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ExperimentNephelometry

ExperimentNephelometry[Samples]⟹Protocol

generates a Protocol object for measuring scattered light from the provided Samples.

    
Nephelometry is a measurement of the intensity of scattered light upon passing through a solution containing insoluble, suspended particles. Samples are exposed to visible light at a specific wavelength, and the intensity of the light that is scattered by the particles in solution is measured. The intensity of scattered light is correlated to the amount of particulate matter suspended in solution by comparison to a standard curve. Nephelometry is often used for immunology applications, measuring amounts of antigen in a sample by adding known amounts of antibody, measuring purity of water, drug solubility screening, and measuring turbidity of cell cultures.
    

Experimental Principles

    Figure 1.1: Procedural overview of an Nephelometry experiment using the NEPHELOstar Plus plate reader. Step 1: Plate is loaded with sample. Step 2: The plate is inserted into the plate reader. Step 3: Injection samples are injected into the plate if specified. Step 4: The turbidity measurement is collected for each of the samples.

Instrumentation

    NEPHELOstar Plus

    Figure 2.1: Instrument schematic of a BMG NEPHELOstar Plus nephelometer plate reader. In the NEPHELOstar Plus, a laser sends photons through each well of the plate. The light that is scattered from particles in solution is then directed through a Ulbricht sphere which collects the scattered light and directs it to be measured by a photodiode detector. The plate chamber can be heated up to 65°C and it can mix the plate at up to 700 RPM before the run. The reader has two 300μL syringe pump injectors which can be used for 0.5 - 300 μL injections of two unique samples prior to the run.

Experiment Options

    General

    Instrument

    The nephelometer used to measure scattered light from particles in solution in this experiment.
    Default Value: Model[Instrument, Nephelometer, NEPHELOstar Plus]
    Pattern Description: An object of type or subtype Model[Instrument, Nephelometer] or Object[Instrument, Nephelometer]
    Programmatic Pattern: ObjectP[{Model[Instrument, Nephelometer], Object[Instrument, Nephelometer]}]

    Method

    The type of experiment nephelometric measurements are collected for. CellCount involves measuring the amount of scattered light from cells suspended in solution and using a Standard Curve that relates RNU (Relative Nephelometric Units) to Cells/mL in order to quantify the number of cells in solution. For Method -> Solubility, scattered light from suspended particles in solution will be measured, at a single time point or over a time period. Reagents can be injected into the samples to study their effects on solubility, and dilutions can be performed to determine the point of saturation.
    Default Value: Automatic
    Default Calculation: Automatically set to CellCount if samples are cells and have a StandardCurve. Otherwise, Method is set to Solubility.
    Pattern Description: Solubility or CellCount.
    Programmatic Pattern: NephelometryMethodTypeP | Automatic

    PreparedPlate

    Indicates if a prepared plate is provided for nephelometric measurement. The prepared plate contains the solutions that are ready for tubidity measurements in a plate reader. If 'PreparedPlate' is True, dilution options and Moat options must be Null.
    Default Value: False
    Pattern Description: True or False.
    Programmatic Pattern: BooleanP

    Analyte

    If the Method->Solublity, the compound whose concentration should be determined during this experiment. If Method->CellCount, the strain of cells whose concentration will be determined during this experiment, based on a previously measured standard curve, ReferenceCellCountCurve in the Model[Cell] composing the sample.
    Default Value: Automatic
    Default Calculation: Automatically set to the first value in the Analytes field of the input sample, or, if not populated, to the first analyte in the Composition field of the input sample.
    Pattern Description: An object of type or subtype Model[Molecule], Model[Molecule, cDNA], Model[Molecule, Oligomer], Model[Molecule, Transcript], Model[Molecule, Protein], Model[Molecule, Protein, Antibody], Model[Molecule, Carbohydrate], Model[Molecule, Polymer], Model[Resin], Model[Resin, SolidPhaseSupport], Model[Lysate], Model[ProprietaryFormulation], Model[Virus], Model[Cell], Model[Cell, Mammalian], Model[Cell, Bacteria], Model[Cell, Yeast], Model[Tissue], Model[Material], or Model[Species]
    Programmatic Pattern: ObjectP[List @@ IdentityModelTypeP] | Automatic
    Index Matches to: experiment samples

    RetainCover

    Indicates if the plate seal or lid on the assay container should not be taken off during measurement to decrease evaporation. When this option is set to True, injections cannot be performed as it's not possible to inject samples through the cover. The cover must be clear, as the laser passes from the top of the plate through to the bottom of the plate.
    Default Value: False
    Pattern Description: True or False.
    Programmatic Pattern: BooleanP

    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: Automatic
    Pattern Description: Manual or Robotic.
    Programmatic Pattern: PreparationMethodP | Automatic

    WorkCell

    The automated workstation with a collection of integrated instruments on which this unit operation will be will be performed if Preparation -> Robotic.
    Default Value: Automatic
    Default Calculation: Automatically set to STAR if Preparation->Robotic.
    Pattern Description: STAR, bioSTAR, or microbioSTAR or Null.
    Programmatic Pattern: ((STAR | bioSTAR | microbioSTAR) | Automatic) | Null

    NumberOfReplicates

    The number of times to repeat nephelometry reading on each provided sample. If Aliquot -> True, this also indicates the number of times each provided sample will be aliquoted.
    Default Value: Automatic
    Pattern Description: Greater than or equal to 2 in increments of 1 or Null.
    Programmatic Pattern: (GreaterEqualP[2, 1] | Automatic) | Null

    Optics

    BeamAperture

    The diameter of the opening allowing the source laser light to pass through to the sample. A larger BeamAperture allows more light to pass through to the sample, leading to a higher signal. A setting of 1.5 millimeters is recommended for all 384 and 96 well plates, and 2.5-3.5 millimeters for 48 or less well plates. For non-homogenous solutions, a higher BeamAperture is recommended, and for samples with a large meniscus effect, a smaller BeamAperture is recommended.
    Default Value: 1.5 millimeters
    Pattern Description: Greater than or equal to 1.5 millimeters and less than or equal to 3.5 millimeters.
    Programmatic Pattern: RangeP[1.5*Millimeter, 3.5*Millimeter]

    BeamIntensity

    The percentage of the total amount of the laser source light passed through to reach the sample. For Solubility experiments, 80% is recommended, and for experiments with highly concentrated or highly turbid samples, such as those involving cells, a BeamIntensity of 10% is recommended.
    Default Value: Automatic
    Default Calculation: Automatically set to 80% if Method->Solubility, and 10% if Method->CellCount.
    Pattern Description: Greater than or equal to 0 percent and less than or equal to 100 percent.
    Programmatic Pattern: RangeP[0*Percent, 100*Percent] | Automatic

    Quantification

    QuantifyCellCount

    Indicates if the number of cells in the sample is automatically converted from the measured RNU (Relative Nephelometric Unit) via a StandardCurve in the Model[Cell].
    Default Value: Automatic
    Default Calculation: Automatically set to True if Method->CellCount, and set to False if Method->Solubility.
    Pattern Description: True or False.
    Programmatic Pattern: BooleanP | Automatic
    Index Matches to: experiment samples

    InputConcentration

    The initial assumed concentrations of the experiment samples.
    Default Value: Automatic
    Default Calculation: Automatically determined from the concentration of the analyte in the original source sample.
    Pattern Description: Greater than 0 molar or greater than 0 grams per liter or Null.
    Programmatic Pattern: ((GreaterP[0*Molar] | GreaterP[0*(Gram/Liter)]) | Automatic) | Null
    Index Matches to: experiment samples

    Sample Preparation

    DilutionCurve

    The collection of dilutions that will be performed on the samples before nephelometric measurements are taken. For Fixed Dilution Volume Dilution Curves, the Sample Amount is the volume of the sample that will be mixed with the Diluent Volume of the Diluent to create the desired concentration. For Fixed Dilution Factor Dilution Curves, the Sample Volume is the volume of the sample that will created after being diluted by the Dilution Factor. For example, a 1M sample with a dilution factor of 0.7 will be diluted to a concentration 0.7M. IMPORTANT: Because the dilution curve does not intrinsically include the original sample, in the case of sample dilution the first diluting factor should be 1 or Diluent Volume should be 0 Microliter to include the original sample. If dilutions and injections are specified, injection samples will be injected into every dilution in the curve corresponding to SamplesIn.
    Figure 3.1: Use the DilutionCuve option to create a collection of dilutions that will be performed on the sample.
    Default Value: Automatic
    Default Calculation: This is automatically set Null if Diluent is set to Null or a Serial Dilution Curve is specified.
    Pattern Description: Fixed Dilution Factor or Fixed Dilution Volume or Null.
    Programmatic Pattern: (({{RangeP[0*Microliter, 300*Microliter], RangeP[0*Microliter, 300*Microliter]}..} | {{RangeP[0*Microliter, 300*Microliter], RangeP[0, 1]}..}) | Automatic) | Null
    Index Matches to: experiment samples

    SerialDilutionCurve

    The collection of dilutions that will be performed on the samples before nephelometric measurements are taken. For Serial Dilution Volumes, the Transfer Volume is taken out of the sample and added to a second well with the Diluent Volume of the Diluent. It is mixed, then the Transfer Volume is taken out of that well to be added to a third well. This is repeated to make Number Of Dilutions diluted samples. For example, if a 100 ug/ ml sample with a Transfer Volume of 20 Microliters, a Diluent Volume of 60 Microliters and a Number of Dilutions of 3 is used, it will create a DilutionCurve of 25 ug/ ml, 6.25 ug/ ml, and 1.5625 ug/ ml with each dilution having a volume of 60 Microliters. For Serial Dilution Factors, the sample will be diluted by the dilution factor at each transfer step. IMPORTANT: Because the dilution curve does not intrinsically include the original sample, in the case of sample dilution the first diluting factor should be 1 or Diluent Volume should be 0 Microliter to include the original sample. If dilutions and injections are specified, injection samples will be injected into every dilution in the curve corresponding to SamplesIn.
    Figure 3.2: Use the SerialDilutionCuve option to create a collection of serial dilutions that will be performed on the sample.
    Default Value: Automatic
    Default Calculation: This is automatically set to Null if Diluent is set to Null or a non-serial Dilution Curve is specified. In all other cases it is automatically set to TransferVolume as one tenth of smallest of sample volume or container max volume, DiluentVolume as smallest of sample volume or container max volume, and Number of Dilutions as 3.
    Pattern Description: Serial Dilution Factor or Serial Dilution Volumes or Null.
    Programmatic Pattern: (({RangeP[0*Microliter, 300*Microliter], RangeP[0*Microliter, 300*Microliter], GreaterP[1, 1]} | {RangeP[0*Microliter, 300*Microliter], {RangeP[0, 1], GreaterP[1, 1]} | {RangeP[0, 1]..}}) | Automatic) | Null
    Index Matches to: experiment samples

    Diluent

    The sample that is used to dilute the sample to make a DilutionCurve or SerialDilutionCurve.
    Default Value: Automatic
    Default Calculation: If the measurement is to be performed with DilutionCurve Null, this is automatically set to Null. Otherwise, it is automatically set to the Solvent of the sample. If the Solvent field is not informed, Diluent is 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: ((ObjectP[{Model[Sample], Object[Sample]}] | _String) | Automatic) | Null
    Index Matches to: experiment samples

    Measurement

    Temperature

    The temperature at which the plate reader chamber is held during the course of the reading.
    Default Value: Automatic
    Default Calculation: Automatically set to Ambient if Method->Solubility or the average of the IncubationTemperatures of the Model[Cell] Analytes, or 37 Celsius if that field is not informed if Method->CellCount.
    Pattern Description: Ambient or greater than or equal to 25 degrees Celsius and less than or equal to 65 degrees Celsius.
    Programmatic Pattern: (RangeP[$AmbientTemperature, 65*Celsius] | Ambient) | Automatic

    EquilibrationTime

    The length of time for which the assay plates equilibrate at the requested temperature in the plate reader before being read.
    Default Value: Automatic
    Default Calculation: Automatically set to 0 second when Temperature is set to Ambient, or 5 minutes when Temperature is above Ambient.
    Pattern Description: Greater than or equal to 0 seconds and less than or equal to 72 hours.
    Programmatic Pattern: RangeP[0*Second, $MaxExperimentTime] | Automatic

    TargetCarbonDioxideLevel

    The target amount of carbon dioxide in the atmosphere in the plate reader chamber.
    Default Value: Automatic
    Default Calculation: Automatically set to 5% for mammalian cells, and Null otherwise.
    Pattern Description: Greater than or equal to 0.1 percent and less than or equal to 20 percent or Null.
    Programmatic Pattern: (RangeP[0.1*Percent, 20*Percent] | Automatic) | Null

    TargetOxygenLevel

    The target amount of oxygen in the atmosphere in the plate reader chamber. If specified, nitrogen gas is pumped into the chamber to force oxygen in ambient air out of the chamber until the desired level is reached.
    Default Value: Null
    Pattern Description: Greater than or equal to 0.1 percent and less than or equal to 20 percent or Null.
    Programmatic Pattern: RangeP[0.1*Percent, 20*Percent] | Null

    PlateReaderMix

    Indicates if samples should be mixed inside the plate reader chamber before the samples are read.
    Default Value: False
    Pattern Description: True or False.
    Programmatic Pattern: BooleanP

    PlateReaderMixTime

    The amount of time samples should be mixed inside the plate reader chamber before the samples are read.
    Default Value: Automatic
    Default Calculation: Automatically set to 30 second if PlateReaderMix is True or any other plate reader mix options are specified.
    Pattern Description: Greater than or equal to 1 second and less than or equal to 72 hours or Null.
    Programmatic Pattern: (RangeP[1*Second, $MaxExperimentTime] | Automatic) | Null

    PlateReaderMixRate

    The rate at which the plate is agitated inside the plate reader chamber before the samples are read.
    Default Value: Automatic
    Default Calculation: Automatically set to 700 RPM if PlateReaderMix is True or any other plate reader mix options are specified.
    Pattern Description: Greater than or equal to 100 revolutions per minute and less than or equal to 700 revolutions per minute or Null.
    Programmatic Pattern: (RangeP[100*RPM, 700*RPM] | Automatic) | Null

    PlateReaderMixMode

    The pattern of motion which should be employed to shake the plate before the samples are read.
    Default Value: Automatic
    Default Calculation: Automatically set to DoubleOrbital if PlateReaderMix is True or any other plate reader mix options are specified.
    Pattern Description: Orbital, DoubleOrbital, or Linear or Null.
    Programmatic Pattern: (MechanicalShakingP | Automatic) | Null

    MoatSize

    Indicates the number of concentric perimeters of wells which should be filled with MoatBuffer in order to decrease evaporation from the assay samples during the run.
    Figure 3.3: Use the moat options, MoatBuffer, MoatVolume and MoatSize to create an outer ring of wells filled with buffer. This has been shown to decrease evaporation during long reads.
    Default Value: Automatic
    Default Calculation: Automatically set to 1 if any other moat options are specified.
    Pattern Description: Greater than or equal to 1 and less than or equal to 7 in increments of 1 or Null.
    Programmatic Pattern: (RangeP[1, 7, 1] | Automatic) | Null

    MoatVolume

    Indicates the volume which should be added to each moat well.
    Default Value: Automatic
    Default Calculation: Automatically set to the RecommendedFillVolume of the assay plate model, or if Null, then 75% of the maximum volume of the assay plate if any other moat options are specified.
    Pattern Description: Greater than or equal to 0 microliters or Null.
    Programmatic Pattern: (GreaterEqualP[0*Microliter] | Automatic) | Null

    MoatBuffer

    Indicates the buffer which should be used to fill each moat well.
    Default Value: Automatic
    Default Calculation: Automatically set to Model[Sample,"Milli-Q water"] if any other moat options are specified.
    Pattern Description: An object of type or subtype Object[Sample] or Model[Sample] or a prepared sample or Null.
    Programmatic Pattern: ((ObjectP[{Object[Sample], Model[Sample]}] | _String) | Automatic) | Null

    ReadDirection

    Indicate the plate path the instrument will follow as it measures scattered light in each well, for instance reading all wells in a row before continuing on to the next row (Row).
    Figure 3.4: Use the ReadDirection option to control how the plate reader scans the plate during each read cycle. Choosing a more efficient path will lead to a shorter minimum CycleTime.
    Default Value: Row
    Pattern Description: Row, Column, SerpentineRow, or SerpentineColumn.
    Programmatic Pattern: ReadDirectionP

    SettlingTime

    The time between the movement of the plate and the beginning of the measurement. It reduces potential vibration of the samples in plate due to the stop and go motion of the plate carrier.
    Default Value: 200 milliseconds
    Pattern Description: Greater than or equal to 0 seconds and less than or equal to 1 second.
    Programmatic Pattern: RangeP[0*Second, 1*Second]

    ReadStartTime

    The time at which nephelometry measurement readings will begin, after the plate is in position and the SettlingTime has passed. If a pause is desired before readings begin, set this time to higher than the SettlingTime. For kinetic experiments, the ReadStartTime is the time at which the first cycle begins.
    Default Value: 0 seconds
    Pattern Description: Greater than or equal to 0 seconds and less than or equal to 1200 seconds.
    Programmatic Pattern: RangeP[0*Second, 1200*Second]

    IntegrationTime

    The amount of time that scattered light is measured. Increasing the IntegrationTime leads to higher measurements.
    Default Value: Automatic
    Default Calculation: Automatically set to 1 second if no SamplingPattern is specified, or if SamplingPattern->Matrix. If SamplingPattern->Ring or Spiral, IntegrationTime is set based on the SamplingDistance.
    Pattern Description: Greater than or equal to 20 milliseconds and less than or equal to 10 seconds.
    Programmatic Pattern: RangeP[20*Millisecond, 10*Second] | Automatic

    Sample Handling

    AtmosphereEquilibrationTime

    The length of time for which the samples equilibrate at the requested oxygen and carbon dioxide level before being read.
    Default Value: Automatic
    Default Calculation: Automatically set to 5 Minute if TargetCarbonDioxideLevel or TargetOxygenLevel is specified. Otherwise, set to Null.
    Pattern Description: Greater than or equal to 0 seconds and less than or equal to 24 hours or Null.
    Programmatic Pattern: (RangeP[0*Second, 24*Hour] | Automatic) | Null

    Injections

    PrimaryInjectionSample

    The sample to be injected in the first round of injections in order to introduce a time sensitive reagent/sample into the plate before/during measurement. The corresponding injection volumes can be set with PrimaryInjectionVolume. If DilutionCurve or SerialDilutionCurve is specified, PrimaryInjectionSample will be injected into all dilutions in the curve.
    Default Value: Null
    Pattern Description: An object of type or subtype Object[Sample] or Model[Sample] or a prepared sample or Null.
    Programmatic Pattern: (ObjectP[{Object[Sample], Model[Sample]}] | _String) | Null
    Index Matches to: experiment samples

    PrimaryInjectionVolume

    The amount of the primary sample injected in the first round of injections.
    Default Value: Null
    Pattern Description: Greater than or equal to 0.5 microliters and less than or equal to 300 microliters or Null.
    Programmatic Pattern: RangeP[0.5*Microliter, 300*Microliter] | Null
    Index Matches to: experiment samples

    SecondaryInjectionSample

    The sample to be injected in the second round of injections. Set the corresponding injection volumes with SecondaryInjectionVolume. If DilutionCurve or SerialDilutionCurve is specified, SecondaryInjectionSample will be injected into all dilutions in the curve.
    Default Value: Null
    Pattern Description: An object of type or subtype Object[Sample] or Model[Sample] or a prepared sample or Null.
    Programmatic Pattern: (ObjectP[{Object[Sample], Model[Sample]}] | _String) | Null
    Index Matches to: experiment samples

    SecondaryInjectionVolume

    The amount of the secondary sample injected in the second round of injections.
    Default Value: Null
    Pattern Description: Greater than or equal to 0.5 microliters and less than or equal to 300 microliters or Null.
    Programmatic Pattern: RangeP[0.5*Microliter, 300*Microliter] | Null
    Index Matches to: experiment samples

    PrimaryInjectionFlowRate

    The speed at which to transfer injection samples into the assay plate in the first round of injections.
    Default Value: Automatic
    Default Calculation: Defaults to 300 Microliter/Second if primary injections are specified.
    Pattern Description: 430 microliters per second, 400 microliters per second, 350 microliters per second, 300 microliters per second, 260 microliters per second, 220 microliters per second, 190 microliters per second, 170 microliters per second, 150 microliters per second, 135 microliters per second, 115 microliters per second, 100 microliters per second, 85 microliters per second, 65 microliters per second, or 50 microliters per second or Null.
    Programmatic Pattern: (BMGFlowRateP | Automatic) | Null

    SecondaryInjectionFlowRate

    The speed at which to transfer injection samples into the assay plate in the second round of injections.
    Default Value: Automatic
    Default Calculation: Defaults to 300 Microliter/Second if secondary injections are specified.
    Pattern Description: 430 microliters per second, 400 microliters per second, 350 microliters per second, 300 microliters per second, 260 microliters per second, 220 microliters per second, 190 microliters per second, 170 microliters per second, 150 microliters per second, 135 microliters per second, 115 microliters per second, 100 microliters per second, 85 microliters per second, 65 microliters per second, or 50 microliters per second or Null.
    Programmatic Pattern: (BMGFlowRateP | Automatic) | Null

    PrimaryInjectionSampleStorageCondition

    The non-default conditions under which any injection samples used by this experiment are stored after the protocol is completed.
    Default Value: Null
    Pattern Description: {AmbientStorage, EnclosedAmbientStorage, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, YeastShakingIncubation, BacterialIncubation, BacterialShakingIncubation, MammalianIncubation, ViralIncubation, CrystalIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, UVVisLightTesting, Oven} or Disposal or Null.
    Programmatic Pattern: (SampleStorageTypeP | Disposal) | Null

    SecondaryInjectionSampleStorageCondition

    The non-default conditions under which any injection samples used by this experiment are stored after the protocol is completed.
    Default Value: Null
    Pattern Description: {AmbientStorage, EnclosedAmbientStorage, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, YeastShakingIncubation, BacterialIncubation, BacterialShakingIncubation, MammalianIncubation, ViralIncubation, CrystalIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, UVVisLightTesting, Oven} or Disposal or Null.
    Programmatic Pattern: (SampleStorageTypeP | Disposal) | Null

    Data Processing

    BlankMeasurement

    Indicates if blank samples are prepared to account for the background signal when measuring scattered light from the assay samples.
    Default Value: True
    Pattern Description: True or False.
    Programmatic Pattern: BooleanP

    Blank

    The source used to generate a blank sample whose scattered light is subtracted as background from the scattered light readings of the input sample.
    Default Value: Automatic
    Default Calculation: Automatically set to Null if BlankMeasurement is False. If BlankMeasurement->True, Blank is set to the Solvent field for each sample. If the Solvent field is not informed, Blank is 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: ((ObjectP[{Model[Sample], Object[Sample]}] | _String) | Automatic) | Null
    Index Matches to: experiment samples

    BlankVolume

    The volume of the blank that should be transferred out and used for blank measurements. Set BlankVolume to Null to indicate blanks should be read inside their current containers.
    Default Value: Automatic
    Default Calculation: If BlankMeasurement is True, automatically set to match the maximum of the volume of each sample or the recommended fill volume of the container. Otherwise set to Null.
    Pattern Description: Greater than or equal to 1 microliter and less than or equal to 4000 microliters or Null.
    Programmatic Pattern: (RangeP[1*Microliter, 4000*Microliter] | Automatic) | Null
    Index Matches to: experiment samples

    Sampling

    SamplingDistance

    Indicates the outer limit of the SamplingPattern.
    Default Value: Automatic
    Default Calculation: Automatically set to 80% of the well diameter of the assay container if SamplingPattern is not Null.
    Pattern Description: Greater than or equal to 1 millimeter and less than or equal to 6 millimeters or Null.
    Programmatic Pattern: (RangeP[1*Millimeter, 6*Millimeter] | Automatic) | Null

    SamplingPattern

    Indicates where in the well measurements are taken. Center indicates that measurements are taken from the center of the well. Ring indicates a ring within the well with a outer diameter of SamplingDistance. Spiral indicates a spiral from the diameter of SamplingDistance to the center of the well. Matrix indicates a grid of readings matching SamplingDimension, filling SamplingDistance. If any part of the grid falls outside of the well, it will not be included in the measurements. Additionally, Spiral will return a much higher background and should only be used bacteria and yeast with a high propensity to clump.
    Default Value: Automatic
    Default Calculation: Resolves to Ring if SamplingDistance is set, and resolves to Matrix if SamplingDimension is set, otherwise resolves to Center.
    Pattern Description: Matrix, Spiral, Ring, or Center.
    Programmatic Pattern: PlateReaderSamplingP | Automatic

    SamplingDimension

    Specifies the size of the grid used for Matrix sampling to fill to SamplingDistance. For example, SamplingDimension->5 will scan a 5 x 5 grid.
    Figure 3.5: When SamplingPattern->Matrix, SamplingDistance is the length of the square that will be measured within the well diameter; SamplingDimension is an integer representing the number of squares forming a grid within the SamplingDistance.
    Default Value: Automatic
    Default Calculation: Automatically set to 5 if SamplingPattern->Matrix, and Null otherwise.
    Pattern Description: Greater than or equal to 2 and less than or equal to 30 or Null.
    Programmatic Pattern: (RangeP[2, 30] | Automatic) | Null

    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 stored according to their current StorageCondition.
    Default Value: Null
    Pattern Description: {AmbientStorage, EnclosedAmbientStorage, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, YeastShakingIncubation, BacterialIncubation, BacterialShakingIncubation, MammalianIncubation, ViralIncubation, CrystalIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, UVVisLightTesting, Oven} or Disposal or Null.
    Programmatic Pattern: (Alternatives[SampleStorageTypeP | Disposal]) | Null
    Index Matches to: experiment samples

    Model Input

    PreparedModelAmount

    Indicates the amount of a Model[Sample] specified as input to the experiment function that will be prepared in the PreparedModelContainer. When set to All and the input model sample is not preparable, the entire amount of the input model sample that comes from one of the Products is prepared. The selected product must have both Amount and DefaultContainerModel populated, and it must not be a KitProduct. When set to All and the input model is preparable such as water, 1 Milliliter of the input model sample is prepared.
    Default Value: Automatic
    Default Calculation: Automatically set to 100 Microliter.
    Pattern Description: All or Count or Count or Mass or Volume or Null.
    Programmatic Pattern: ((Null | (RangeP[1*Microliter, 20*Liter] | RangeP[1*Milligram, 20*Kilogram] | GreaterP[0*Unit, 1*Unit] | GreaterP[0., 1.] | All)) | Automatic) | Null
    Index Matches to: experiment samples

    PreparedModelContainer

    Indicates the container in which a Model[Sample] specified as input to the experiment function will be prepared.
    Default Value: Automatic
    Default Calculation: If PreparedModelAmount is set to All and the input model has a product associated with both Amount and DefaultContainerModel populated, automatically set to the DefaultContainerModel value in the product. Otherwise, automatically set to Model[Container, Plate, "96-well UV-Star Plate"].
    Pattern Description: An object of type or subtype Model[Container] or Null.
    Programmatic Pattern: ((Null | ObjectP[Model[Container]]) | Automatic) | Null
    Index Matches to: experiment samples

Sample Prep Options

    Sample Preparation

    PreparatoryUnitOperations

    Specifies a sequence of transferring, aliquoting, consolidating, or mixing of new or existing samples before the main experiment. These prepared samples can be used in the main experiment by referencing their defined name. For more information, please reference the documentation for ExperimentSamplePreparation.
    Default Value: Null
    Pattern Description: List of one or more unit Operation ManualSamplePreparation or RoboticSamplePreparation or unit Operation must match SamplePreparationP entries or Null.
    Programmatic Pattern: {((ManualSamplePreparationMethodP | RoboticSamplePreparationMethodP) | SamplePreparationP)..} | Null

    Preparatory Incubation

    Incubate

    Indicates if the SamplesIn should be incubated at a fixed temperature prior to starting the experiment or any aliquoting. Sample Preparation occurs in the order of Incubation, Centrifugation, Filtration, and then Aliquoting (if specified).
    Default Value: Automatic
    Default Calculation: Resolves to True if any of the corresponding Incubation options are set. Otherwise, resolves to False.
    Pattern Description: True or False.
    Programmatic Pattern: BooleanP | Automatic
    Index Matches to: experiment samples

    IncubationTemperature

    Temperature at which the SamplesIn should be incubated for the duration of the IncubationTime prior to starting the experiment.
    Default Value: Automatic
    Pattern Description: Ambient or greater than or equal to -20 degrees Celsius and less than or equal to 500 degrees Celsius or Null.
    Programmatic Pattern: ((Ambient | RangeP[$MinIncubationTemperature, $MaxIncubationTemperature]) | Automatic) | Null
    Index Matches to: experiment samples

    IncubationTime

    Duration for which SamplesIn should be incubated at the IncubationTemperature, prior to starting the experiment.
    Default Value: Automatic
    Pattern Description: Greater than or equal to 1 minute and less than or equal to 72 hours or Null.
    Programmatic Pattern: (RangeP[1*Minute, $MaxExperimentTime] | Automatic) | Null
    Index Matches to: experiment samples

    Mix

    Indicates if this sample should be mixed while incubated, prior to starting the experiment.
    Default Value: Automatic
    Default Calculation: Automatically resolves to True if any Mix related options are set. Otherwise, resolves to False.
    Pattern Description: True or False or Null.
    Programmatic Pattern: (BooleanP | Automatic) | Null
    Index Matches to: experiment samples

    MixType

    Indicates the style of motion used to mix the sample, prior to starting the experiment.
    Default Value: Automatic
    Default Calculation: Automatically resolves based on the container of the sample and the Mix option.
    Pattern Description: Roll, Vortex, Sonicate, Pipette, Invert, Stir, Shake, Homogenize, Swirl, Disrupt, or Nutate or Null.
    Programmatic Pattern: (MixTypeP | Automatic) | Null
    Index Matches to: experiment samples

    MixUntilDissolved

    Indicates if the mix should be continued up to the MaxIncubationTime or MaxNumberOfMixes (chosen according to the mix Type), in an attempt dissolve any solute. Any mixing/incubation will occur prior to starting the experiment.
    Default Value: Automatic
    Default Calculation: Automatically resolves to True if MaxIncubationTime or MaxNumberOfMixes is set.
    Pattern Description: True or False or Null.
    Programmatic Pattern: (BooleanP | Automatic) | Null
    Index Matches to: experiment samples

    MaxIncubationTime

    Maximum duration of time for which the samples will be mixed while incubated in an attempt to dissolve any solute, if the MixUntilDissolved option is chosen. This occurs prior to starting the experiment.
    Default Value: Automatic
    Default Calculation: Automatically resolves based on MixType, MixUntilDissolved, and the container of the given sample.
    Pattern Description: Greater than or equal to 1 minute and less than or equal to 72 hours or Null.
    Programmatic Pattern: (RangeP[1*Minute, $MaxExperimentTime] | Automatic) | Null
    Index Matches to: experiment samples

    IncubationInstrument

    The instrument used to perform the Mix and/or Incubation, prior to starting the experiment.
    Default Value: Automatic
    Default Calculation: Automatically resolves based on the options Mix, Temperature, MixType and container of the sample.
    Pattern Description: An object of type or subtype Model[Instrument, Roller], Model[Instrument, OverheadStirrer], Model[Instrument, Vortex], Model[Instrument, Shaker], Model[Instrument, BottleRoller], Model[Instrument, Roller], Model[Instrument, Sonicator], Model[Instrument, HeatBlock], Model[Instrument, Homogenizer], Model[Instrument, Disruptor], Model[Instrument, Nutator], Model[Instrument, Thermocycler], Model[Instrument, EnvironmentalChamber], Model[Instrument, Pipette], Object[Instrument, Roller], Object[Instrument, OverheadStirrer], Object[Instrument, Vortex], Object[Instrument, Shaker], Object[Instrument, BottleRoller], Object[Instrument, Roller], Object[Instrument, Sonicator], Object[Instrument, HeatBlock], Object[Instrument, Homogenizer], Object[Instrument, Disruptor], Object[Instrument, Nutator], Object[Instrument, Thermocycler], Object[Instrument, EnvironmentalChamber], or Object[Instrument, Pipette] or Null.
    Programmatic Pattern: (ObjectP[Join[MixInstrumentModels, MixInstrumentObjects]] | Automatic) | Null
    Index Matches to: experiment samples

    AnnealingTime

    Minimum duration for which the SamplesIn should remain in the incubator allowing the system to settle to room temperature after the IncubationTime has passed but prior to starting the experiment.
    Default Value: Automatic
    Pattern Description: Greater than or equal to 0 minutes and less than or equal to 72 hours or Null.
    Programmatic Pattern: (RangeP[0*Minute, $MaxExperimentTime] | Automatic) | Null
    Index Matches to: experiment samples

    IncubateAliquotContainer

    The desired type of container that should be used to prepare and house the incubation samples which should be used in lieu of the SamplesIn for the experiment.
    Default Value: Automatic
    Pattern Description: An object of type or subtype Model[Container] or {Index, Container} or Null.
    Programmatic Pattern: ((ObjectP[Model[Container]] | {GreaterEqualP[1, 1] | (Automatic | Null), (ObjectP[{Model[Container], Object[Container]}] | _String) | Automatic}) | Automatic) | Null
    Index Matches to: experiment samples

    IncubateAliquotDestinationWell

    The desired position in the corresponding IncubateAliquotContainer in which the aliquot samples will be placed.
    Default Value: Automatic
    Default Calculation: Automatically resolves to A1 in containers with only one position. For plates, fills wells in the order provided by the function AllWells.
    Pattern Description: Any well from A1 to H12 or Null.
    Programmatic Pattern: (WellPositionP | Automatic) | Null
    Index Matches to: experiment samples

    IncubateAliquot

    The amount of each sample that should be transferred from the SamplesIn into the IncubateAliquotContainer when performing an aliquot before incubation.
    Default Value: Automatic
    Default Calculation: Automatically set as the smaller between the current sample volume and the maximum volume of the destination container.
    Pattern Description: All or greater than or equal to 1 microliter and less than or equal to 20 liters or Null.
    Programmatic Pattern: ((RangeP[1*Microliter, 20*Liter] | All) | Automatic) | Null
    Index Matches to: experiment samples

    Preparatory Centrifugation

    Centrifuge

    Indicates if the SamplesIn should be centrifuged prior to starting the experiment or any aliquoting. Sample Preparation occurs in the order of Incubation, Centrifugation, Filtration, and then Aliquoting (if specified).
    Default Value: Automatic
    Default Calculation: Resolves to True if any of the corresponding Centrifuge options are set. Otherwise, resolves to False.
    Pattern Description: True or False.
    Programmatic Pattern: BooleanP | Automatic
    Index Matches to: experiment samples

    CentrifugeInstrument

    The centrifuge that will be used to spin the provided samples prior to starting the experiment.
    Default Value: Automatic
    Pattern Description: An object of type or subtype Model[Instrument, Centrifuge] or Object[Instrument, Centrifuge] or Null.
    Programmatic Pattern: (ObjectP[{Model[Instrument, Centrifuge], Object[Instrument, Centrifuge]}] | Automatic) | Null
    Index Matches to: experiment samples

    CentrifugeIntensity

    The rotational speed or the force that will be applied to the samples by centrifugation prior to starting the experiment.
    Default Value: Automatic
    Pattern Description: Greater than 0 revolutions per minute or greater than 0 standard accelerations due to gravity on the surface of the earth or Null.
    Programmatic Pattern: ((GreaterP[0*RPM] | GreaterP[0*GravitationalAcceleration]) | Automatic) | Null
    Index Matches to: experiment samples

    CentrifugeTime

    The amount of time for which the SamplesIn should be centrifuged prior to starting the experiment.
    Default Value: Automatic
    Pattern Description: Greater than 0 minutes or Null.
    Programmatic Pattern: (GreaterP[0*Minute] | Automatic) | Null
    Index Matches to: experiment samples

    CentrifugeTemperature

    The temperature at which the centrifuge chamber should be held while the samples are being centrifuged prior to starting the experiment.
    Default Value: Automatic
    Pattern Description: Ambient or greater than or equal to -10 degrees Celsius and less than or equal to 40 degrees Celsius or Null.
    Programmatic Pattern: ((Ambient | RangeP[-10*Celsius, 40*Celsius]) | Automatic) | Null
    Index Matches to: experiment samples

    CentrifugeAliquotContainer

    The desired type of container that should be used to prepare and house the centrifuge samples which should be used in lieu of the SamplesIn for the experiment.
    Default Value: Automatic
    Pattern Description: An object of type or subtype Model[Container] or {Index, Container} or Null.
    Programmatic Pattern: ((ObjectP[Model[Container]] | {GreaterEqualP[1, 1] | (Automatic | Null), (ObjectP[{Model[Container], Object[Container]}] | _String) | Automatic}) | Automatic) | Null
    Index Matches to: experiment samples

    CentrifugeAliquotDestinationWell

    The desired position in the corresponding AliquotContainer in which the aliquot samples will be placed.
    Default Value: Automatic
    Default Calculation: Automatically resolves to A1 in containers with only one position. For plates, fills wells in the order provided by the function AllWells.
    Pattern Description: Any well from A1 to H12 or Null.
    Programmatic Pattern: (WellPositionP | Automatic) | Null
    Index Matches to: experiment samples

    CentrifugeAliquot

    The amount of each sample that should be transferred from the SamplesIn into the CentrifugeAliquotContainer when performing an aliquot before centrifugation.
    Default Value: Automatic
    Default Calculation: Automatically set as the smaller between the current sample volume and the maximum volume of the destination container.
    Pattern Description: All or greater than or equal to 1 microliter and less than or equal to 20 liters or Null.
    Programmatic Pattern: ((RangeP[1*Microliter, 20*Liter] | All) | Automatic) | Null
    Index Matches to: experiment samples

    Preparatory Filtering

    Filtration

    Indicates if the SamplesIn should be filter prior to starting the experiment or any aliquoting. Sample Preparation occurs in the order of Incubation, Centrifugation, Filtration, and then Aliquoting (if specified).
    Default Value: Automatic
    Default Calculation: Resolves to True if any of the corresponding Filter options are set. Otherwise, resolves to False.
    Pattern Description: True or False.
    Programmatic Pattern: BooleanP | Automatic
    Index Matches to: experiment samples

    FiltrationType

    The type of filtration method that should be used to perform the filtration.
    Default Value: Automatic
    Default Calculation: Will automatically resolve to a filtration type appropriate for the volume of sample being filtered.
    Pattern Description: PeristalticPump, Centrifuge, Vacuum, Syringe, or AirPressure or Null.
    Programmatic Pattern: (FiltrationTypeP | Automatic) | Null
    Index Matches to: experiment samples

    FilterInstrument

    The instrument that should be used to perform the filtration.
    Default Value: Automatic
    Default Calculation: Will automatically resolved to an instrument appropriate for the filtration type.
    Pattern Description: An object of type or subtype Model[Instrument, FilterBlock], Object[Instrument, FilterBlock], Model[Instrument, PeristalticPump], Object[Instrument, PeristalticPump], Model[Instrument, VacuumPump], Object[Instrument, VacuumPump], Model[Instrument, Centrifuge], Object[Instrument, Centrifuge], Model[Instrument, SyringePump], or Object[Instrument, SyringePump] or Null.
    Programmatic Pattern: (ObjectP[{Model[Instrument, FilterBlock], Object[Instrument, FilterBlock], Model[Instrument, PeristalticPump], Object[Instrument, PeristalticPump], Model[Instrument, VacuumPump], Object[Instrument, VacuumPump], Model[Instrument, Centrifuge], Object[Instrument, Centrifuge], Model[Instrument, SyringePump], Object[Instrument, SyringePump]}] | Automatic) | Null
    Index Matches to: experiment samples

    Filter

    The filter that should be used to remove impurities from the SamplesIn prior to starting the experiment.
    Default Value: Automatic
    Default Calculation: Will automatically resolve to a filter appropriate for the filtration type and instrument.
    Pattern Description: An object of type or subtype Model[Container, Plate, Filter], Model[Container, Vessel, Filter], or Model[Item, Filter] or Null.
    Programmatic Pattern: (ObjectP[{Model[Container, Plate, Filter], Model[Container, Vessel, Filter], Model[Item, Filter]}] | Automatic) | Null
    Index Matches to: experiment samples

    FilterMaterial

    The membrane material of the filter that should be used to remove impurities from the SamplesIn prior to starting the experiment.
    Default Value: Automatic
    Default Calculation: Resolves to an appropriate filter material for the given sample is Filtration is set to True.
    Pattern Description: Cellulose, Cotton, Polyethylene, Polypropylene, PTFE, Nylon, PES, PLUS, PVDF, GlassFiber, GHP, UHMWPE, EPDM, DuraporePVDF, GxF, ZebaDesaltingResin, NickelResin, AgaroseResin, CobaltResin, Silica, HLB, or AnoporeAlumina or Null.
    Programmatic Pattern: (FilterMembraneMaterialP | Automatic) | Null
    Index Matches to: experiment samples

    PrefilterMaterial

    The material from which the prefilter filtration membrane should be made of to remove impurities from the SamplesIn prior to starting the experiment.
    Default Value: Automatic
    Default Calculation: By default, no prefiltration is performed on samples, even when Filter->True.
    Pattern Description: Cellulose, Cotton, Polyethylene, Polypropylene, PTFE, Nylon, PES, PLUS, PVDF, GlassFiber, GHP, UHMWPE, EPDM, DuraporePVDF, GxF, ZebaDesaltingResin, NickelResin, AgaroseResin, CobaltResin, Silica, HLB, or AnoporeAlumina or Null.
    Programmatic Pattern: (FilterMembraneMaterialP | Automatic) | Null
    Index Matches to: experiment samples

    FilterPoreSize

    The pore size of the filter that should be used when removing impurities from the SamplesIn prior to starting the experiment.
    Default Value: Automatic
    Default Calculation: Resolves to an appropriate filter pore size for the given sample is Filtration is set to True.
    Pattern Description: 0.008 micrometers, 0.02 micrometers, 0.1 micrometers, 0.2 micrometers, 0.22 micrometers, 0.45 micrometers, 1. micrometer, 1.1 micrometers, 2.5 micrometers, 6. micrometers, 20. micrometers, 30. micrometers, or 100. micrometers or Null.
    Programmatic Pattern: (FilterSizeP | Automatic) | Null
    Index Matches to: experiment samples

    PrefilterPoreSize

    The pore size of the filter; all particles larger than this should be removed during the filtration.
    Default Value: Automatic
    Default Calculation: By default, no prefiltration is performed on samples, even when Filter->True.
    Pattern Description: 0.008 micrometers, 0.02 micrometers, 0.1 micrometers, 0.2 micrometers, 0.22 micrometers, 0.45 micrometers, 1. micrometer, 1.1 micrometers, 2.5 micrometers, 6. micrometers, 20. micrometers, 30. micrometers, or 100. micrometers or Null.
    Programmatic Pattern: (FilterSizeP | Automatic) | Null
    Index Matches to: experiment samples

    FilterSyringe

    The syringe used to force that sample through a filter.
    Default Value: Automatic
    Default Calculation: Resolves to an syringe appropriate to the volume of sample being filtered, if Filtration is set to True.
    Pattern Description: An object of type or subtype Model[Container, Syringe] or Object[Container, Syringe] or a prepared sample or Null.
    Programmatic Pattern: ((ObjectP[{Model[Container, Syringe], Object[Container, Syringe]}] | _String) | Automatic) | Null
    Index Matches to: experiment samples

    FilterHousing

    The filter housing that should be used to hold the filter membrane when filtration is performed using a standalone filter membrane.
    Default Value: Automatic
    Default Calculation: Resolve to an housing capable of holding the size of the membrane being used, if filter with Membrane FilterType is being used and Filtration is set to True.
    Pattern Description: An object of type or subtype Model[Instrument, FilterHousing], Object[Instrument, FilterHousing], Model[Instrument, FilterBlock], or Object[Instrument, FilterBlock] or Null.
    Programmatic Pattern: (ObjectP[{Model[Instrument, FilterHousing], Object[Instrument, FilterHousing], Model[Instrument, FilterBlock], Object[Instrument, FilterBlock]}] | Automatic) | Null
    Index Matches to: experiment samples

    FilterIntensity

    The rotational speed or force at which the samples will be centrifuged during filtration.
    Default Value: Automatic
    Default Calculation: Will automatically resolve to 2000 GravitationalAcceleration if FiltrationType is Centrifuge and Filtration is True.
    Pattern Description: Greater than 0 revolutions per minute or greater than 0 standard accelerations due to gravity on the surface of the earth or Null.
    Programmatic Pattern: ((GreaterP[0*RPM] | GreaterP[0*GravitationalAcceleration]) | Automatic) | Null
    Index Matches to: experiment samples

    FilterTime

    The amount of time for which the samples will be centrifuged during filtration.
    Default Value: Automatic
    Default Calculation: Will automatically resolve to 5 Minute if FiltrationType is Centrifuge and Filtration is True.
    Pattern Description: Greater than 0 minutes or Null.
    Programmatic Pattern: (GreaterP[0*Minute] | Automatic) | Null
    Index Matches to: experiment samples

    FilterTemperature

    The temperature at which the centrifuge chamber will be held while the samples are being centrifuged during filtration.
    Default Value: Automatic
    Default Calculation: Will automatically resolve to 22 Celsius if FiltrationType is Centrifuge and Filtration is True.
    Pattern Description: Greater than or equal to 4 degrees Celsius or Null.
    Programmatic Pattern: ((Alternatives[GreaterEqualP[4*Celsius]]) | Automatic) | Null
    Index Matches to: experiment samples

    FilterContainerOut

    The desired container filtered samples should be produced in or transferred into by the end of filtration, with indices indicating grouping of samples in the same plates, if desired.
    Default Value: Automatic
    Default Calculation: Automatically set as the PreferredContainer for the Volume of the sample. For plates, attempts to fill all wells of a single plate with the same model before using another one.
    Pattern Description: An object of type or subtype Model[Container] or Object[Container] or a prepared sample or {Index, Container} or Null.
    Programmatic Pattern: (((ObjectP[{Model[Container], Object[Container]}] | _String) | {GreaterEqualP[1, 1] | Automatic, (ObjectP[{Model[Container], Object[Container]}] | _String) | Automatic}) | Automatic) | Null
    Index Matches to: experiment samples

    FilterAliquotDestinationWell

    The desired position in the corresponding AliquotContainer in which the aliquot samples will be placed.
    Default Value: Automatic
    Default Calculation: Automatically resolves to A1 in containers with only one position. For plates, fills wells in the order provided by the function AllWells.
    Pattern Description: Any well from A1 to H12 or Null.
    Programmatic Pattern: (WellPositionP | Automatic) | Null
    Index Matches to: experiment samples

    FilterAliquotContainer

    The desired type of container that should be used to prepare and house the filter samples which should be used in lieu of the SamplesIn for the experiment.
    Default Value: Automatic
    Pattern Description: An object of type or subtype Model[Container] or {Index, Container} or Null.
    Programmatic Pattern: ((ObjectP[Model[Container]] | {GreaterEqualP[1, 1] | (Automatic | Null), (ObjectP[{Model[Container], Object[Container]}] | _String) | Automatic}) | Automatic) | Null
    Index Matches to: experiment samples

    FilterAliquot

    The amount of each sample that should be transferred from the SamplesIn into the FilterAliquotContainer when performing an aliquot before filtration.
    Default Value: Automatic
    Default Calculation: Automatically set as the smaller between the current sample volume and the maximum volume of the destination container.
    Pattern Description: All or greater than or equal to 1 microliter and less than or equal to 20 liters or Null.
    Programmatic Pattern: ((RangeP[1*Microliter, 20*Liter] | All) | Automatic) | Null
    Index Matches to: experiment samples

    FilterSterile

    Indicates if the filtration of the samples should be done in a sterile environment.
    Default Value: Automatic
    Default Calculation: Resolve to False if Filtration is indicated. If sterile filtration is desired, this option must manually be set to True.
    Pattern Description: True or False or Null.
    Programmatic Pattern: (BooleanP | Automatic) | Null
    Index Matches to: experiment samples

    Aliquoting

    Aliquot

    Indicates if aliquots should be taken from the SamplesIn and transferred into new AliquotSamples used in lieu of the SamplesIn for the experiment. Note that if NumberOfReplicates is specified this indicates that the input samples will also be aliquoted that number of times. Note that Aliquoting (if specified) occurs after any Sample Preparation (if specified).
    Default Value: Automatic
    Pattern Description: True or False.
    Programmatic Pattern: BooleanP | Automatic
    Index Matches to: experiment samples

    AliquotAmount

    The amount of a sample that should be transferred from the input samples into aliquots.
    Default Value: Automatic
    Default Calculation: Automatically set as the smaller between the current sample volume and the maximum volume of the destination container if a liquid, or the current Mass or Count if a solid or counted item, respectively.
    Pattern Description: All or Count or Count or Mass or Volume or Null.
    Programmatic Pattern: ((RangeP[1*Microliter, 20*Liter] | RangeP[1*Milligram, 20*Kilogram] | GreaterP[0*Unit, 1*Unit] | GreaterP[0., 1.] | All) | Automatic) | Null
    Index Matches to: experiment samples

    TargetConcentration

    The desired final concentration of analyte in the AliquotSamples after dilution of aliquots of SamplesIn with the ConcentratedBuffer and BufferDiluent which should be used in lieu of the SamplesIn for the experiment.
    Default Value: Automatic
    Default Calculation: Automatically calculated based on aliquot and buffer volumes.
    Pattern Description: Greater than 0 molar or greater than 0 grams per liter or Null.
    Programmatic Pattern: ((GreaterP[0*Molar] | GreaterP[0*(Gram/Liter)]) | Automatic) | Null
    Index Matches to: experiment samples

    TargetConcentrationAnalyte

    The substance whose final concentration is attained with the TargetConcentration option.
    Default Value: Automatic
    Default Calculation: Automatically set to the first value in the Analytes field of the input sample, or, if not populated, to the first analyte in the Composition field of the input sample, or if none exist, the first identity model of any kind in the Composition field.
    Pattern Description: An object of type or subtype Model[Molecule], Model[Molecule, cDNA], Model[Molecule, Oligomer], Model[Molecule, Transcript], Model[Molecule, Protein], Model[Molecule, Protein, Antibody], Model[Molecule, Carbohydrate], Model[Molecule, Polymer], Model[Resin], Model[Resin, SolidPhaseSupport], Model[Lysate], Model[ProprietaryFormulation], Model[Virus], Model[Cell], Model[Cell, Mammalian], Model[Cell, Bacteria], Model[Cell, Yeast], Model[Tissue], Model[Material], or Model[Species] or Null.
    Programmatic Pattern: (ObjectP[IdentityModelTypes] | Automatic) | Null
    Index Matches to: experiment samples

    AssayVolume

    The desired total volume of the aliquoted sample plus dilution buffer.
    Default Value: Automatic
    Default Calculation: Automatically determined based on Volume and TargetConcentration option values.
    Pattern Description: Greater than or equal to 1 microliter and less than or equal to 20 liters or Null.
    Programmatic Pattern: (RangeP[1*Microliter, 20*Liter] | Automatic) | Null
    Index Matches to: experiment samples

    ConcentratedBuffer

    The concentrated buffer which should be diluted by the BufferDilutionFactor in the final solution (i.e., the combination of the sample, ConcentratedBuffer, and BufferDiluent). The ConcentratedBuffer and BufferDiluent will be combined and then mixed with the sample, where the combined volume of these buffers is the difference between the AliquotAmount and the total AssayVolume.
    Default Value: Automatic
    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

    BufferDilutionFactor

    The dilution factor by which the concentrated buffer should be diluted in the final solution (i.e., the combination of the sample, ConcentratedBuffer, and BufferDiluent). The ConcentratedBuffer and BufferDiluent will be combined and then mixed with the sample, where the combined volume of these buffers is the difference between the AliquotAmount and the total AssayVolume.
    Default Value: Automatic
    Default Calculation: If ConcentratedBuffer is specified, automatically set to the ConcentratedBufferDilutionFactor of that sample; otherwise, set to Null.
    Pattern Description: Greater than or equal to 1 or Null.
    Programmatic Pattern: (GreaterEqualP[1] | Automatic) | Null
    Index Matches to: experiment samples

    BufferDiluent

    The buffer used to dilute the aliquot sample such that ConcentratedBuffer is diluted by BufferDilutionFactor in the final solution. The ConcentratedBuffer and BufferDiluent will be combined and then mixed with the sample, where the combined volume of these buffers is the difference between the AliquotAmount and the total AssayVolume.
    Default Value: Automatic
    Default Calculation: Automatically resolves to Model[Sample, "Milli-Q water"] if ConcentratedBuffer is specified; otherwise, resolves to Null.
    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

    AssayBuffer

    The buffer that should be added to any aliquots requiring dilution, where the volume of this buffer added is the difference between the AliquotAmount and the total AssayVolume.
    Default Value: Automatic
    Default Calculation: Automatically resolves to Model[Sample, "Milli-Q water"] if ConcentratedBuffer is not specified; otherwise, resolves to Null.
    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

    AliquotSampleStorageCondition

    The non-default conditions under which any aliquot samples generated by this experiment should be stored after the protocol is completed.
    Default Value: Automatic
    Pattern Description: {AmbientStorage, EnclosedAmbientStorage, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, YeastShakingIncubation, BacterialIncubation, BacterialShakingIncubation, MammalianIncubation, ViralIncubation, CrystalIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, UVVisLightTesting, Oven} or Disposal or Null.
    Programmatic Pattern: ((SampleStorageTypeP | Disposal) | Automatic) | Null
    Index Matches to: experiment samples

    DestinationWell

    The desired position in the corresponding AliquotContainer in which the aliquot samples will be placed.
    Default Value: Automatic
    Default Calculation: Automatically resolves to A1 in containers with only one position. For plates, fills wells in the order provided by the function AllWells.
    Pattern Description: Any well from A1 to H12 or list of one or more any well from A1 to H12 or any well from A1 to H12 entries or Null.
    Programmatic Pattern: ((WellPositionP | {((Automatic | Null) | WellPositionP)..}) | Automatic) | Null

    AliquotContainer

    The desired type of container that should be used to prepare and house the aliquot samples, with indices indicating grouping of samples in the same plates, if desired. This option will resolve to be the length of the SamplesIn * NumberOfReplicates.
    Default Value: Automatic
    Default Calculation: Automatically set as the PreferredContainer for the AssayVolume of the sample. For plates, attempts to fill all wells of a single plate with the same model before aliquoting into the next.
    Pattern Description: An object of type or subtype Model[Container] or Object[Container] or a prepared sample or Automatic or Null or {Index, Container} or list of one or more an object of type or subtype Model[Container] or Object[Container] or a prepared sample or Automatic or Null entries or list of one or more Automatic or Null or {Index, Container} entries.
    Programmatic Pattern: (((ObjectP[{Model[Container], Object[Container]}] | _String) | (Automatic | Null) | {GreaterEqualP[1, 1] | (Automatic | Null), (ObjectP[{Model[Container], Object[Container]}] | _String) | (Automatic | Null)} | {((ObjectP[{Model[Container], Object[Container]}] | _String) | (Automatic | Null))..} | {({GreaterEqualP[1, 1] | (Automatic | Null), (ObjectP[{Model[Container], Object[Container]}] | _String) | (Automatic | Null)} | (Automatic | Null))..}) | Automatic) | Null

    AliquotPreparation

    Indicates the desired scale at which liquid handling used to generate aliquots will occur.
    Default Value: Automatic
    Default Calculation: Automatic resolution will occur based on manipulation volumes and container types.
    Pattern Description: Manual or Robotic or Null.
    Programmatic Pattern: (PreparationMethodP | Automatic) | Null

    ConsolidateAliquots

    Indicates if identical aliquots should be prepared in the same container/position.
    Default Value: Automatic
    Pattern Description: True or False or Null.
    Programmatic Pattern: (BooleanP | Automatic) | 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.
    Default Value: Null
    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.
    Default Value: Null
    Pattern Description: A string or Null.
    Programmatic Pattern: _String | Null

    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: Automatic
    Pattern Description: True or False or Null.
    Programmatic Pattern: (BooleanP | Automatic) | 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: Automatic
    Pattern Description: True or False or Null.
    Programmatic Pattern: (BooleanP | Automatic) | 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: Automatic
    Pattern Description: True or False or Null.
    Programmatic Pattern: (BooleanP | Automatic) | Null

Example Calls

    Method

    Setting Method->Solubility will obtain a RNU (Relative Nephelometric Unit) measurement from the sample:
    Cell samples that already have a Standard Curve (in the StandardCurves field of the Model[Cell]) that relates RNU to Cell/mL should use Method->CellCount to have the RNU value automatically be converted to Cell/mL. To obtain a Standard Curve, please call ExperimentQuantifyCells:

    PreparedPlate

    If samples and blanks are already in a plate on the list BMGCompatiblePlate[Nephelometry], and no moat or dilutions are desired, set PreparedPlate to True:

    Analyte

    To specify the component of the sample to be measured and quantified, specify Analyte:

    Optics

    To control the amount of light reaching the sample, set BeamIntensity and BeamAperture:

    Quantification

    If QuantifyCellCount is set to True, each sample must have a Model[Cell] Analyte with a StandardCurve that can convert RNU to Cell/mL. The number of cells in each sample will be calculated based on the nephelometry reading and the previously determined fit in StandardCurves. If there are multiple standard curves that can convert between RNU and Cell/mL, the standard curve with the acquisition parameters (BeamAperture, BeamIntensity, IntegrationTime) closest to the acquisition parameters specified in the current experiment is used :
    Set the sample to set as the blank to subtract when quantifying. If not specified, will be set to the Solvent of the sample, or water if Null:

    Dilutions

    To specify dilutions, use the DilutionCurve and SerialDilutionCurve options, depending on the type of dilution desired. Dilutions can be specified based on volumes, specifying the sample and diluent volumes for standard dilutions or the volume of the sample that should be transferred, the volume of diluent the sample should be added to and the number of times the sample should be diluted for serial dilutions:
    Dilutions can also be specified based on dilution factors, either fixed or variable for a serial dilution curve. For standard dilutions, specify the volume of the sample and dilution factor at each point of the curve. For serial dilutions diluting by a fixed factor at each step, provide the volume of the sample, a dilution factor and the number of times the sample should be diluted. For serial dilutions diluting by variable factors at each step, provide the volume of the sample and a series of dilution factors.

    Atmosphere

    To regulate the atmosphere inside the sample chamber, use option TargetCarbonDioxideLevel and TargetOxygenLevel:

    Plate Reader Mixing

    The assay plate can be mixed during readings by specifying any of the PlateReaderMix options:

    Moat

    A moat may be specified to limit evaporation during long read times; use the MoatSize, MoatVolume, and MoatBuffer options to specify:

    Injections

    To specify injections, use the InjectionSample and InjectionVolume options. The sample and volume options are index matched to the input samples allowing you to control the wells which receive injections and the volumes of those injections. In the example below, 50 Microliter of myInjectionSample1 is injected into each well, and then myInjectionSample2 is injected at different volumes into the first two wells but not the third:

Preferred Input Containers

    The NEPHELOstar Plus plate reader can read standard SBS shallow well plates.
    The NEPHELOstar Plus plate reader can inject samples from samples in 2mL, 15mL and 50 mL tubes while measuring turbidity.

Warnings and Errors

    Messages  (32)

    DuplicateName  (1)

    The Name option must not be the name of an already-existing Nephelometry protocol:

    InvalidInput  (1)

    Throw an error if one or multiple of the input samples are discarded:

    NephelometryAnalyteMissing  (1)

    If Analyte is not set and cannot be determined from the sample Analyte field or Composition:

    NephelometryConflictingDilutionCurveTypes  (1)

    If both a serial dilution curve and a custom dilution curve is given, an error will be thrown:

    NephelometryIncompatibleGasLevels  (2)

    If TargetOxygenLevel and TargetCarbonDioxideLevel are incompatible (carbon dioxde level is high when oxygen level is low), an error is thrown:

    If TargetOxygenLevel and TargetCarbonDioxideLevel are incompatible (oxygen level is high when carbon dioxde level is high), an error is thrown:

    NephelometryIncomputableConcentration  (5)

    A warning will be shown if InputConcentrations cannot be resolved when the analyte concentration is in mass concentration units in the sample composition and MolecularWeight for the analyte is unknown:

    A warning will be shown if InputConcentrations cannot be resolved when the analyte concentration is in MassPercent units in the sample composition and Density for the analyte is unknown:

    A warning will be shown if InputConcentrations cannot be resolved when the analyte concentration is in MassPercent units in the sample composition and MolecularWeight for the analyte is unknown:

    A warning will be shown if InputConcentrations cannot be resolved when the analyte concentration is in VolumePercent units in the sample composition and Density for the analyte is unknown:

    A warning will be shown if InputConcentrations cannot be resolved when the analyte concentration is in VolumePercent units in the sample composition and MolecularWeight for the analyte is unknown:

    NephelometryIntegrationTimeTooLarge  (3)

    If IntegrationTime is longer than is allowed for SamplingPattern->Ring and SamplingDistance->3 Millimeter, an error is thrown:

    If IntegrationTime is longer than is allowed for SamplingPattern->Spiral and SamplingDistance->3 Millimeter, an error is thrown:

    If IntegrationTime is longer than is allowed for SamplingPattern->Spiral, an error is thrown:

    NephelometryMethodQuantificationMismatch  (1)

    If Method is not CellCount, QuantifyCellCount cannot be true:

    NephelometryMissingDiluent  (1)

    If a dilution curve is given with no diluent, an error will be thrown:

    NephelometryMissingDilutionCurve  (1)

    Throw error if Diluent is specified but there's no DilutionCurve or SerialDilutionCurve:

    NephelometryNonCellAnalyte  (2)

    If Method is CellCount, the samples must be cells:

    When Method is set to CellCount, the sample's Analyte must be a Model[Cell]:

    NephelometryNoStandardCurve  (1)

    If Method is CellCount, the sample Analyte(s) specified must be Model[Cell]s with a StandardCurve that relates NephelometricTurbidityUnit to Cell/mL:

    NephelometryPreparedPlateContainerInvalid  (2)

    If PreparedPlate is True, the samples must all be in compatible plates:

    If PreparedPlate is True, the samples must all be in compatible plates:

    NephelometryPreparedPlateInvalidOptions  (1)

    If PreparedPlate is True, Dilutions, moat options, and BlankVolume cannot be specified:

    NephelometrySampleMustContainAnalyte  (1)

    The samples must contain the specified Analyte in their composition, if not, an error is thrown:

    NonLiquidSamples  (1)

    If the provided sample is not Liquid, an error will be thrown:

    ObjectDoesNotExist  (6)

    Do NOT throw a message if we have a simulated container but a simulation is specified that indicates that it is simulated:

    Do NOT throw a message if we have a simulated sample but a simulation is specified that indicates that it is simulated:

    Throw a message if we have a container that does not exist (ID form):

    Throw a message if we have a container that does not exist (name form):

    Throw a message if we have a sample that does not exist (ID form):

    Throw a message if we have a sample that does not exist (name form):

    TemperatureNoEquilibration  (1)

    A warning will be shown if Temperature is set above Ambient and EquilibrationTime is set to zero:

Possible Issues

    Impurities in plates

    If a plate is scratched on the bottom, this can effect the light scattering reading. It is recommended to measure at least 4 replicates in case of effects from the plate.

    Meniscus effects

    The meniscus of a sample can change the light scattering intensity from a sample. Sample wells should be filled as close to the MaxVolume of the wells as possible to minimize meniscus effects. When comparing Blank data to sample data, if the sample contains detergent or other similar compounds that effect the meniscus, blank measurements can be higher than sample measurements, leading to negative measurements when the blank measurement is subtracted. In these cases, raw measurements with blank data not subtracted should be used.
Last modified on Thu 4 Sep 2025 14:39:56

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