper limit for the count of colonies in the population.
    Default Value: Automatic
    Default Calculation: If Select is Min or Max, up to 10 colonies are selected, otherwise All colonies are selected.
    Pattern Description: All or greater than or equal to 2 in increments of 1 or Null.
    Programmatic Pattern: ((GreaterEqualP[2, 1] | All) | Automatic) | Null

    NumberOfDivisions

    The number of partitions to group colonies into. Partitions are ordered by the Unit Operation feature. If the Select option is Min or Max, the lowest or highest partition will be used, respectively.
    Default Value: Automatic
    Default Calculation: If Select is Min or Max, set to 2.
    Pattern Description: Greater than or equal to 2 in increments of 1 or Null.
    Programmatic Pattern: (GreaterEqualP[2, 1] | Automatic) | Null

    PopulationName

    The name used to reference the population of colonies.
    Default Value: Automatic
    Default Calculation: By default, each population is labeled as ColonySelection with sequential integers.
    Pattern Description: A string.
    Programmatic Pattern: _String | Automatic

    Include

    Coordinates of colonies included in the selection even if they do not match the selection criteria.
    Default Value: {}
    Pattern Description: {} or list of one or more {X, Y} entries or None.
    Programmatic Pattern: {{GreaterP[0*Millimeter], GreaterP[0*Millimeter]}..} | None

    Exclude

    Coordinates of colonies excluded from the selection even if they match the selection criteria.
    Default Value: {}
    Pattern Description: {} or list of one or more {X, Y} entries or None or Null.
    Programmatic Pattern: ({{GreaterP[0*Millimeter], GreaterP[0*Millimeter]}..} | None) | Null

Isolation

    isolationRules

    Key/value pairs that define a set of colonies into a population based on their isolation.
    Pattern: {_Rule..}

    Characterization

    Select

    The method used to group colonies into a population. Colonies are first ordered by their Isolation, the shortest distance from the boundary of the colony to the boundary of another. If the Select option is Min or Max, the ordered colonies are divided into partitions based on the NumberOfDivisions. From there, the least isolated or most isolated partition is grouped into a population depending on if the Select option is Min or Max. For example, if the Select option is set to Max and the NumberOfDivisions is 10, the colonies will be divided into 10 partitions sorted from least isolated to most isolated and the partition with the most isolated colonies will be selected as the population. Alternatively, if the Select option is AboveThreshold or BelowThreshold, an absolute cutoff is used to group ordered colonies into a population. The threshold is set by the ThresholdDistance option. For example, if the Select option is AboveThreshold and the ThresholdDistance is 1 Millimeter, all colonies with separation greater than 1 Millimeter are grouped into a population.
    Default Value: Automatic
    Default Calculation: If the Threshold is specified, set to AboveThreshold, otherwise set to Max.
    Pattern Description: Min, Max, AboveThreshold, or BelowThreshold.
    Programmatic Pattern: (Min | Max | AboveThreshold | BelowThreshold) | Automatic

    ThresholdDistance

    The min or max possible isolation for a colony to be included in the population. When the Select option is AboveThreshold or BelowThreshold, all colonies with an isolation distance larger or smaller than the ThresholdDistance, respectively, are grouped into a population. The isolation is the shortest distance from the boundary of the colony to the boundary of another.
    Default Value: Null
    Pattern Description: Greater than or equal to 0 millimeters or Null.
    Programmatic Pattern: GreaterEqualP[0*Millimeter] | Null

    NumberOfColonies

    The upper limit for the count of colonies in the population.
    Default Value: Automatic
    Default Calculation: If Select is Min or Max, up to 10 colonies are selected, otherwise All colonies are selected.
    Pattern Description: All or greater than or equal to 2 in increments of 1 or Null.
    Programmatic Pattern: ((GreaterEqualP[2, 1] | All) | Automatic) | Null

    NumberOfDivisions

    The number of partitions to group colonies into. Partitions are ordered by the Unit Operation feature. If the Select option is Min or Max, the lowest or highest partition will be used, respectively.
    Default Value: Automatic
    Default Calculation: If Select is Min or Max, set to 2.
    Pattern Description: Greater than or equal to 2 in increments of 1 or Null.
    Programmatic Pattern: (GreaterEqualP[2, 1] | Automatic) | Null

    PopulationName

    The name used to reference the population of colonies.
    Default Value: Automatic
    Default Calculation: By default, each population is labeled as ColonySelection with sequential integers.
    Pattern Description: A string.
    Programmatic Pattern: _String | Automatic

    Include

    Coordinates of colonies included in the selection even if they do not match the selection criteria.
    Default Value: {}
    Pattern Description: {} or list of one or more {X, Y} entries or None.
    Programmatic Pattern: {{GreaterP[0*Millimeter], GreaterP[0*Millimeter]}..} | None

    Exclude

    Coordinates of colonies excluded from the selection even if they match the selection criteria.
    Default Value: {}
    Pattern Description: {} or list of one or more {X, Y} entries or None or Null.
    Programmatic Pattern: ({{GreaterP[0*Millimeter], GreaterP[0*Millimeter]}..} | None) | Null

Circularity

    circularityRules

    Key/value pairs that define a set of colonies into a population based on their circularity.
    Pattern: {_Rule..}

    Characterization

    Select

    The method used to group colonies into a population. Colonies are first ordered by their Circularity, the ratio of the minor axis to the major axis of the best fit ellipse. If the Select option is Min or Max, the ordered colonies are divided into partitions based on the NumberOfDivisions. From there, the least circular or most circular partition is grouped into a population depending on if the Select option is Min or Max. For example, if the Select option is set to Max and the NumberOfDivisions is 10, the colonies will be divided into 10 partitions sorted from least circular to most circular and the partition with the most circular colonies will be selected as the population. Alternatively, if the Select option is AboveThreshold or BelowThreshold, an absolute cutoff is used to group ordered colonies into a population. The threshold is set by the ThresholdCircularity option. For example, if the Select option is AboveThreshold and the ThresholdCircularity is 0.9, all colonies with a circularity ratio greater than 0.9 are grouped into a population.
    Default Value: Automatic
    Default Calculation: If the Threshold is specified, set to AboveThreshold, otherwise set to Max.
    Pattern Description: Min, Max, AboveThreshold, or BelowThreshold.
    Programmatic Pattern: (Min | Max | AboveThreshold | BelowThreshold) | Automatic

    ThresholdCircularity

    The min or max possible circularity ratio for a colony to be included in the population. When the Select option is AboveThreshold or BelowThreshold, all colonies with a circularity ratio larger or smaller than the ThresholdCircularity, respectively, are grouped into a population. The colony circularity ratio is the ratio of the minor axis to the major axis of the best fit ellipse.
    Default Value: Null
    Pattern Description: Greater than or equal to 0 and less than or equal to 1 or Null.
    Programmatic Pattern: RangeP[0, 1] | Null

    NumberOfColonies

    The upper limit for the count of colonies in the population.
    Default Value: Automatic
    Default Calculation: If Select is Min or Max, up to 10 colonies are selected, otherwise All colonies are selected.
    Pattern Description: All or greater than or equal to 2 in increments of 1 or Null.
    Programmatic Pattern: ((GreaterEqualP[2, 1] | All) | Automatic) | Null

    NumberOfDivisions

    The number of partitions to group colonies into. Partitions are ordered by the Unit Operation feature. If the Select option is Min or Max, the lowest or highest partition will be used, respectively.
    Default Value: Automatic
    Default Calculation: If Select is Min or Max, set to 2.
    Pattern Description: Greater than or equal to 2 in increments of 1 or Null.
    Programmatic Pattern: (GreaterEqualP[2, 1] | Automatic) | Null

    PopulationName

    The name used to reference the population of colonies.
    Default Value: Automatic
    Default Calculation: By default, each population is labeled as ColonySelection with sequential integers.
    Pattern Description: A string.
    Programmatic Pattern: _String | Automatic

    Include

    Coordinates of colonies included in the selection even if they do not match the selection criteria.
    Default Value: {}
    Pattern Description: {} or list of one or more {X, Y} entries or None.
    Programmatic Pattern: {{GreaterP[0*Millimeter], GreaterP[0*Millimeter]}..} | None

    Exclude

    Coordinates of colonies excluded from the selection even if they match the selection criteria.
    Default Value: {}
    Pattern Description: {} or list of one or more {X, Y} entries or None or Null.
    Programmatic Pattern: ({{GreaterP[0*Millimeter], GreaterP[0*Millimeter]}..} | None) | Null

Regularity

    regularityRules

    Key/value pairs that define a set of colonies into a population based on their regularity.
    Pattern: {_Rule..}

    Characterization

    Select

    The method used to group colonies into a population. Colonies are first ordered by their Regularity, the ratio of the area of the colony to the area of a circle with the same perimeter. If the Select option is Min or Max, the ordered colonies are divided into partitions based on the NumberOfDivisions. From there, the least regular or most regular partition is grouped into a population depending on if the Select option is Min or Max. For example, if the Select option is set to Max and the NumberOfDivisions is 10, the colonies will be divided into 10 partitions sorted from least regular to most regular and the partition with the most regular colonies will be selected as the population. Alternatively, if the Select option is AboveThreshold or BelowThreshold, an absolute cutoff is used to group ordered colonies into a population. The threshold is set by the ThresholdRegularity option. For example, if the Select option is AboveThreshold and the ThresholdRegularity is 0.9, all colonies with a regularity ratio greater than 0.9 are grouped into a population.
    Default Value: Automatic
    Default Calculation: If the Threshold is specified, set to AboveThreshold, otherwise set to Max.
    Pattern Description: Min, Max, AboveThreshold, or BelowThreshold.
    Programmatic Pattern: (Min | Max | AboveThreshold | BelowThreshold) | Automatic

    ThresholdRegularity

    The min or max possible regularity ratio for a colony to be included in the population. When the Select option is AboveThreshold or BelowThreshold, all colonies with a regularity ratio larger or smaller than the ThresholdRegularity, respectively, are grouped into a population. The colony regularity ratio is the ratio of the area of the colony to the area of a circle with the same perimeter.
    Default Value: Null
    Pattern Description: Greater than or equal to 0 and less than or equal to 1 or Null.
    Programmatic Pattern: RangeP[0, 1] | Null

    NumberOfColonies

    The upper limit for the count of colonies in the population.
    Default Value: Automatic
    Default Calculation: If Select is Min or Max, up to 10 colonies are selected, otherwise All colonies are selected.
    Pattern Description: All or greater than or equal to 2 in increments of 1 or Null.
    Programmatic Pattern: ((GreaterEqualP[2, 1] | All) | Automatic) | Null

    NumberOfDivisions

    The number of partitions to group colonies into. Partitions are ordered by the Unit Operation feature. If the Select option is Min or Max, the lowest or highest partition will be used, respectively.
    Default Value: Automatic
    Default Calculation: If Select is Min or Max, set to 2.
    Pattern Description: Greater than or equal to 2 in increments of 1 or Null.
    Programmatic Pattern: (GreaterEqualP[2, 1] | Automatic) | Null

    PopulationName

    The name used to reference the population of colonies.
    Default Value: Automatic
    Default Calculation: By default, each population is labeled as ColonySelection with sequential integers.
    Pattern Description: A string.
    Programmatic Pattern: _String | Automatic

    Include

    Coordinates of colonies included in the selection even if they do not match the selection criteria.
    Default Value: {}
    Pattern Description: {} or list of one or more {X, Y} entries or None.
    Programmatic Pattern: {{GreaterP[0*Millimeter], GreaterP[0*Millimeter]}..} | None

    Exclude

    Coordinates of colonies excluded from the selection even if they match the selection criteria.
    Default Value: {}
    Pattern Description: {} or list of one or more {X, Y} entries or None or Null.
    Programmatic Pattern: ({{GreaterP[0*Millimeter], GreaterP[0*Millimeter]}..} | None) | Null

Fluorescence

    fluorescenceRules

    Key/value pairs that define a set of colonies into a population based on their fluorescence.
    Pattern: {_Rule..}

    Characterization

    Dye

    The fluorophore used to detect colonies that fluoresce at an EmissionWavelength when exposed to an ExcitationWavelength.
    Default Value: Automatic
    Default Calculation: Automatically set to the fluorophore within the excitation/emission range. For VioletFluorescence, set to DAPI. For GreenFluorescence, set to GFP. For OrangeFluorescence, set to Cy3. For RedFluorescence, set to TxRed. For DarkRedFluorescence, set to Cy5.
    Pattern Description: DAPI, UltraViolet, GFP, RGBColor[0, 0, 1], Cy3, TxRed, Cy5, or RGBColor[1, 0, 0]
    Programmatic Pattern: (DAPI | UltraViolet | GFP | Blue | Cy3 | TxRed | Cy5 | Red) | Automatic

    ExcitationWavelength

    The wavelength of light that adds energy to colonies and causes them to fluoresce. Pairs with an EmissionWavelength.
    Default Value: Automatic
    Default Calculation: Automatically set to the excitation wavelength specified in the FluorescentExcitationWavelength field of model cell in CellTypes.
    Pattern Description: 377 nanometers, 457 nanometers, 531 nanometers, or 628 nanometers.
    Programmatic Pattern: (377*Nanometer | 457*Nanometer | 531*Nanometer | 628*Nanometer) | Automatic

    EmissionWavelength

    The light that the instrument measures to detect colonies fluorescing at a particular wavelength. Pairs with an ExcitationWavelength.
    Default Value: Automatic
    Default Calculation: Automatically set to the emission wavelength specified in the FluorescentEmissionWavelength field of model cell in CellTypes.
    Pattern Description: 447 nanometers, 536 nanometers, 593 nanometers, 624 nanometers, or 692 nanometers.
    Programmatic Pattern: (447*Nanometer | 536*Nanometer | 593*Nanometer | 624*Nanometer | 692*Nanometer) | Automatic

    Select

    The method used to group colonies into a population. Colonies are first ordered by their Fluorescence, the average pixel value inside the colony boundary from an image generated using an excitation wavelength and emission filter. If the Select option is Min or Max, the ordered colonies are divided into partitions based on the NumberOfDivisions. From there, the least fluorescing or most fluorescing partition is grouped into a population depending on if the Select option is Min or Max. For example, if the Select option is set to Max and the NumberOfDivisions is 10, the colonies will be divided into 10 partitions sorted from least fluorescing to most fluorescing and the most fluorescing partition will be selected as the population. Alternatively, if the Select option is Positive or Negative, the ordered colonies are first clustered into two groups based on their Fluorescence above or below background intensity. Then, if the Select option is Positive, the group with the higher fluorescing values is selected as the population. However, if the Select option is Negative, the group without fluorescence values are chosen as the population.
    Default Value: Automatic
    Default Calculation: If the NumberOfDivisions is specified, set to Max, otherwise set to Positive.
    Pattern Description: Min, Max, Positive, or Negative.
    Programmatic Pattern: (Min | Max | Positive | Negative) | Automatic

    NumberOfColonies

    The upper limit for the count of colonies in the population.
    Default Value: Automatic
    Default Calculation: If Select is Min or Max, up to 10 colonies are selected, otherwise All colonies are selected.
    Pattern Description: All or greater than or equal to 2 in increments of 1 or Null.
    Programmatic Pattern: ((GreaterEqualP[2, 1] | All) | Automatic) | Null

    NumberOfDivisions

    The number of partitions to group colonies into. Partitions are ordered by the Unit Operation feature. If the Select option is Min or Max, the lowest or highest partition will be used, respectively.
    Default Value: Automatic
    Default Calculation: If Select is Min or Max, set to 2.
    Pattern Description: Greater than or equal to 2 in increments of 1 or Null.
    Programmatic Pattern: (GreaterEqualP[2, 1] | Automatic) | Null

    PopulationName

    The name used to reference the population of colonies.
    Default Value: Automatic
    Default Calculation: By default, each population is labeled as ColonySelection with sequential integers.
    Pattern Description: A string.
    Programmatic Pattern: _String | Automatic

    Include

    Coordinates of colonies included in the selection even if they do not match the selection criteria.
    Default Value: {}
    Pattern Description: {} or list of one or more {X, Y} entries or None.
    Programmatic Pattern: {{GreaterP[0*Millimeter], GreaterP[0*Millimeter]}..} | None

    Exclude

    Coordinates of colonies excluded from the selection even if they match the selection criteria.
    Default Value: {}
    Pattern Description: {} or list of one or more {X, Y} entries or None or Null.
    Programmatic Pattern: ({{GreaterP[0*Millimeter], GreaterP[0*Millimeter]}..} | None) | Null

BlueWhiteScreen

    blueWhiteScreenRules

    Key/value pairs that define a set of colonies into a population based on their BlueWhiteScreen feature.
    Pattern: {_Rule..}

    Characterization

    Color

    The color to block with the absorbance filter which is inserted between the light source and the sample. Default to blue to eliminate blue colonies from the image, even when the colonies are newly formed and appear powder blue.
    Default Value: RGBColor[0, 0, 1]
    Pattern Description: RGBColor[0, 0, 1]
    Programmatic Pattern: Blue

    FilterWavelength

    The mean wavelength of light blocked by the absorbance filter. Blue colonies, which have a wavelength around 450 nanometers, appear darker.
    Default Value: 400 nanometers
    Pattern Description: 400 nanometers.
    Programmatic Pattern: 400*Nanometer

    Select

    The method used to group colonies into a population. Colonies are first ordered by their intensities from BlueWhiteScreen images, the average pixel value inside the colony boundary from an image generated using an absorbance filter. If the Select option is Positive or Negative, the ordered colonies are first clustered into two groups based on their Absorbance. Then, if the Select option is Positive, the group with the higher brightness is selected as the population, and in this case white colonies. However, if the Select option is Negative, the group with the lower brightness values are chosen as the population, and in this case blue colonies. Alternatively, if the Select option is Min or Max, the ordered colonies are divided into partitions based on the NumberOfDivisions. From there, the least bright or most bright partition is grouped into a population depending on if the Select option is Min or Max. For example, if the Select option is set to Max and the NumberOfDivisions is 10, the colonies will be divided into 10 partitions sorted from least bright to most bright and the most bright partition will be selected as the population.
    Default Value: Automatic
    Default Calculation: If the NumberOfDivisions is specified, set to Max, otherwise set to Positive.
    Pattern Description: Min, Max, Positive, or Negative.
    Programmatic Pattern: (Min | Max | Positive | Negative) | Automatic

    NumberOfColonies

    The upper limit for the count of colonies in the population.
    Default Value: Automatic
    Default Calculation: If Select is Min or Max, up to 10 colonies are selected, otherwise All colonies are selected.
    Pattern Description: All or greater than or equal to 2 in increments of 1 or Null.
    Programmatic Pattern: ((GreaterEqualP[2, 1] | All) | Automatic) | Null

    NumberOfDivisions

    The number of partitions to group colonies into. Partitions are ordered by the Unit Operation feature. If the Select option is Min or Max, the lowest or highest partition will be used, respectively.
    Default Value: Automatic
    Default Calculation: If Select is Min or Max, set to 2.
    Pattern Description: Greater than or equal to 2 in increments of 1 or Null.
    Programmatic Pattern: (GreaterEqualP[2, 1] | Automatic) | Null

    PopulationName

    The name used to reference the population of colonies.
    Default Value: Automatic
    Default Calculation: By default, each population is labeled as ColonySelection with sequential integers.
    Pattern Description: A string.
    Programmatic Pattern: _String | Automatic

    Include

    Coordinates of colonies included in the selection even if they do not match the selection criteria.
    Default Value: {}
    Pattern Description: {} or list of one or more {X, Y} entries or None.
    Programmatic Pattern: {{GreaterP[0*Millimeter], GreaterP[0*Millimeter]}..} | None

    Exclude

    Coordinates of colonies excluded from the selection even if they match the selection criteria.
    Default Value: {}
    Pattern Description: {} or list of one or more {X, Y} entries or None or Null.
    Programmatic Pattern: ({{GreaterP[0*Millimeter], GreaterP[0*Millimeter]}..} | None) | Null

AllColonies

    allColoniesRules

    Key/value pairs that define a set of colonies within a single classification.
    Pattern: {_Rule..}

    Characterization

    PopulationName

    The name used to reference the population of colonies.
    Default Value: Automatic
    Default Calculation: By default, each population is labeled as ColonySelection with sequential integers.
    Pattern Description: A string.
    Programmatic Pattern: _String | Automatic

    Include

    Coordinates of colonies included in the selection even if they do not match the selection criteria.
    Default Value: {}
    Pattern Description: {} or list of one or more {X, Y} entries or None.
    Programmatic Pattern: {} | ({{GreaterP[0*Millimeter], GreaterP[0*Millimeter]}..} | None)

    Exclude

    Coordinates of colonies excluded from the selection even if they match the selection criteria.
    Default Value: {}
    Pattern Description: {} or list of one or more {X, Y} entries or None or Null.
    Programmatic Pattern: ({} | (Null | ({{GreaterP[0*Millimeter], GreaterP[0*Millimeter]}..} | None))) | Null

MultiFeatured

    multiFeaturedRules

    Key/value pairs that define a set of colonies into a population by multiple features, including Diameter, Regularity, Isolation, Circularity, BlueWhiteScreen, and Fluorescence.
    Pattern: {_Rule..}

    Characterization

    Features

    The characteristics selected from Diameter, Regularity, Isolation, Circularity, BlueWhiteScreen, and Fluorescence of the colony by which the population will be isolated. For example, if Features is set to {Isolation, Diameter}, the colonies that are both larger than the median colony and more fluorescing than the median colony will be grouped into a population. More than one feature must be specified, otherwise the individual feature Unit Operation should be used. Colonies that match all features in the MultiFeatured unit operation will be included in the population.
    Default Value: {Isolation, Diameter}
    Pattern Description: Diameter, Isolation, Regularity, Circularity, Fluorescence, BlueWhiteScreen, or Absorbance or {Isolation, Diameter}
    Programmatic Pattern: ColonySelectionFeatureP
    Index Matches to: Features

    Select

    The method used to group colonies into a population. Colonies are first ordered by their Feature. If the Select option is Min or Max, the ordered colonies are divided into partitions based on the NumberOfDivisions. From there, the smallest or largest partition is grouped into a population depending on if the Select option is Min or Max. For example, if the Select option is set to Max and the NumberOfDivisions is 10, the colonies will be divided into 10 partitions sorted by the Feature and the highest partition will become the selected population. If the Select option is AboveThreshold or BelowThreshold, an absolute cutoff is used to group ordered colonies into a population. The threshold values is set by the Threshold option. For example, if the Select option is BelowThreshold, the Feature is Diameter, and the Threshold is 0.8 Millimeter, all colonies with Diameter less than 0.8 Millimeter will be selected as the population. If the Select option is Positive or Negative, the colonies are first clustered into two groups based on their Fluorescence or BlueWhiteScreen image intensity compared with background. Then, if the Select option is Positive, the group with the higher intensity values is selected as the population. However, if the Select option is Negative, the group without Fluorescence or BlueWhiteScreen signal is chosen as the population.
    Default Value: Automatic
    Default Calculation: For Diameter, Isolation, Regularity, and Circularity features the default is Max unless a Threshold is specified, in which case the default is AboveThreshold. For Fluorescence and BlueWhiteScreen the default is Positive, unless the NumberOfDivisions is specified, in which case the default is Max.
    Pattern Description: Min, Max, AboveThreshold, BelowThreshold, Positive, or Negative.
    Programmatic Pattern: (Min | Max | AboveThreshold | BelowThreshold | Positive | Negative) | Automatic
    Index Matches to: Features

    NumberOfDivisions

    The number of partitions to group colonies into. Partitions are ordered by the Features. If the Select option is Min or Max, the lowest or highest partition will be used, respectively.
    Default Value: Automatic
    Default Calculation: If the Select option is set to Min or Max, set NumberOfDivisions to 2.
    Pattern Description: Greater than or equal to 2 in increments of 1 or Null.
    Programmatic Pattern: (GreaterEqualP[2, 1] | Automatic) | Null
    Index Matches to: Features

    Threshold

    The min or max possible feature value (e.g., Diameter or Regularity) for a colony to be included in the population. When the Select option is AboveThreshold or BelowThreshold, all colonies with a feature value larger or smaller than the Threshold, respectively, are grouped into a population.
    Default Value: Null
    Pattern Description: Greater than or equal to 0 and less than or equal to 1 or greater than or equal to 0 millimeters or Null.
    Programmatic Pattern: (GreaterEqualP[0*Millimeter] | RangeP[0, 1]) | Null
    Index Matches to: Features

    Color

    The color to block with the absorbance filter which is inserted between the light source and the sample. Default to blue to eliminate blue colonies from the image, even when the colonies are newly formed and appear powder blue.
    Default Value: Automatic
    Default Calculation: If the feature is BlueWhiteScreen, set to Blue.
    Pattern Description: RGBColor[0, 0, 1] or Null.
    Programmatic Pattern: (Blue | Automatic) | Null
    Index Matches to: Features

    FilterWavelength

    The mean wavelength of light blocked by the absorbance filter. Blue colonies, which have a wavelength around 450 nanometers, appear darker.
    Default Value: Automatic
    Default Calculation: If the feature is BlueWhiteScreen, set to 400 Nanometer.
    Pattern Description: 400 nanometers or Null.
    Programmatic Pattern: (400*Nanometer | Automatic) | Null
    Index Matches to: Features

    Dye

    The coloring used to detect colonies that fluoresce at an EmissionWavelength when exposed to an ExcitationWavelength.
    Default Value: Automatic
    Default Calculation: Automatically set to the fluorophore within the excitation/emission range. For VioletFluorescence, set to DAPI. For GreenFluorescence, set to GFP. For OrangeFluorescence, set to Cy3. For RedFluorescence, set to TxRed. For DarkRedFluorescence, set to Cy5.
    Pattern Description: DAPI, UltraViolet, GFP, RGBColor[0, 0, 1], Cy3, TxRed, Cy5, or RGBColor[1, 0, 0] or Null.
    Programmatic Pattern: ((DAPI | UltraViolet | GFP | Blue | Cy3 | TxRed | Cy5 | Red) | Automatic) | Null
    Index Matches to: Features

    ExcitationWavelength

    The wavelength of light that adds energy to colonies and causes them to fluoresce. Pairs with an EmissionWavelength.
    Default Value: Automatic
    Default Calculation: Automatically set to the excitation wavelength specified in the FluorescentExcitationWavelength field of model cell in CellTypes.
    Pattern Description: 377 nanometers, 457 nanometers, 531 nanometers, or 628 nanometers or Null.
    Programmatic Pattern: ((377*Nanometer | 457*Nanometer | 531*Nanometer | 628*Nanometer) | Automatic) | Null
    Index Matches to: Features

    EmissionWavelength

    The light that the instrument measures to detect colonies fluorescing at a particular wavelength. Pairs with an ExcitationWavelength.
    Default Value: Automatic
    Default Calculation: Automatically set to the emission wavelength specified in the FluorescentEmissionWavelength field of model cell in CellTypes.
    Pattern Description: 447 nanometers, 536 nanometers, 593 nanometers, 624 nanometers, or 692 nanometers or Null.
    Programmatic Pattern: ((447*Nanometer | 536*Nanometer | 593*Nanometer | 624*Nanometer | 692*Nanometer) | Automatic) | Null
    Index Matches to: Features

    PopulationName

    The name used to reference the population of colonies.
    Default Value: Automatic
    Default Calculation: By default, each population is labeled as ColonySelection with sequential integers.
    Pattern Description: A string.
    Programmatic Pattern: _String | Automatic

    NumberOfColonies

    The upper limit for the count of colonies in the population.
    Default Value: Automatic
    Default Calculation: If Select is Min or Max, up to 10 colonies are selected, otherwise All colonies are selected.
    Pattern Description: All or greater than or equal to 2 in increments of 1 or Null.
    Programmatic Pattern: ((Null | (GreaterEqualP[2, 1] | All)) | Automatic) | Null

    Include

    Coordinates of colonies included in the selection even if they do not match the selection criteria.
    Default Value: {}
    Pattern Description: {} or list of one or more {X, Y} entries or None.
    Programmatic Pattern: {} | ({{GreaterP[0*Millimeter], GreaterP[0*Millimeter]}..} | None)

    Exclude

    Coordinates of colonies excluded from the selection even if they match the selection criteria.
    Default Value: {}
    Pattern Description: {} or list of one or more {X, Y} entries or None or Null.
    Programmatic Pattern: ({} | (Null | ({{GreaterP[0*Millimeter], GreaterP[0*Millimeter]}..} | None))) | Null

Experiment Options

    General

    Instrument

    The robotic instrument that is used to transfer colonies incubating on solid media to fresh liquid or solid media.
    Figure 3.1: Diagram of the deck layout of the ColonyHandler. The ColonyHandler is equipped with colony picking tool. In the picking configuration, the deck features designated positions for multi-well plates, single-well plates inside of light table, and wash baths.
    Default Value: Automatic
    Pattern Description: An object of type or subtype Model[Instrument, ColonyHandler] or Object[Instrument, ColonyHandler]
    Programmatic Pattern: ObjectP[{Model[Instrument, ColonyHandler], Object[Instrument, ColonyHandler]}] | Automatic

    NumberOfReplicates

    The number of times a colony selection should be picked from the input and placed in or on liquid or solid media.
    Default Value: Null
    Pattern Description: Greater than or equal to 2 in increments of 1 or Null.
    Programmatic Pattern: GreaterEqualP[2, 1] | Null

    Preparation

    Indicates if this unit operation is carried out primarily robotically or manually. Manual unit operations are executed by a laboratory operator and robotic unit operations are executed by a liquid handling work cell.
    Default Value: Robotic
    Pattern Description: Robotic.
    Programmatic Pattern: Robotic

    WorkCell

    Indicates the work cell that this primitive will be run on if Preparation->Robotic.
    Default Value: qPix
    Pattern Description: QPix.
    Programmatic Pattern: qPix

    Characterization

    Populations

    For each sample, the criteria used to group colonies together into a population to pick. Criteria are based on the ordering of colonies by the desired feature(s): Diameter, Regularity, Circularity, Isolation, Fluorescence, and BlueWhiteScreen. Additionally, CustomCoordinates can be specified, which work in conjunction with the PickCoordinates option to select colonies based on pre-determined locations. For more information see documentation on colony population Unit Operations: Diameter, Isolation, Regularity, Circularity, Fluorescence, BlueWhiteScreen, MultiFeatured, and AllColonies under Experiment Principles section.
    Default Value: Automatic
    Default Calculation: If the Model[Cell] information in the sample object matches one of the fluorescent excitation and emission pairs of the colony picking instrument, Populations is set to Fluorescence. Otherwise, Populations is set to All.
    Pattern Description: AllColonies or BlueWhiteScreen or Circularity or Diameter or Fluorescence or Fluorescence, BlueWhiteScreen, Diameter, Isolation, Circularity, Regularity, or All or Isolation or Known Coordinates or MultiFeatured or Regularity.
    Programmatic Pattern: ((Fluorescence | BlueWhiteScreen | Diameter | Isolation | Circularity | Regularity | All) | FluorescencePrimitiveP | BlueWhiteScreenPrimitiveP | DiameterPrimitiveP | IsolationPrimitiveP | CircularityPrimitiveP | RegularityPrimitiveP | AllColoniesPrimitiveP | MultiFeaturedPrimitiveP | CustomCoordinates) | Automatic
    Index Matches to: experiment samples
    Nested Index Matches to: experiment samples

    Selection

    MinDiameter

    For each sample, the smallest diameter value from which colonies will be included. The diameter is defined as the diameter of a circle with the same area as the colony.
    Figure 3.2: Diameter is the distance of the longest line connecting 2 points on the edge of the colony that goes through the centerpoint.
    Default Value: 0.5 millimeters
    Pattern Description: Greater than or equal to 0.2 millimeters and less than or equal to 10 millimeters or Null.
    Programmatic Pattern: (Null | RangeP[$QPixMinDiameter, 10*Millimeter]) | Null
    Index Matches to: experiment samples

    MaxDiameter

    For each sample, the largest diameter value from which colonies will be included. The diameter is defined as the diameter of a circle with the same area as the colony.
    Figure 3.3: Diameter is the distance of the longest line connecting 2 points on the edge of the colony that goes through the centerpoint.
    Default Value: 2 millimeters
    Pattern Description: Greater than or equal to 0.2 millimeters and less than or equal to 10 millimeters or Null.
    Programmatic Pattern: (Null | RangeP[$QPixMinDiameter, 10*Millimeter]) | Null
    Index Matches to: experiment samples

    MinColonySeparation

    For each sample, the closest distance included colonies can be from each other from which colonies will be included. The separation of a colony is the shortest path between the perimeter of the colony and the perimeter of any other colony.
    Figure 3.4: Isolation is the distance between the 2 closest points of 2 colonies.
    Default Value: 0.2 millimeters
    Pattern Description: Greater than 0 millimeters or Null.
    Programmatic Pattern: (Null | GreaterP[0*Millimeter]) | Null
    Index Matches to: experiment samples

    MinRegularityRatio

    For each sample, the smallest regularity ratio from which colonies will be included. The regularity ratio is the ratio of the area of the colony to the area of a circle with the colony's perimeter. For example, jagged edged shapes will have a longer perimeter than smoother ones and therefore a smaller regularity ratio.
    Figure 3.5: Regularity is the ratio of the area of the colony to the area of a circle with the colony's perimeter.
    Default Value: 0.65
    Pattern Description: Greater than or equal to 0 and less than or equal to 1 or Null.
    Programmatic Pattern: (Null | RangeP[0, 1]) | Null
    Index Matches to: experiment samples

    MaxRegularityRatio

    For each sample, the largest regularity ratio from which colonies will be included. The regularity ratio is the ratio of the area of the colony to the area of a circle with the colony's perimeter. For example, jagged edged shapes will have a longer perimeter than smoother ones and therefore a smaller regularity ratio.
    Figure 3.6: Regularity is the ratio of the area of the colony to the area of a circle with the colony's perimeter.
    Default Value: 1.
    Pattern Description: Greater than or equal to 0 and less than or equal to 1 or Null.
    Programmatic Pattern: (Null | RangeP[0, 1]) | Null
    Index Matches to: experiment samples

    MinCircularityRatio

    For each sample, the smallest circularity ratio from which colonies will be included. The circularity ratio is defined as the ratio of the minor axis to the major axis of the best fit ellipse. For example, a very oblong colony will have a much larger major axis compared to its minor axis and therefore a low circularity ratio.
    Figure 3.7: Circularity is a measure of the ratio of the minor axis to the major axis of the best fit ellipse.
    Default Value: 0.65
    Pattern Description: Greater than or equal to 0 and less than or equal to 1 or Null.
    Programmatic Pattern: (Null | RangeP[0, 1]) | Null
    Index Matches to: experiment samples

    MaxCircularityRatio

    For each sample, the largest circularity ratio from which colonies will be included. The circularity ratio is defined as the ratio of the minor axis to the major axis of the best fit ellipse. For example, a very oblong colony will have a much larger major axis compared to its minor axis and therefore a low circularity ratio.
    Figure 3.8: Circularity is a measure of the ratio of the minor axis to the major axis of the best fit ellipse.
    Default Value: 1.
    Pattern Description: Greater than or equal to 0 and less than or equal to 1 or Null.
    Programmatic Pattern: (Null | RangeP[0, 1]) | Null
    Index Matches to: experiment samples

    Picking

    ColonyPickingTool

    For each sample, the tool used to stab the source colonies plates from SamplesIn and either deposit any material stuck to the picking head onto the destination plate or into a destination well.
    Figure 3.9: Various colony picking tools. In Picking application, the ColonyHandlerHeadCassette containing either 96/24-pin picking head is installed into the robot gantry, and is designed to stab source colonies and deposit any material stuck to the probe onto the destination plate or into a destination well.
    Default Value: Automatic
    Default Calculation: If the DestinationContainer has 24 wells, set to Model[Part,ColonyHandlerHeadCassette, "24-pin picking head for E. coli" ]. If the DestinationContainer has 96 or 384 wells, or is an OmniTray, will use the PreferredColonyHandlerHeadCassette of the first Model[Cell] in the composition of the input sample. If the Composition field is not filled or there are not Model[Cell]'s in the composition, this option is automatically set to Model[Part,ColonyHandlerHeadCassette, "96-pin picking head for E. coli - Deep well"] if the destination is a deep well plate and Model[Part,ColonyHandlerHeadCassette, "96-pin picking head for E. coli"] otherwise.
    Pattern Description: An object of type or subtype Model[Part, ColonyHandlerHeadCassette] or Object[Part, ColonyHandlerHeadCassette]
    Programmatic Pattern: ObjectP[{Model[Part, ColonyHandlerHeadCassette], Object[Part, ColonyHandlerHeadCassette]}] | Automatic
    Index Matches to: experiment samples

    HeadDiameter

    For each sample, the width of the metal probe used to stab the source colonies and deposit any material stuck to the probe onto the destination plate or into a destination well.
    Default Value: Automatic
    Default Calculation: Resolves from the ColonyPickingTool[HeadDiameter].
    Pattern Description: Greater than 0 millimeters.
    Programmatic Pattern: GreaterP[0*Millimeter] | Automatic
    Index Matches to: experiment samples

    HeadLength

    For each sample, the length of the metal probe used to stab the source colonies and deposit any material stuck to the probe onto the destination plate or into a destination well.
    Default Value: Automatic
    Default Calculation: Resolves from the ColonyPickingTool[HeadLength].
    Pattern Description: Greater than 0 millimeters.
    Programmatic Pattern: GreaterP[0*Millimeter] | Automatic
    Index Matches to: experiment samples

    NumberOfHeads

    For each sample, the number of metal probes on the ColonyHandlerHeadCassette used to stab the source colonies and deposit any material stuck to the probe onto the destination plate or into a destination well.
    Default Value: Automatic
    Default Calculation: Resolves from the ColonyPickingTool[NumberOfHeads].
    Pattern Description: Greater than 0 in increments of 1.
    Programmatic Pattern: GreaterP[0, 1] | Automatic
    Index Matches to: experiment samples

    ColonyHandlerHeadCassetteApplication

    For each sample, the designed use of the ColonyPickingTool used to stab the source colonies and deposit any material stuck to the probe onto the destination plate or into a destination well..
    Default Value: Automatic
    Default Calculation: Resolves from the ColonyPickingTool[Application].
    Pattern Description: Pick, Spread, or Streak.
    Programmatic Pattern: ColonyHandlerHeadCassetteTypeP | Automatic
    Index Matches to: experiment samples

    ColonyPickingDepth

    For each sample, the distance the picking head penetrates into the agar when picking a colony.
    Default Value: 2 millimeters
    Pattern Description: Greater than or equal to 0 millimeters and less than or equal to 20 millimeters.
    Programmatic Pattern: RangeP[0*Millimeter, 20*Millimeter]
    Index Matches to: experiment samples
    Nested Index Matches to: experiment samples

    PickCoordinates

    For each sample, the coordinates, in Millimeters, from which colonies will be picked from the source plate where {0 Millimeter, 0 Millimeter} is the center of the source well.
    Default Value: Automatic
    Default Calculation: Automatically set to Null if not specified.
    Pattern Description: List of one or more {XCoordinate, YCoordinate} entries or Null.
    Programmatic Pattern: ({{RangeP[-63*Millimeter, 63*Millimeter], RangeP[-43*Millimeter, 43*Millimeter]}..} | Automatic) | Null
    Index Matches to: experiment samples

    Imaging

    ImagingStrategies

    For each Sample, the end goals for capturing images. ImagingStrategies can be either a single end goal of simple visualization or a list of multiple end goals. The options include BrightField, BlueWhiteScreen, and multiple fluorescence imaging techniques. BrightField imaging is essential for obtaining baseline images and is required if other imaging strategies are employed. BlueWhiteScreen is used to distinguish recombinant colonies with disrupted lacZ (white colonies) from blue colonies using an absorbance filter. Fluorescence imaging allows for the visualization of colonies with fluorescent dyes or proteins.
    Figure 3.10: Diagram of the imaging module of the ColonyHandler with various imaging strategies. For BlueWhiteScreen, an absorbance filter which blocks blue light between the sample and the light source, eliminating blue colonies from the image, even when they are newly formed and appear powder blue. For VioletFluorescence, GreenFluorescence, OrangeFluorescence, RedFluorescence, or DarkRedFluorescence, an LED-based light source with a specific fluorescence excitation wavelength illuminates the sample, and emission is filtered before reaching the CCD camera. The transition to capture multiple types of images is accomplished by the robotic gantry of the QPix colony handler, which moves seamlessly between imaging strategies and samples.
    Default Value: Automatic
    Default Calculation: Automatically set to include the BlueWhiteScreen along with BrightField if option Populations is set to include BlueWhiteScreen, set to include fluorescence along with BrightField if the Model[Cell] information in the sample matches one of the fluorescent excitation and emission pairs of the imaging instrument. Otherwise, set to BrightField as a BrightField image is always taken.
    Pattern Description: Multiple Imaging Strategies or Single Imaging Strategy.
    Programmatic Pattern: (DuplicateFreeListableP[BrightField | BlueWhiteScreen | VioletFluorescence | GreenFluorescence | OrangeFluorescence | RedFluorescence | DarkRedFluorescence] | BrightField) | Automatic
    Index Matches to: experiment samples

    ExposureTimes

    For each Sample, and for each imaging strategy, a single length of time to allow the camera to capture an image. An increased exposure time leads to brighter images based on a linear scale. When set as Automatic, optimal exposure time is automatically determined during experiment. This is done by running AnalyzeImageExposure on images taken with suggested initial exposure times. The process adjusts the exposure time for subsequent image acquisitions until the optimal exposure time is found.
    Figure 3.11: This table outlines the suggested exposure times for various imaging strategies and lists the corresponding fields where the raw image data is stored for each imaging strategy.
    Default Value: Automatic
    Pattern Description: Multiple Exposure Times or Single Exposure Time.
    Programmatic Pattern: ({(RangeP[1*Millisecond, 2000*Millisecond] | Automatic)..} | (RangeP[1*Millisecond, 2000*Millisecond] | Automatic)) | Automatic
    Index Matches to: experiment samples

    Placing

    DestinationMediaType

    For each Sample, the type of media (liquid or solid) the picked colonies will be transferred in to.
    Default Value: Automatic
    Default Calculation: Automatically set to State that matches DestinationMedia if specified. Otherwise is set to LiquidMedia if there is a PreferredLiquidMedia specified in the Model[Cell] in the input sample. If there is no PreferredLiquidMedia but there is a PreferredSolidMedia, resolves to SolidMedia. If there is neither PreferredLiquidMedia or PreferredSolidMedia in the Model[Cell] in the input sample, defaults to LiquidMedia.
    Pattern Description: SolidMedia or LiquidMedia.
    Programmatic Pattern: DestinationMediaTypeP | Automatic
    Index Matches to: experiment samples
    Nested Index Matches to: experiment samples

    DestinationMedia

    For each sample, the media in which the picked colonies should be placed.
    Default Value: Automatic
    Default Calculation: If DestinationMediaType is LiquidMedia, automatically set to the value in the PreferredLiquidMedia field for the first Model[Cell] in the input sample Composition. If DestinationMediaType is SolidMedia, automatically set to the value in the PreferredSolidMedia field for the first Model[Cell] in the input sample.
    Pattern Description: An object of type or subtype Object[Sample] or Model[Sample] or a prepared sample.
    Programmatic Pattern: (ObjectP[{Object[Sample], Model[Sample]}] | _String) | Automatic
    Index Matches to: experiment samples
    Nested Index Matches to: experiment samples

    DestinationMediaContainer

    For each Sample, the desired container to have picked colonies deposited in.
    Default Value: Automatic
    Default Calculation: Automatically set based on the DestinationMediaType and DestinationMedia options. Will default to Model[Container, Plate, "96-well 2mL Deep Well Plate"] if DestinationMediaType is LiquidMedia and will default to Model[Container, Plate, "Omni Tray Sterile Media Plate"] if DestinationMediaType is SolidMedia.
    Pattern Description: A single container or A single model of container or Multiple containers.
    Programmatic Pattern: (ObjectP[Model[Container]] | (ObjectP[Object[Container]] | _String) | {(ObjectP[Object[Container]] | _String)..}) | Automatic
    Index Matches to: experiment samples
    Nested Index Matches to: experiment samples

    DestinationFillDirection

    For each Sample, indicates if the DestinationMediaContainer is filled with picked colonies in row order, column order, or by custom coordinates. Row/Column completely fills spots in available row/column before moving to the next. If set to CustomCoordinates, ignores MaxDestinationNumberOfColumns and MaxDestinationNumberOfRows to fill at locations specified by DestinationCoordinates. CustomCoordinates is only applicable when DestinationMediaType is SolidMedia.
    Default Value: Row
    Pattern Description: Row, Column, or CustomCoordinates.
    Programmatic Pattern: DestinationFillDirectionP

    MaxDestinationNumberOfColumns

    For each sample, the maximum number of columns of colonies to deposit in the destination container.
    Figure 3.12: Picked colonies will be deposited on solid media and spaced out according to this chart.
    Default Value: Automatic
    Default Calculation: Automatically set based on the below table after the number of colonies to pick has been determined.
    Pattern Description: Greater than 0 in increments of 1 or Null.
    Programmatic Pattern: (GreaterP[0, 1] | Automatic) | Null
    Index Matches to: experiment samples
    Nested Index Matches to: experiment samples

    MaxDestinationNumberOfRows

    For each sample, the maximum number of rows of colonies to deposit in the destination container.
    Figure 3.13: Picked colonies will be deposited on solid media and spaced out according to this chart.
    Default Value: Automatic
    Default Calculation: Automatically set based on the below table after the number of colonies to pick has been determined.
    Pattern Description: Greater than 0 in increments of 1 or Null.
    Programmatic Pattern: (GreaterP[0, 1] | Automatic) | Null
    Index Matches to: experiment samples
    Nested Index Matches to: experiment samples

    DestinationCoordinates

    For each sample, the xy coordinates, in Millimeters, to deposit the picked colonies on solid media where {0 Millimeter, 0 Millimeter} is the center of the destination well. DestinationCoordinates is only applicable when Destination is SolidMedia.
    Figure 3.14: The specified coordinates will snap to the center of a 384 well grid on the solid media.
    Default Value: Null
    Pattern Description: List of one or more {XCoordinate, YCoordinate} entries or Null.
    Programmatic Pattern: {{RangeP[-60*Millimeter, 60*Millimeter], RangeP[-40*Millimeter, 40*Millimeter]}..} | Null
    Index Matches to: experiment samples
    Nested Index Matches to: experiment samples

    MediaVolume

    For each sample, the amount of liquid media in which the picked colonies are placed. MediaVolume is only applicable when DestinationMediaType -> LiquidMedia.
    Default Value: Automatic
    Default Calculation: Automatically set to the minimum of $MaxRoboticSingleTransferVolume and either the RecommendedFillVolume of the DestinationMediaContainer, or 40% of the MaxVolume if the field is not populated.
    Pattern Description: Greater than 0 microliters or Null.
    Programmatic Pattern: (GreaterP[0*Microliter] | Automatic) | Null
    Index Matches to: experiment samples
    Nested Index Matches to: experiment samples

    DestinationMix

    For each sample, indicates if the picking head is swirled in the destination plate while inoculating the liquid media. DestinationMix is only applicable when Destination -> LiquidMedia.
    Default Value: Automatic
    Default Calculation: If Destination is LiquidMedia or if DestinationNumberOfMixes is specified, automatically resolves to True.
    Pattern Description: True or False or Null.
    Programmatic Pattern: (BooleanP | Automatic) | Null
    Index Matches to: experiment samples
    Nested Index Matches to: experiment samples

    DestinationNumberOfMixes

    For each sample, the number of times the picking pin will be swirled in the liquid media during inoculation. DestinationNumberOfMixes is only applicable when Destination -> LiquidMedia.
    Default Value: Automatic
    Default Calculation: Automatically set to 5 if DestinationMix is True.
    Pattern Description: Greater than or equal to 0 and less than or equal to 50 in increments of 1 or Null.
    Programmatic Pattern: (RangeP[0, $MaxNumberOfMixes, 1] | Automatic) | Null
    Index Matches to: experiment samples
    Nested Index Matches to: experiment samples

    Post Experiment

    SamplesInStorageCondition

    The non-default conditions under which the SamplesIn of this experiment should be stored after the protocol is completed. If left unset, SamplesIn will be disposed.
    Default Value: Disposal
    Pattern Description: {AmbientStorage, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, YeastShakingIncubation, BacterialIncubation, BacterialShakingIncubation, MammalianIncubation, ViralIncubation, CrystalIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, UVVisLightTesting} or Disposal.
    Programmatic Pattern: Alternatives[SampleStorageTypeP | Disposal]
    Index Matches to: experiment samples

    SamplesOutStorageCondition

    The non-default conditions under which any new samples generated by this experiment should be stored after the protocol is completed. If left unset, the new samples will be stored according to their Models' DefaultStorageCondition.
    Default Value: Null
    Pattern Description: {AmbientStorage, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, YeastShakingIncubation, BacterialIncubation, BacterialShakingIncubation, MammalianIncubation, ViralIncubation, CrystalIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, UVVisLightTesting} or Disposal or Null.
    Programmatic Pattern: (Alternatives[SampleStorageTypeP | Disposal]) | Null
    Index Matches to: experiment samples
    Nested Index Matches to: experiment samples

    Sanitization

    PrimaryWash

    For each sample, indicates if the PrimaryWash stage should be turned on during the sanitization process.
    Default Value: True
    Pattern Description: True or False.
    Programmatic Pattern: BooleanP
    Index Matches to: experiment samples

    PrimaryWashSolution

    For each sample, the first wash solution that is used during the sanitization process prior to each round of picking.
    Default Value: Automatic
    Default Calculation: Automatically set to Model[Sample,StockSolution,"70% Ethanol"], if PrimaryWash is True.
    Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.
    Programmatic Pattern: ((ObjectP[{Model[Sample], Object[Sample]}] | _String) | Automatic) | Null
    Index Matches to: experiment samples

    NumberOfPrimaryWashes

    For each sample, the number of times the ColonyHandlerHeadCassette moves in a circular motion in the PrimaryWashSolution to clean any material off the head.
    Default Value: Automatic
    Default Calculation: Automatically set to 5 if PrimaryWash is True.
    Pattern Description: Greater than 0 in increments of 1 or Null.
    Programmatic Pattern: (GreaterP[0, 1] | Automatic) | Null
    Index Matches to: experiment samples

    PrimaryDryTime

    For each sample, the length of time the ColonyHandlerHeadCassette is dried over the halogen fan after the cassette is washed in PrimaryWashSolution.
    Default Value: Automatic
    Default Calculation: Automatically set to 10 seconds if PrimaryWash is True.
    Pattern Description: Greater than 0 seconds or Null.
    Programmatic Pattern: (GreaterP[0*Second] | Automatic) | Null
    Index Matches to: experiment samples

    SecondaryWash

    For each sample, indicates if the SecondaryWash stage should be turned on during the sanitization process.
    Default Value: Automatic
    Default Calculation: Automatically set to False if PrimaryWash is False.
    Pattern Description: True or False.
    Programmatic Pattern: BooleanP | Automatic
    Index Matches to: experiment samples

    SecondaryWashSolution

    For each sample, the second wash solution that can be used during the sanitization process prior to each round of picking.
    Default Value: Automatic
    Default Calculation: Automatically set to Model[Sample,"Milli-Q water"] if SecondaryWash is True.
    Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.
    Programmatic Pattern: ((ObjectP[{Model[Sample], Object[Sample]}] | _String) | Automatic) | Null
    Index Matches to: experiment samples

    NumberOfSecondaryWashes

    For each sample, the number of times the ColonyHandlerHeadCassette moves in a circular motion in the SecondaryWashSolution to clean any material off the head.
    Default Value: Automatic
    Default Calculation: Automatically set to 5 if SecondaryWash is True.
    Pattern Description: Greater than 0 in increments of 1 or Null.
    Programmatic Pattern: (GreaterP[0, 1] | Automatic) | Null
    Index Matches to: experiment samples

    SecondaryDryTime

    For each sample, the length of time the ColonyHandlerHeadCassette is dried over the halogen fan after the cassette is washed in SecondaryWashSolution.
    Default Value: Automatic
    Default Calculation: Automatically set to 10 seconds if SecondaryWash is True.
    Pattern Description: Greater than 0 seconds or Null.
    Programmatic Pattern: (GreaterP[0*Second] | Automatic) | Null
    Index Matches to: experiment samples

    TertiaryWash

    For each sample, indicates if the TertiaryWash stage should be turned on during the sanitization process.
    Default Value: Automatic
    Default Calculation: Automatically set to False if SecondaryWash is False.
    Pattern Description: True or False.
    Programmatic Pattern: BooleanP | Automatic
    Index Matches to: experiment samples

    TertiaryWashSolution

    For each sample, the third wash solution that can be used during the sanitization process prior to each round of picking.
    Default Value: Automatic
    Default Calculation: Automatically set to Model[Sample, StockSolution, "10% Bleach"] if TertiaryWash is True.
    Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.
    Programmatic Pattern: ((ObjectP[{Model[Sample], Object[Sample]}] | _String) | Automatic) | Null
    Index Matches to: experiment samples

    NumberOfTertiaryWashes

    For each sample, the number of times the ColonyHandlerHeadCassette moves in a circular motion in the TertiaryWashSolution to clean any material off the head.
    Default Value: Automatic
    Default Calculation: Automatically set to 5 if TertiaryWash is True.
    Pattern Description: Greater than 0 in increments of 1 or Null.
    Programmatic Pattern: (GreaterP[0, 1] | Automatic) | Null
    Index Matches to: experiment samples

    TertiaryDryTime

    For each sample, the length of time to dry the ColonyHandlerHeadCassette over the halogen fan after the cassette is washed in TertiaryWashSolution.
    Default Value: Automatic
    Default Calculation: Automatically set to 10 seconds if TertiaryWash is True.
    Pattern Description: Greater than 0 seconds or Null.
    Programmatic Pattern: (GreaterP[0*Second] | Automatic) | Null
    Index Matches to: experiment samples

    QuaternaryWash

    For each sample, indicates if the QuaternaryWash stage should be turned on during the sanitization process.
    Default Value: Automatic
    Default Calculation: Automatically set to False if TertiaryWash is False.
    Pattern Description: True or False.
    Programmatic Pattern: BooleanP | Automatic
    Index Matches to: experiment samples

    QuaternaryWashSolution

    For each sample, the fourth wash solution that can be used during the process prior to each round of picking.
    Default Value: Automatic
    Default Calculation: Automatically set to Model[Sample,StockSolution,"70% Ethanol"] if QuaternaryWash is True.
    Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.
    Programmatic Pattern: ((ObjectP[{Model[Sample], Object[Sample]}] | _String) | Automatic) | Null
    Index Matches to: experiment samples

    NumberOfQuaternaryWashes

    For each sample, the number of times the ColonyHandlerHeadCassette moves in a circular motion in the QuaternaryWashSolution to clean any material off the head
    Default Value: Automatic
    Default Calculation: Automatically set to 5 if QuaternaryWash is True.
    Pattern Description: Greater than 0 in increments of 1 or Null.
    Programmatic Pattern: (GreaterP[0, 1] | Automatic) | Null
    Index Matches to: experiment samples

    QuaternaryDryTime

    For each sample, the length of time the ColonyHandlerHeadCassette is dried over the halogen fan after the cassette is washed in QuaternaryWashSolution
    Default Value: Automatic
    Default Calculation: Automatically set to 10 seconds if QuaternaryWash is True.
    Pattern Description: Greater than 0 seconds or Null.
    Programmatic Pattern: (GreaterP[0*Second] | Automatic) | Null
    Index Matches to: experiment samples

Protocol Options

    Post Experiment

    MeasureWeight

    Indicates if any solid samples that are modified in the course of the experiment should have their weights measured and updated after running the experiment. Please note that public samples are weighed regardless of the value of this option.
    Default Value: False
    Pattern Description: True or False or Null.
    Programmatic Pattern: (Null | BooleanP) | Null

    MeasureVolume

    Indicates if any liquid samples that are modified in the course of the experiment should have their volumes measured and updated after running the experiment. Please note that public samples are volume measured regardless of the value of this option.
    Default Value: False
    Pattern Description: True or False or Null.
    Programmatic Pattern: (Null | BooleanP) | Null

    ImageSample

    Indicates if any samples that are modified in the course of the experiment should be freshly imaged after running the experiment. Please note that public samples are imaged regardless of the value of this option.
    Default Value: False
    Pattern Description: True or False or Null.
    Programmatic Pattern: (Null | BooleanP) | Null

    Organizational Information

    Name

    A object name which should be used to refer to the output object in lieu of an automatically generated ID number.
    Default Value: Null
    Pattern Description: A string or Null.
    Programmatic Pattern: _String | Null

Example Calls

    Picking

    Pick colonies that are fluorescing using the Fluorescence primitive:
    Use the Absorbance primitive to perform a blue white screen:
    Pick colonies after they have been classified by multiple features. In this case the large fluorescing colonies would be picked:

    Inoculate Media

    Have the picked colonies placed into LiquidMedia and then mixed by pipette, so they can be further grown:
    Have the picked colonies placed onto SolidMedia so they can be further grown:
    Have the picked colonies placed onto SolidMedia by specifying a custom placement pattern, so they can be further grown. {0 Millimeter, 0 Millimeter is the center of the destination well}:

Preferred Input Containers

    Single-Well OmniTray Plate

Warnings and Errors

    Messages  (46)

    ColonyHandlerHeadCassetteApplicationMismatch  (1)

    If the specified ColonyHandlerHeadCassetteApplication does not match the value in the Application field of the specified ColonyPickingTool, an error will be thrown:

    DestinationFillDirectionMismatch  (1)

    If DestinationFillDirection->CustomCoordinates and MaxDestinationNumberOfColumns or MaxDestinationNumberOfRows is not Null, an error will be thrown:

    DestinationMediaTypeMismatch  (1)

    If the State of DestinationMedia does not match DestinationMediaType, an error will be thrown:

    DestinationMixMismatch  (1)

    If DestinationMix->False and DestinationNumberOfMixes->an Integer, an error will be thrown:

    DuplicatedSamples  (1)

    Throws an error if the input samples contain duplicates:

    HeadDiameterMismatch  (1)

    If the specified HeadDiameter does not match the value in the HeadDiameter field of the specified ColonyPickingTool, an error will be thrown:

    HeadLengthMismatch  (1)

    If the specified HeadLength does not match the value in the HeadLength field of the specified ColonyPickingTool, an error will be thrown:

    ImagingOptionMismatch  (2)

    If ImagingStrategies and ExposureTimes are set to a single value and a list, an error will be thrown:

    If ImagingStrategies and ExposureTimes are set to lists with different lengths, an error will be thrown:

    IncompatibleMaterials  (2)

    If a wash solution is not compatible with the wetted materials of the instrument, an error will be thrown:

    If the input sample is not compatible with the wetted materials of the instrument, an error will be thrown:

    IndexMatchingPrimitive  (1)

    An error is thrown if some options in MultiFeatured are not index matched:

    InstrumentPrecision  (6)

    If a ColonyPickingDepth with a greater precision than 0.01 Millimeter is given, it is rounded:

    If an ExposureTime with a greater precision than 1 Millisecond is given, it is rounded:

    If a PrimaryDryTime with a greater precision than 1 Second is given, it is rounded:

    If a QuaternaryDryTime with a greater precision than 1 Second is given, it is rounded:

    If a SecondaryDryTime with a greater precision than 1 Second is given, it is rounded:

    If a TertiaryDryTime with a greater precision than 1 Second is given, it is rounded:

    InvalidColonyPickingDepths  (1)

    If the specified ColonyPickingDepth is greater than the depth of a well of an input container, an error will be thrown:

    InvalidDestinationMediaContainer  (1)

    If the DestinationMediaContainer does not have 1, 24, or 96 wells or is deep well but does not have 96 wells, an error will be thrown:

    InvalidDestinationMediaState  (1)

    If the DestinationMedia has a non Liquid or Solid State, an error will be thrown:

    InvalidMixOption  (1)

    If DestinationMediaType->SolidMedia and the DestinationMix gets set to True, an error will be thrown:

    MissingDestinationCoordinates  (1)

    If DestinationFillDirection->CustomCoordinates and DestinationCoordinates are not specified, an error will be thrown:

    MissingImagingStrategies  (1)

    If there are imaging strategies specified in a Population that are not specified in ImagingStrategies, an error will be thrown:

    MultiplePopulationMethods  (1)

    If Populations -> population primitive and PickCoordinates are specified an error will be thrown:

    NoAutomaticWavelength  (1)

    If for a MultiFeatured population, Features -> Fluorescence and no fluorescent wavelength is given or can be found in the composition of the input sample, an error will be thrown:

    NoAvailablePickingTool  (1)

    If there is no ColonyPickingTool that satisfies the colony picking tool parameter options, an error will be thrown:

    NonOmniTrayContainer  (1)

    Return $Failed if the input samples are not in an omnitray:

    NonSolidSamples  (1)

    Return $Failed if the samples the colonies are being picked from are not solid:

    NotPreferredColonyHandlerHead  (1)

    If the specified ColonyPickingTool is not preferred for the cell type in the input sample, a warning will be thrown:

    NumberOfHeadsMismatch  (1)

    If the specified NumberOfHeads does not match the value in the NumberOfHeads field of the specified ColonyPickingTool, an error will be thrown:

    OutOfOrderWashStages  (1)

    If a wash stage is specified but not all of the prerequisite stages are specified, an error will be thrown:

    OverlappingPopulations  (1)

    If Populations is specified as a mix of population primitives and CustomCoordinates for a single sample, an error will be thrown:

    PickCoordinatesMissing  (1)

    If Populations ->CustomCoordinates and PickCoordinates are not specified an error will be thrown:

    PickingToolIncompatibleWithDestinationMediaContainer  (1)

    If the specified ColonyPickingTool is incompatible with a DestinationMediaContainer, an error will be thrown:

    PrimaryWashMismatch  (1)

    If PrimaryWash->True and other PrimaryWash options are Null, an error will be thrown:

    QPixWashSolutionInsufficientVolume  (1)

    If there is not sufficient volume (150mL) left in a specified Object[Sample] for any wash solution options, an error will be thrown:

    QuaternaryWashMismatch  (1)

    If QuaternaryWash->True and other QuaternaryWash options are Null, an error will be thrown:

    RepeatedPopulationNames  (1)

    If the same PopulationName is used in multiple Populations, an error will be thrown :

    SecondaryWashMismatch  (1)

    If SecondaryWash -> True and other SecondaryWash options are Null, an error will be thrown:

    SingleAutomaticWavelength  (1)

    If when trying to determine the fluorescent wavelength pair to use if it is not specified, and the Model[Cell] in the composition input sample only matches half of a wavelength pair, a warning will be thrown:

    TertiaryWashMismatch  (1)

    If TertiaryWash->True and other TertiaryWash options are Null, an error will be thrown:

    TooManyDestinationCoordinates  (1)

    If the length of the specified DestinationCoordinates is longer than 384, a warning will be thrown:

    TooManyDestinationMediaContainers  (1)

    If there are more than 6 unique DestinationMediaContainers, an error will be thrown:

    TooManyInputContainers  (1)

    Return $Failed if the input samples are contained in more than 4 unique containers:

    TooManyWashSolutions  (1)

    If there are more than 3 different sample models across PrimaryWashSolution, SecondaryWashSolution, TertiaryWashSolution, and QuaternaryWashSolution, an error will be thrown:

Last modified on Sat 2 Nov 2024 18:51:23


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