ExperimentInoculateLiquidMedia
ExperimentInoculateLiquidMedia[Objects]⟹Protocol
creates a Protocol that takes colonies from the provided sample or container Objects and deposit them into liquid media.
InoculateLiquidMedia allows for the transfer of microbial cells to a new or existing container containing liquid media for further growth and analysis. The microbial cells growing as colonies on solid media are picked by a colony-picking robot and deposited in liquid media. Microbial cells in a bacterial stab are collected and transferred to liquid media via a pipette tip. Microbial cells in suspension are transferred by pipette to the destination container. Freeze-dried microbial cells are resuspended and transferred to liquid media. Microbial Cells in frozen glycerol are scraped and deposited into liquid media via pipette tips, while the source tube is transported in a portable cooler to remain frozen. The transfer can occur manually in a Biosafety Cabinet or robotically on a liquid handling or colony handling workcell.
Experimental Principles
Figure 1.1: Procedural overview of ExperimentInoculateLiquidMedia if the source cells are in a suspension. Step 1: The samples are detected to be growing in liquid media. Step 2: Samples are transferred by Pipette to the destination container.
Figure 1.2: Procedural overview of ExperimentInoculateLiquidMedia if the source cells are growing on solid media. Step 1: The samples are detected to be growing on solid media. Step 2: Samples are imaged using the CCD camera on the instrument. Step 3: The images are analyzed by the function AnalyzeColonies in order to find the locations of the colonies on the plates. Step 4: The selected colonies are picked by the QPix 420 HT colony picking tool. Step 5: The picked colonies are placed on the desired media. Step 6: The colony picking tool is washed in sanitization solution. Step 7: The colony picking tool is dried by a fan.
Figure 1.3: Procedural overview of ExperimentInoculateLiquidMedia if the source cells are in a bacterial stab. Step 1: The samples are detected to be in a bacterial stab and a Biosafety Cabinet is selected. Step 2: A pipette tip is dipped into the stab to collect cells. Step 3: The pipette tip is dipped in the destination container containing liquid media. Step 4: The destination container is mixed by pipette or via swirling.
Figure 1.4: Procedural overview of ExperimentInoculateLiquidMedia if the source cells are in the form of freeze-dried powder. Step 1: The samples are detected to be solid in a glass ampoule. Step 2: The ampoule is broken open and media is added to the powder. Step 3: The reconstituted cell suspension is mixed by pipette. Step 4: Samples are transferred by Pipette to the destination container.
Figure 1.5: Procedural overview of ExperimentInoculateLiquidMedia if the source cells are in frozen glycerol. Step 1: The samples are detected to be stored in freezer or lower temperature. Step 2: Samples are acquired by scraping the top of the sample with a pipette, while the source sample is kept in a portable cooler to prevent thawing. Step 3: The pipette tip with scraped samples is dipped into the media in the destination container. Step 4: The deposited samples are mixed by pipette in the destination container.
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.
microbioSTAR
pipetus, Microbial
Figure 2.3.1: The above diagram lists the compatible serological tip sizes that are available at the ECL.
Eppendorf Research Plus P2.5, Microbial
Figure 2.4.1: The diagram above lists the available pipette sizes and corresponding tip types that are available in the ECL.
Eppendorf Research Plus P20, Microbial
Figure 2.5.1: The diagram above lists the available pipette sizes and corresponding tip types that are available in the ECL.
Eppendorf Research Plus P200, Microbial
Figure 2.6.1: The diagram above lists the available pipette sizes and corresponding tip types that are available in the ECL.
Eppendorf Research Plus P1000, Microbial
Figure 2.7.1: The diagram above lists the available pipette sizes and corresponding tip types that are available in the ECL.
Eppendorf Research Plus P5000, Microbial
Diameter
diameterRules
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.
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.
Pattern Description: Greater than or equal to 0.2 millimeters and less than or equal to 10 millimeters or Null.
NumberOfColonies
Default Calculation: If Select is Min or Max, up to 10 colonies are selected, otherwise All colonies are selected.
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.
PopulationName
Default Calculation: By default, each population is labeled as ColonySelection with sequential integers.
Include
Exclude
Isolation
isolationRules
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.
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.
NumberOfColonies
Default Calculation: If Select is Min or Max, up to 10 colonies are selected, otherwise All colonies are selected.
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.
PopulationName
Default Calculation: By default, each population is labeled as ColonySelection with sequential integers.
Include
Exclude
Circularity
circularityRules
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.
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.
NumberOfColonies
Default Calculation: If Select is Min or Max, up to 10 colonies are selected, otherwise All colonies are selected.
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.
PopulationName
Default Calculation: By default, each population is labeled as ColonySelection with sequential integers.
Include
Exclude
Regularity
regularityRules
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.
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.
NumberOfColonies
Default Calculation: If Select is Min or Max, up to 10 colonies are selected, otherwise All colonies are selected.
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.
PopulationName
Default Calculation: By default, each population is labeled as ColonySelection with sequential integers.
Include
Exclude
Fluorescence
fluorescenceRules
Characterization
Dye
The fluorophore used to detect colonies that fluoresce at an EmissionWavelength when exposed to an ExcitationWavelength.
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]
ExcitationWavelength
The wavelength of light that adds energy to colonies and causes them to fluoresce. Pairs with an EmissionWavelength.
Default Calculation: Automatically set to the excitation wavelength specified in the FluorescentExcitationWavelength field of model cell in CellTypes.
EmissionWavelength
The light that the instrument measures to detect colonies fluorescing at a particular wavelength. Pairs with an ExcitationWavelength.
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.
NumberOfColonies
Default Calculation: If Select is Min or Max, up to 10 colonies are selected, otherwise All colonies are selected.
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.
PopulationName
Default Calculation: By default, each population is labeled as ColonySelection with sequential integers.
Include
Exclude
BlueWhiteScreen
blueWhiteScreenRules
Key/value pairs that define a set of colonies into a population based on their BlueWhiteScreen feature.
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.
FilterWavelength
The mean wavelength of light blocked by the absorbance filter. Blue colonies, which have a wavelength around 450 nanometers, appear darker.
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.
NumberOfColonies
Default Calculation: If Select is Min or Max, up to 10 colonies are selected, otherwise All colonies are selected.
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.
PopulationName
Default Calculation: By default, each population is labeled as ColonySelection with sequential integers.
Include
Exclude
AllColonies
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.
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.
Pattern Description: Diameter, Isolation, Regularity, Circularity, Fluorescence, BlueWhiteScreen, or Absorbance or {Isolation, Diameter}
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 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.
Programmatic Pattern: (Min | Max | AboveThreshold | BelowThreshold | Positive | Negative) | Automatic
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.
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.
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.
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.
FilterWavelength
The mean wavelength of light blocked by the absorbance filter. Blue colonies, which have a wavelength around 450 nanometers, appear darker.
Dye
The coloring used to detect colonies that fluoresce at an EmissionWavelength when exposed to an ExcitationWavelength.
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
ExcitationWavelength
The wavelength of light that adds energy to colonies and causes them to fluoresce. Pairs with an EmissionWavelength.
Default Calculation: Automatically set to the excitation wavelength specified in the FluorescentExcitationWavelength field of model cell in CellTypes.
Programmatic Pattern: ((377*Nanometer | 457*Nanometer | 531*Nanometer | 628*Nanometer) | Automatic) | Null
EmissionWavelength
The light that the instrument measures to detect colonies fluorescing at a particular wavelength. Pairs with an ExcitationWavelength.
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
PopulationName
Default Calculation: By default, each population is labeled as ColonySelection with sequential integers.
NumberOfColonies
Default Calculation: If Select is Min or Max, up to 10 colonies are selected, otherwise All colonies are selected.
Include
Exclude
Experiment Options
General
InoculationSource
The type of the media (Solid, Liquid, AgarStab, FreezeDried, or FrozenGlycerol) where the source cells are stored before the experiment. Note that for source type of FrozenGlycerol, the samples are scraped from top and resuspended into liquid media via pipette tips, while the source tube is chilled to remain frozen.
Default Calculation: If the source cells are in liquid media, automatically set to LiquidMedia. Otherwise if the source container is a plate, automatically set to SolidMedia, and if the source container is a vial or tube, automatically set to AgarStab. If the source container model is hermetic or an ampoule, automatically set to FreezeDried. If the source container is stored in freezer or -80 Celsius, automatically set to FrozenGlycerol.
Instrument
The instrument that is used to move cells to fresh liquid media in order to initiate a culture growth.
Default Calculation: If the source cells are on solid media and in a Object[Container,Plate], set to Object[Instrument,ColonyHandler,"Pinhead"]. If the source cells are in liquid media or freeze-dried powder and Preparation->Manual, set to the smallest Microbial pipette that fits the Volume. If the source cells are in an agar stab and Preparation->Manual, set to Model[Instrument, Pipette, "Eppendorf Research Plus P1000, Microbial"] if that will reach the bottom of DestinationMediaContainer. If that tip does not reach, set to a serological pipette. If the source cells are in frozen glycerol and Preparation->Manual, set to Model[Instrument, Pipette, "Eppendorf Research Plus P1000, Microbial"].
Pattern Description: An object of type or subtype Model[Instrument, ColonyHandler], Object[Instrument, ColonyHandler], Object[Instrument, Pipette], or Model[Instrument, Pipette] or Null.
Programmatic Pattern: (ObjectP[{Model[Instrument, ColonyHandler], Object[Instrument, ColonyHandler], Object[Instrument, Pipette], Model[Instrument, Pipette]}] | Automatic) | Null
TransferEnvironment
For each sample, the environment in which the inoculation will be performed. Containers involved in the inoculation will first be moved into the TransferEnvironment (with covers on), uncovered inside of the TransferEnvironment, then covered after the inoculation has finished -- before they're moved back onto the operator cart. This option is only applicable if InoculationSource is LiquidMedia or AgarStab and Preparation->Manual.
Default Calculation: If InoculationSource is LiquidMedia or AgarStab and Preparation->Manual, Automatically set to a biosafety Cabinet.
Pattern Description: An object of type or subtype Model[Instrument, BiosafetyCabinet] or Object[Instrument, BiosafetyCabinet] or Null.
Programmatic Pattern: (ObjectP[{Model[Instrument, BiosafetyCabinet], Object[Instrument, BiosafetyCabinet]}] | Automatic) | Null
Volume
For each sample, if the source cells are in liquid media or freeze dried powder, the amount of suspended source cells to transfer to the destination container.
Default Calculation: If InoculationSource is LiquidMedia or FreezeDried, automatically set to the larger of 1 Microliter and 1/10th of the sample volume.
MediaVolume
For each sample, the starting amount of liquid media in which the source colonies are deposited prior to the colonies being added.
Default Calculation: If InoculationSource is SolidMedia, automatically set to the RecommendedFillVolume of the Destination container, or 40% of the MaxVolume if the field is not populated. Otherwise set to Null
DestinationMedia
Default Calculation: If InoculationSource is FreezeDried and ResuspensionMedia is specified, automatically set to match the ResuspensionMedia. In other cases, DestinationMedia is automatically set to the value in the PreferredLiquidMedia field for the first Model[Cell] in the input sample Composition. If there is no PreferredLiquidMedia, automatically set to Model[Sample, Media, "LB Broth, Miller"].
Pattern Description: An object of type or subtype Object[Sample] or Model[Sample] or a prepared sample or Null.
DestinationMediaContainer
Default Calculation: Automatically set to Model[Container, Plate, "96-well 2mL Deep Well Plate"] if the sample will fit. Otherwise set to the PreferredContainer[] of the output sample.
Programmatic Pattern: (ObjectP[Model[Container]] | (ObjectP[Object[Container]] | _String) | {(ObjectP[Object[Container]] | _String)..}) | Automatic
DestinationWell
Default Calculation: If InoculationSource is LiquidMedia, AgarStab, FreezeDried, or FrozenGlycerol, automatically set to the first empty position of the DestinationMediaContainer. If no empty position is found, automatically set to "A1".
DestinationMix
For each sample, indicates if mixing will occur after the cells are dispensed into the destination container.
Default Calculation: If Destination is LiquidMedia or if DestinationNumberOfMixes is specified, automatically resolves to True.
DestinationMixType
For each sample, the type of mixing that will occur immediately after the cells are dispensed into the destination container. Pipette performs DestinationNumberOfMixes aspiration/dispense cycle(s) of DestinationMixVolume using a pipette. Swirl has the operator place the container on the surface of the TransferEnvironment and perform DestinationNumberOfMixes clockwise rotations of the container. Shake moves the pin on the ColonyHandlerHeadCassette used to pick the colony in a circular motion DestinationNumberOfMixes times in the DestinationWell. If InoculationSource is SolidMedia, Shake is applicable. If InoculationSource is LiquidMedia or AgarStab and Prepartion->Robotic, Pipette is applicable. If InoculationSource is LiquidMedia, FreezeDried, FrozenGlycerol, or AgarStab and Prepartion->Manual, Pipette and Swirl are applicable. See the below table.
Figure 3.1: The possible DestinationMixTypes depend on the InoculationSource and the Preparation options.
Default Calculation: If DestinationMix->True, automatically set based on InoculationSource. If InoculationSource is SolidMedia, set to shake. Otherwise, set to Pipette.
DestinationNumberOfMixes
Pattern Description: Greater than or equal to 0 and less than or equal to 50 in increments of 1 or Null.
DestinationMixVolume
For each sample, the volume that will be repeatedly aspirated and dispensed via pipette from the destination sample in order to mix the destination sample immediately after the inoculation occurs. The same pipette and tips used in the inoculation will be used to mix the destination sample. This option is only applicable if InoculationSource is LiquidMedia or AgarStab.
Default Calculation: If InoculationSource is LiquidMedia, AgarStab, FreezeDried, or FrozenGlycerol, automatically set to 1/2 the volume of the destination sample or the maximum volume of the pipette being used, depending on which value is smaller.
Pattern Description: Greater than or equal to 0 microliters and less than or equal to 50 milliliters or Null.
Tips
Default Calculation: If InoculationSource is LiquidMedia, AgarStab, FreezeDried, or FrozenGlycerol, automatically set to a tip that does not conflict with the incompatible materials of the cells that the tip will come in contact with, the amount being inoculated, and the source and destination containers of the inoculation (accessibility). For more information, please refer to the function TransferDevices[].
Programmatic Pattern: ((Null | ObjectP[{Model[Item, Tips], Object[Item, Tips]}]) | Automatic) | Null
TipType
For each sample, the type of pipette tips used to aspirate and dispense the cells during the inoculation. This option is only applicable if InoculationSource is LiquidMedia.
Default Calculation: If InoculationSource is LiquidMedia, AgarStab, FreezeDried, or FrozenGlycerol, automatically set to the TipType field of the calculated Tips that will be used to perform the inoculation.
TipMaterial
For each sample, the material of the pipette tips used to aspirate and dispense the cells during the inoculation.
Default Calculation: If InoculationSource is LiquidMedia, AgarStab, FreezeDried, or FrozenGlycerol, automatically set to the chemistry of the calculated Tips that will be used to perform the inoculation.
Pattern Description: {ABS, PLA, Acrylic, AmorphousFluoropolymer, CPVC, CTFE, Cycloolefine, COC, Delrin, ECTFE, EPDM, ETFE, EVA, FEP, FFKM, HDPE, Hypalon, LDPE, NaturalRubber, NBR, Neoprene, Nitrile, Noryl, Nylon, PEEK, PEI, Perlast, PharmaPure, Polycarbonate, Polyester, Polyethylene, Polyisoprene, Polyolefin, Polyoxymethylene, Polypropylene, Polystyrene, Polyurethane, PVC, PCTFE, PETG, PF, PFA, PPS, PTFE, PVDF, SEBS, Silicone, SyntheticRubber, TFM, TPE, Tygon, UVPlastic, UVXPO, Viton}, {Aluminum, Alloy, AnodisedAluminum, Brass, Bronze, CarbonSteel, CastIron, Chrome, Copper, Elgiloy, Gold, Hastelloy, Lead, Magnesium, Molybdenum, Nickel, Niobium, Platinum, Silver, Steel, StainlessSteel, Titanium, Tungsten, Zinc}, {Cellulose, Cotton, Polyethylene, Polypropylene, PTFE, Nylon, PES, PLUS, PVDF, GlassFiber, GHP, UHMWPE, EPDM, DuraporePVDF, GxF, ZebaDesaltingResin, NickelResin, Silica, HLB}, {Silica, Alumina, ResinParticlesWithLatexMicroBeads, CrossLinkedDextranBeads, CrossLinkedPolystyrene, AerisCoreShell, KinetexCoreShell, CrossLinkedAgarose, Vydac218MS, JordiGel, Styrene, SilicaCompositeTWIN, BEH, CSH, HSS, CarboPacPA1, CarboPacPA10, BEH}, Polysulfone, Agate, AluminiumOxide, ZirconiumOxide, Cardboard, Ceramic, Epoxy, EpoxyResin, BorosilicateGlass, Glass, GlassyCarbon, Graphite, OpticalGlass, Porcelain, Quartz, UVQuartz, ESQuartz, FusedQuartz, IRQuartz, Oxidizer, Ruby, Sapphire, Silicon, Silver, Viton, Styrofoam, {VacuumMeltedStainlessSteel}, or Wood or Null.
NumberOfReplicates
WorkCell
Default Calculation: Automatically set to microbioSTAR if Preparation->Robotic and InoculationSource is LiquidMedia. Automatically set to qPix if Preparation is Robotic and InoculationSource is SolidMedia. Otherwise set to 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.
Inoculate From Freeze Dried
ResuspensionMix
For each sample, indicates if the cells in resuspension is mixed after adding ResuspensionMedia to the source sample.
Default Calculation: If InoculationSource is FreezeDried, or if any of the other ResuspensionMix options are set, automatically set to True.
NumberOfResuspensionMixes
For each sample, the number of times that the cells in resuspension is mixed after adding ResuspensionMedia to the source sample.
Default Calculation: If InoculationSource is FreezeDried, or if any of the other ResuspensionMix options are set, automatically set to 5.
Pattern Description: Greater than or equal to 1 and less than or equal to 50 in increments of 1 or Null.
ResuspensionMixVolume
For each sample, the volume that will be repeatedly aspirated and dispensed via pipette from the cells in resuspension in order to mix after adding ResuspensionMedia to the source sample. The same pipette and tips used to add the ResuspensionMedia will be used to mix the cell resuspension.
Default Calculation: If InoculationSource is FreezeDried, or if any of the other ResuspensionMix options are set, automatically set to 1/2 the ResuspensionMediaVolume or 1/2 of the maximum volume of the pipette being used, depending on which value is smaller.
Pattern Description: Greater than or equal to 0.5 microliters and less than or equal to 50 milliliters or Null.
ResuspensionMedia
Default Calculation: Automatically set to match the specified DestinationMedia. If DestinationMedia is not specified, ResuspensionMedia is automatically set to the PreferredLiquidMedia of the Model[Cell] in the sample. If PreferredLiquidMedia is not informed, automatically set to Model[Sample, "Nutrient Broth"].
Pattern Description: An object of type or subtype Model[Sample], Object[Sample], or Object[Container] or a prepared sample or Null.
Programmatic Pattern: ((ObjectP[{Model[Sample], Object[Sample], Object[Container]}] | _String) | Automatic) | Null
ResuspensionMediaVolume
For each sample, the amount of liquid media added to the source samples in order to resuspend the cells.
Inoculate From Frozen Glycerol
NumberOfSourceScrapes
For each sample, the number of times that the sample is scraped with the tip before it is dipped into the liquid media and swirled.
Pattern Description: Greater than or equal to 1 and less than or equal to 20 in increments of 1 or Null.
Inoculate From Solid Media
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. This option is only applicable if InoculationSource is SolidMedia.
Default Calculation: If InoculationSource is SolidMedia, and if the Model[Cell] information in the sample object matches one of the fluorescent excitation and emission pairs of the colony picking instrument, Populations will group the fluorescent colonies into a population. Otherwise, Populations will be 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 or Null.
Programmatic Pattern: (((Fluorescence | BlueWhiteScreen | Diameter | Isolation | Circularity | Regularity | All) | FluorescencePrimitiveP | BlueWhiteScreenPrimitiveP | DiameterPrimitiveP | IsolationPrimitiveP | CircularityPrimitiveP | RegularityPrimitiveP | AllColoniesPrimitiveP | MultiFeaturedPrimitiveP | CustomCoordinates) | Automatic) | Null
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. This option is only applicable if InoculationSource is SolidMedia.
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.
Pattern Description: Greater than or equal to 0.2 millimeters and less than or equal to 10 millimeters or Null.
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. This option is only applicable if InoculationSource is SolidMedia.
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.
Pattern Description: Greater than or equal to 0.2 millimeters and less than or equal to 10 millimeters or Null.
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. This option is only applicable if InoculationSource is SolidMedia.
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. This option is only applicable if InoculationSource is SolidMedia.
Figure 3.5: Regularity is the ratio of the area of the colony to the area of a circle with the colony's perimeter.
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. This option is only applicable if InoculationSource is SolidMedia.
Figure 3.6: Regularity is the ratio of the area of the colony to the area of a circle with the colony's perimeter.
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. This option is only applicable if InoculationSource is SolidMedia.
Figure 3.7: Circularity is a measure of the ratio of the minor axis to the major axis of the best fit ellipse.
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. This option is only applicable if InoculationSource is SolidMedia.
Figure 3.8: Circularity is a measure of the ratio of the minor axis to the major axis of the best fit ellipse.
ImagingStrategies
For each sample, the end goals for capturing images. The options include BrightField imaging, BlueWhite Screening, and Fluorescence imaging. Images can be taken even if they are not used during Analysis. This option is only applicable if InoculationSource is SolidMedia.
Figure 3.9: 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 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.
Programmatic Pattern: ((DuplicateFreeListableP[BrightField | BlueWhiteScreen | VioletFluorescence | GreenFluorescence | OrangeFluorescence | RedFluorescence | DarkRedFluorescence] | BrightField) | Automatic) | Null
ExposureTimes
For each Sample and for each imaging strategy, the length of time to allow the camera to capture an image. An increased ExposureTime leads to brighter images based on a linear scale. This option is only applicable if InoculationSource is SolidMedia.
Figure 3.10: 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 Calculation: If InoculationSource is SolidMedia and ExposureTimes is not specified, optimal exposure time is automatically determined during experiment. This is done by running AnalyzeImageExposure on suggested initial exposure time and calculating pixel gray levels. The process adjusts the exposure time for subsequent image acquisitions until the optimal exposure time is found.
Programmatic Pattern: (({(RangeP[1*Millisecond, 2000*Millisecond] | Automatic)..} | (RangeP[1*Millisecond, 2000*Millisecond] | Automatic)) | Automatic) | Null
ColonyPickingTool
For each sample, the part used to collect the source colonies and deposit them into a destination well. This option is only applicable if InoculationSource is SolidMedia.
Figure 3.11: 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 Calculation: If InoculationSource is SolidMedia, if the DestinationContainer has 24 wells, set to Model[Part,ColonyHandlerHeadCassette, "Qpix 24 pin picking head - E. coli" ]. If the DestinationContainer has 96 or 384 wells, or is an OmniTray, will use the PreferredColonyHanderHeadCassette 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, " Qpix 96 pin picking head, deepwell - E. coli"] if the destination is a deep well plate and Model[Part,ColonyHandlerHeadCassette, " Qpix 96 pin picking head, deepwell - E. coli"] otherwise.
Pattern Description: An object of type or subtype Model[Part, ColonyHandlerHeadCassette] or Object[Part, ColonyHandlerHeadCassette] or Null.
Programmatic Pattern: (ObjectP[{Model[Part, ColonyHandlerHeadCassette], Object[Part, ColonyHandlerHeadCassette]}] | Automatic) | Null
HeadDiameter
For each sample, the width of the metal probe that will pick the colonies. This option is only applicable if InoculationSource is SolidMedia.
Default Calculation: If InoculationSource is SolidMedia, resolves from the ColonyPickingTool[HeadDiameter].
HeadLength
For each sample, the length of the metal probe that will pick the colonies. This option is only applicable if InoculationSource is SolidMedia.
Default Calculation: If InoculationSource is SolidMedia, resolves from the ColonyPickingTool[HeadLength].
NumberOfHeads
For each sample, the number of metal probes on the ColonyHandlerHeadCassette that will pick the colonies. This option is only applicable if InoculationSource is SolidMedia.
Default Calculation: If InoculationSource is SolidMedia, resolves from the ColonyPickingTool[NumberOfHeads].
ColonyHandlerHeadCassetteApplication
For each sample, the designed use of the ColonyPickingTool. This option is only applicable if InoculationSource is SolidMedia.
Default Calculation: If InoculationSource is SolidMedia, resolves from the ColonyPickingTool[Application].
ColonyPickingDepth
For each sample, the deepness to reach into the agar when collecting a colony. This option is only applicable if InoculationSource is SolidMedia.
Pattern Description: Greater than or equal to 0 millimeters and less than or equal to 20 millimeters or Null.
PickCoordinates
For each sample, the coordinates, in Millimeters, from which colonies will be collected from the source plate where {0 Millimeter, 0 Millimeter} is the center of the source well. This option is only applicable if InoculationSource is SolidMedia.
Programmatic Pattern: ((Null | {{RangeP[-63*Millimeter, 63*Millimeter], RangeP[-43*Millimeter, 43*Millimeter]}..}) | Automatic) | Null
DestinationFillDirection
For each Sample, indicates if the destination will be filled with picked colonies in row order or column order. This option is only applicable if InoculationSource is SolidMedia.
MaxDestinationNumberOfColumns
For each sample, the number of columns of colonies to deposit in the destination container. This option is only applicable if InoculationSource is SolidMedia.
Default Calculation: If InoculationSource is SolidMedia, automatically set based on the below Table.
MaxDestinationNumberOfRows
For each sample, the number of rows of colonies to deposit in the destination container. This option is only applicable if InoculationSource is SolidMedia.
Default Calculation: If InoculationSource is SolidMedia, automatically set based on the below Table.
PrimaryWash
For each sample, whether the PrimaryWash stage should be turned on during the sanitization process. This option is only applicable if InoculationSource is SolidMedia.
PrimaryWashSolution
For each sample, the first wash solution that is used during the sanitization process prior to each round of picking. This option is only applicable if InoculationSource is SolidMedia.
Default Calculation: If InoculationSource is SolidMedia, automatically set to Model[Sample,StockSolution,"70% Ethanol"], if PrimaryWash -> True.
Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.
Programmatic Pattern: ((Null | (ObjectP[{Model[Sample], Object[Sample]}] | _String)) | Automatic) | Null
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. This option is only applicable if InoculationSource is SolidMedia.
PrimaryDryTime
For each sample, the length of time the ColonyHandlerHeadCassette is dried over the halogen fan after the cassette is washed in PrimaryWashSolution.. This option is only applicable if InoculationSource is SolidMedia.
SecondaryWash
For each sample, whether the SecondaryWash stage should be turned on during the sanitization process. This option is only applicable if InoculationSource is SolidMedia.
Default Calculation: If InoculationSource is SolidMedia, automatically set to False if PrimaryWash is False.
SecondaryWashSolution
For each sample, the second wash solution that can be used during the sanitization process prior to each round of picking. This option is only applicable if InoculationSource is SolidMedia.
Default Calculation: If InoculationSource is SolidMedia, automatically set to Model[Sample,"Milli-Q water"].
Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.
Programmatic Pattern: ((Null | (ObjectP[{Model[Sample], Object[Sample]}] | _String)) | Automatic) | Null
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. This option is only applicable if InoculationSource is SolidMedia.
SecondaryDryTime
For each sample, the length of time the ColonyHandlerHeadCassette is dried over the halogen fan after the cassette is washed in SecondaryWashSolution. This option is only applicable if InoculationSource is SolidMedia.
TertiaryWash
For each sample, whether the TertiaryWash stage should be turned on during the sanitization process. This option is only applicable if InoculationSource is SolidMedia.
Default Calculation: If InoculationSource is SolidMedia, automatically set to False if SecondaryWash is False.
TertiaryWashSolution
For each sample, the third wash solution that can be used during the sanitization process prior to each round of picking. This option is only applicable if InoculationSource is SolidMedia.
Default Calculation: If InoculationSource is SolidMedia, automatically set to Model[Sample, StockSolution, "10% Bleach"].
Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.
Programmatic Pattern: ((Null | (ObjectP[{Model[Sample], Object[Sample]}] | _String)) | Automatic) | Null
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. This option is only applicable if InoculationSource is SolidMedia.
TertiaryDryTime
For each sample, length of time the ColonyHandlerHeadCassette is dried over the halogen fan after the cassette is washed in TertiaryWashSolution. This option is only applicable if InoculationSource is SolidMedia.
QuaternaryWash
For each sample, whether the QuaternaryWash stage should be turned on during the sanitization process. This option is only applicable if InoculationSource is SolidMedia.
Default Calculation: If InoculationSource is SolidMedia, automatically set to False if TertiaryWash is False.
QuaternaryWashSolution
For each sample, the fourth wash solution that can be used during the process prior to each round of picking. This option is only applicable if InoculationSource is SolidMedia.
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: ((Null | (ObjectP[{Model[Sample], Object[Sample]}] | _String)) | Automatic) | Null
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. This option is only applicable if InoculationSource is SolidMedia.
QuaternaryDryTime
For each sample, the length of time the ColonyHandlerHeadCassette is dried over the halogen fan after the cassette is washed in QuaternaryWashSolution. This option is only applicable if InoculationSource is SolidMedia.
Inoculate From Liquid Media
SourceMix
For each sample, indicates if mixing of the cells in liquid media will occur during aspiration from the source sample.
Default Calculation: If InoculationSource is LiquidMedia,AgarStab, FreezeDried, or FrozenGlycerol, automatically set to True if any of the other SourceMix options are set.
SourceMixType
For each sample, the type of mixing of the cells that will occur immediately before aspiration from the source container. Pipette performs NumberOfSourceMixes aspiration/dispense cycle(s) of SourceMixVolume using a pipette. Swirl has the operator place the container on the surface of the TransferEnvironment and perform DestinationNumberOfMixes clockwise rotations of the container. This option is only applicable if InoculationSource is LiquidMedia. Swirl is only applicable if Preparation->Manual.
Default Calculation: If InoculationSource is LiquidMedia, automatically set to Pipette if any of the other SourceMix options are set.
NumberOfSourceMixes
For each sample, the number of times that the source cells will be mixed during aspiration. This option is only applicable if InoculationSource is LiquidMedia.
Default Calculation: If InoculationSource is LiquidMedia, automatically set to 5 if any of the other SourceMix options are set.
Pattern Description: Greater than or equal to 0 and less than or equal to 50 in increments of 1 or Null.
SourceMixVolume
For each sample, the volume that will be repeatedly aspirated and dispensed via pipette from the source cells in order to mix the source cells immediately before the inoculation occurs. The same pipette and tips used in the inoculation will be used to mix the source cells. This option is only applicable if InoculationSource is LiquidMedia.
Default Calculation: If InoculationSource is LiquidMedia, and SourceMixType is Pipette, automatically set to 1/2 the volume of the source cells or the maximum volume of the pipette being used, depending on which value is smaller.
Pattern Description: Greater than or equal to 0 microliters and less than or equal to 50 milliliters or Null.
PipettingMethod
For each sample, the pipetting parameters used to manipulate the source cells. If other pipetting options are specified, the parameters from the method here are overwritten. This option can only be specified if InoculationSource is LiquidMedia and Preparation->Robotic.
Default Calculation: If InoculationSource is LiquidMedia, automatically set to the PipettingMethod of the model of the sample if available.
Post Experiment
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.
Pattern Description: {AmbientStorage, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, YeastShakingIncubation, BacterialIncubation, BacterialShakingIncubation, MammalianIncubation, ViralIncubation, CrystalIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, UVVisLightTesting} or Disposal or Null.
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 stored according to their current StorageCondition.
Pattern Description: {AmbientStorage, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, YeastShakingIncubation, BacterialIncubation, BacterialShakingIncubation, MammalianIncubation, ViralIncubation, CrystalIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, UVVisLightTesting} or Disposal or Null.
Protocol Options
Organizational Information
Template
A template protocol whose methodology should be reproduced in running this experiment. Option values will be inherited from the template protocol, but can be individually overridden by directly specifying values for those options to this Experiment function.
Pattern Description: An object of type or subtype Object[Protocol] or an object of type or subtype of Object[Protocol] with UnresolvedOptions, ResolvedOptions specified or Null.
Programmatic Pattern: (ObjectP[Object[Protocol]] | FieldReferenceP[Object[Protocol], {UnresolvedOptions, ResolvedOptions}]) | Null
Name
A object name which should be used to refer to the output object in lieu of an automatically generated ID number.
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.
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.
ImageSample
Example Calls
Warnings and Errors
Messages (60)
ColonyHandlerHeadCassetteApplicationMismatch (1)
DestinationMixMismatch (1)
DuplicatedFreezeDriedSamples (1)
HeadDiameterMismatch (1)
HeadLengthMismatch (1)
ImagingOptionMismatch (1)
IncompatibleBiosafetyCabinetAndCellType (2)
IncompatibleMaterials (2)
IndexMatchingPrimitive (1)
InoculationSourceInputMismatch (1)
InoculationSourceOptionMismatch (2)
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)
InvalidDestinationMediaContainer (1)
InvalidDestinationMediaState (1)
InvalidDestinationWellPosition (1)
InvalidInstrument (3)
InvalidMixType (1)
InvalidTransferWellSpecification (1)
MissingImagingStrategies (1)
MixMismatch (1)
MultipleDestinationMediaContainers (1)
MultipleInoculationSourceInInput (1)
MultiplePopulationMethods (1)
NoAutomaticWavelength (1)
NoAvailablePickingTool (1)
NoCompatibleTips (1)
NonOmniTrayContainer (1)
NoPreferredLiquidMedia (1)
NoResuspensionMixForFreezeDriedSample (1)
NoTipsFound (1)
NotPreferredColonyHandlerHead (1)
NumberOfHeadsMismatch (1)
OutOfOrderWashStages (1)
OverAspiratedTransfer (1)
OverlappingPopulations (1)
PickCoordinatesMissing (1)
PickingToolIncompatibleWithDestinationMediaContainer (1)
PrimaryWashMismatch (1)
QPixWashSolutionInsufficientVolume (1)
QuaternaryWashMismatch (1)
RepeatedPopulationNames (1)
SecondaryWashMismatch (1)
TertiaryWashMismatch (1)
TipConnectionMismatch (1)
TipOptionMismatch (1)
TooManyDestinationMediaContainers (1)
TooManyInputContainers (1)
Last modified on Sat 2 Nov 2024 16:59:51