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ExperimentRamanSpectroscopy

ExperimentRamanSpectroscopy[Samples]⟹Protocol

generates a Protocol object for performing Raman Spectroscopy on the provided Samples in the THz and IR region (10 cm-1 to 3800 cm-1).

    
Raman spectroscopy is a generally non-destructive analytical technique which provides information about chemical structure and bulk characteristics including morphology, phase, crystallinity, and intermolecular interactions. It is based on the scattering of intense single wavelength light, which is dependent on the interaction of the incident light with chemical bonds within the sample. Stokes and anti-Stokes scattering give information about the spacing of the energetic states in the sample, while the Rayleigh scattering is removed to allow sensitivity in the THz region. Transitions with energies in the THZ or IR region (10 cm-1 to 3800 cm -1) are recorded as peaks on the Raman spectrum with their frequencies reported relative to the excitation frequency. Only transitions which result in change in polarizablity will be visible with this technique; Raman-silent modes can generally be seen by IR spectroscopy. This technique can be applied to crude or purified solids and liquids, and provides information about sample identity, sample purity, as well as sample homogeneity. The experimental results include an averaged spectrum for the entire sample and spatially resolved Raman response generated by measurements at specified coordinates or along a sampling pattern.
    

Experimental Principles

    Figure 1.1: Procedural overview of a Raman Spectroscopy experiment. Step 1: Solid, liquid, or tablet samples are prepared and moved into the sample plate, which is then placed on the sample stage. Step 2: Appropriate adjustments are made to the input power, focus and exposure to maximize the signal-to-noise ratio without saturating the detector. The sample is then irradiated with visible or near-IR light to induce Raman scattering. Step 3: The Raman spectrum is measured over the low frequency/THz region and the IR region, giving information about the structural and chemical composition of the sample respectively. Measurement is performed at a single point or as a function of location by scanning over individual wells or multiple wells in the XY direction. Spatially resolved Raman signals from mapping measurements can be used for principle component analysis based on specific peak intensities.

Instrumentation

    THz Raman WPS

    Figure 2.1: The THz-Raman Well Plate System (WPS) is a plate-based Raman spectrometer composed of a laser source, focusing and filtering optics, a sample stage, and detector. Panel 1: The input signal is generated with a continuous wave diode laser (785 nm, up to 400 mW). Input light is filtered to remove stray frequency photons and directed towards the bottom of the sample plate via a beamsplitter. The input is focused on the bottom of the sample plate using a 2x, 4x, 10x, or 20x objective. Backscattered light from the sample is collected and passed through a pinhole aperture to remove out of focus signal, then filtered through a narrow bandpass notch filter to reduce the intensity of the Rayleigh scattering. Panel 2: The filtered signal is transmitted to a spectrometer module, composed of gratings and a CCD detector, which records the intensity of scattered light from the THz (5 wavenumber) to IR (2800 wavenumber) regime. The Raman spectrum is plotted as scattering intensity against frequency of the scattered light referenced to the Rayleigh frequency. Scattering with higher energy than the Rayleigh line (anti-Stokes scattering) is recorded on the negative axis to -800 wavenumber, while lower energy scattering (Stokes scattering) is recorded on the positive axis to 2800 wavenumber. Raman maps are generated using the relative intensity of constituent scattering peaks measured at each spatial position. Panel 3: The sample stage can be translated in the X, Y, and Z axes, allowing the instrument to scan using predetermined patterns within an individual well or between multiple wells. An optical camera is also mounted under the motorized sample stage to image the sample and identify areas from which data was collected.

Experiment Options

    General

    SampleType

    For each member of SamplesIn, specifies the form factor of the sample as liquid or solid (powder or tablet) which will occupy a well in the sample plate.
    Default Value: Automatic
    Default Calculation: The sample type is determined from the State and Tablet fields of the Object[Sample], and by Aliquot options specifying dilution and the TabletProcessing option. For example, a solid sample with TargetConcentration specified will have SampleType -> Liquid, and a tablet sample with TabletProcessing -> Grind will have SampletType -> Solid.
    Pattern Description: Powder, Liquid, or Tablet.
    Programmatic Pattern: (Powder | Liquid | Tablet) | Automatic
    Index Matches to: experiment samples

    Instrument

    The THz-Raman Spectrometer used to characterize Raman scattering.
    Default Value: Model[Instrument, RamanSpectrometer, THz Raman WPS]
    Pattern Description: An object of type or subtype Model[Instrument, RamanSpectrometer] or Object[Instrument, RamanSpectrometer]
    Programmatic Pattern: ObjectP[{Model[Instrument, RamanSpectrometer], Object[Instrument, RamanSpectrometer]}]

    TabletProcessing

    For each member of SamplesIn, specifies if a tablet should be ground or cut prior to analysis. LargestCrossSection and SmallestCrossSection specify that the tablet is to be cut in half along an axis to expose either the largest or smallest amount of the tablet interior. The largest cross section is obtained by cleaving the tablet parallel to the longest axis, while the smallest cross section will be obtained by cleaving the tablet perpendicular to the longest axis. For scored round tablets, the direction of the score is considered the long axis, and for unscored round tablets LargestCrossSection and SmallestCrossSection are equivalent. The cut face of the tablet is placed facing downward and is subjected to Raman analysis.
    Default Value: Automatic
    Default Calculation: If SampleType -> Solid for a Tablet input, TabletProcessing is set to Grind. For Tablet samples with SampleType -> Automatic or Tablet, TabletProcessing is set to Whole and for all other samples it is set to Null.
    Pattern Description: Whole, LargestCrossSection, SmallestCrossSection, or Grind or Null.
    Programmatic Pattern: ((Whole | LargestCrossSection | SmallestCrossSection | Grind) | Automatic) | Null
    Index Matches to: experiment samples

    Data Processing

    Blank

    For each member of SamplesIn, the source used to generate a blank sample whose Raman scattering response is subtracted as background from every Raman spectrum collected for that sample. Window indicates that a stored spectrum of the window material wil be subtracted, while None indicates that there will be no blank subtraction.
    Default Value: Automatic
    Default Calculation: Automatically set to Window for samples with SampleType -> Liquid or Powder, and None when SampleType -> Tablet.
    Pattern Description: Sample or Window.
    Programmatic Pattern: ((ObjectP[{Model[Sample], Object[Sample]}] | _String) | (Window | None)) | Automatic
    Index Matches to: experiment samples

    Optics

    FloodLight

    For each member of SamplesIn, indicates if spectroscopic measurements are performed with an objective that creates a broad spot size of approximately 1 Millimeter. FloodLight is best used to obtain a rapid average over the entire sample in cases where spatial resolution of the Raman scattering is not the primary goal.
    Default Value: Automatic
    Default Calculation: If the ObjectiveMagnification is set to Null, FloodLight will be used.
    Pattern Description: True or False.
    Programmatic Pattern: BooleanP | Automatic
    Index Matches to: experiment samples

    ObjectiveMagnification

    For each member of SamplesIn, specifies the magnification factor objective to be used for the excitation beam, optical imaging, and Raman backscattering.
    Default Value: Automatic
    Default Calculation: If FloodLight is True, the ObjectiveMagnification will be set to Null if no optical image is requested, and 2X if optical images are to be taken along with spectroscopic measurements. Otherwise ObjectiveMagnification is set to 10.
    Pattern Description: 2, 4, 10, or 20 or Null.
    Programmatic Pattern: ((2 | 4 | 10 | 20) | Automatic) | Null
    Index Matches to: experiment samples

    LaserPower

    For each member of SamplesIn, specifies the percent of the maximum laser output (400 mW) at the objective. Insufficient LaserPower may result in low signal-to-noise ratio, while excessively LaserPower can result in detector saturation (and loss or spectral resolution) and sample damage. If you are unsure of an appropriate LaserPower, select Optimize.
    Default Value: 20 percent
    Pattern Description: Greater than or equal to 1 percent and less than or equal to 100 percent or Optimize.
    Programmatic Pattern: Optimize | RangeP[1*Percent, 100*Percent]
    Index Matches to: experiment samples

    ExposureTime

    For each member of SamplesIn, specifies the amount of time over which the Raman scattering signal is summed by the CCD detector for each measurement. Insufficient ExposureTime results in weak signal, while excessive ExposureTime may lead to detector saturation and loss of spectral resolution. If you are unsure of an appropriate ExposureTime, select Optimize.
    Default Value: 100 milliseconds
    Pattern Description: Greater than or equal to 1 millisecond or Optimize.
    Programmatic Pattern: Optimize | GreaterEqualP[1*Millisecond]
    Index Matches to: experiment samples

    AdjustmentSample

    For each member of SamplesIn, specifies the sample that should be used to adjust the LaserPower and ExposureTime. If All is selected, the LaserPower and ExposureTime will be adjusted for each sample individually.
    Default Value: Automatic
    Default Calculation: If LaserPower or ExposureTime are set to Optimize, the first measured sample will be used as the adjustment sample.
    Pattern Description: Use Each Sample or Use Selected Sample or Null.
    Programmatic Pattern: ((All | (ObjectP[{Object[Sample], Model[Sample]}] | _String)) | Automatic) | Null
    Index Matches to: experiment samples

    AdjustmentEmissionWavelength

    For each member of SamplesIn, specifies the Raman shift wavelength to be used for optimizing signal intensity. "Max" indicates that the most intense scattering peak will be used.
    Default Value: Automatic
    Default Calculation: If AdjustmentSample is specified or All, AdjustmentEmissionWavelength will be set to use the most intense scattering peak. Otherwise, this option will be set to Null.
    Pattern Description: Single Wavelength or Use Maximum or Null.
    Programmatic Pattern: ((Max | (RangeP[-600*(1/Centimeter), -10*(1/Centimeter)] | RangeP[10*(1/Centimeter), 3800*(1/Centimeter)])) | Automatic) | Null
    Index Matches to: experiment samples

    AdjustmentTarget

    For each member of SamplesIn, specifies the target intensity for an optimized signal as a percentage of the saturation threshold of the detector.
    Default Value: Automatic
    Default Calculation: If AdjustmentSample is specified or All, or Optimize is indicated in ExposureTime or LaserPower, AdjustmentTarget is set to 50 Percent, otherwise this option is set to Null.
    Pattern Description: Greater than or equal to 1 percent and less than or equal to 100 percent or Null.
    Programmatic Pattern: (RangeP[1*Percent, 100*Percent] | Automatic) | Null
    Index Matches to: experiment samples

    BackgroundRemove

    For each member of SamplesIn, indicates if a dark background is subtracted from the sample spectrum. The background is collected with the beam shutter closed and accounts for noise in the CCD detector.
    Default Value: True
    Pattern Description: True or False.
    Programmatic Pattern: BooleanP
    Index Matches to: experiment samples

    CosmicRadiationFilter

    For each member of SamplesIn, indicates if spectra are processed to remove features arising from cosmic rays. Cosmic rays are random and intense bursts of radiation that overwhelm the Raman scattering signal. It is highly recommended that this option is used to eradicate cosmic radiation features which can obfuscate the sample scatting. Note that NumberOfShots should be set to more than 1 (if applicable) in order for this feature to function optimally.
    Default Value: True
    Pattern Description: True or False.
    Programmatic Pattern: BooleanP
    Index Matches to: experiment samples

    CalibrationCheck

    Indicates if the instrument collects a spectrum using a PMMA internal standard prior to measuring the samples. The calibration check reports a value from 0 to 1 representing the similarity between the collected spectrum and the manufacturer collected spectrum (1 is a perfect match). Note that this assessment will not adjust the instrument in any way.
    Default Value: True
    Pattern Description: True or False.
    Programmatic Pattern: BooleanP

    Optical Imaging

    InvertedMicroscopeImage

    For each member of SamplesIn, indicates if an optical image of the sample is taken using an inverted microscope configuration. The optical camera will utilize ObjectiveMagnification.
    Default Value: Automatic
    Default Calculation: If MicroscopeImageExposureTime or MicroscopeImageLightIntensity are informed, InvertedMicroscopeImage is set to True.
    Pattern Description: True or False.
    Programmatic Pattern: BooleanP | Automatic
    Index Matches to: experiment samples

    MicroscopeImageExposureTime

    For each member of SamplesIn, specifies the exposure time for optical microscope images. Optimize will automatically adjust the exposure for best image quality.
    Default Value: Automatic
    Default Calculation: If InvertedMicroscopeImage is True, the default value is Optimize.
    Pattern Description: Optimize or Set Time or Null.
    Programmatic Pattern: ((RangeP[1*Millisecond, 9999*Millisecond] | Optimize) | Automatic) | Null
    Index Matches to: experiment samples

    MicroscopeImageLightIntensity

    For each member of SamplesIn, specifies the power of the blue LED light that illuminates the sample stage for optical imaging.
    Default Value: Automatic
    Default Calculation: If InvertedMicroscopeImage is True, the default value is 10 Percent.
    Pattern Description: Set Percent or Null.
    Programmatic Pattern: ((Alternatives[RangeP[0*Percent, 100*Percent]]) | Automatic) | Null
    Index Matches to: experiment samples

    Reading

    ReadPattern

    Specifies the sequence in which the sample plate is measured.
    Default Value: Row
    Pattern Description: Custom or Predefined.
    Programmatic Pattern: (Row | Column | Serpentine | TransposedSerpentine) | {WellP..}

    NumberOfReads

    For each member of SamplesIn, specifies the number of times that the SamplingPattern is repeated on the sample.
    Default Value: 1
    Pattern Description: Greater than or equal to 1 and less than or equal to 9999 in increments of 1.
    Programmatic Pattern: RangeP[1, 9999, 1]
    Index Matches to: experiment samples

    ReadRestTime

    For each member of SamplesIn, specifies the delay between executing the SamplingPattern in a given well.
    Default Value: 1 second
    Pattern Description: Greater than or equal to 1 second and less than or equal to 9999 seconds.
    Programmatic Pattern: RangeP[1*Second, 9999*Second]
    Index Matches to: experiment samples

    Sampling

    SamplingPattern

    For each member of SamplesIn, specifies pattern or set of points that are samples within each well. SinglePoint: Collects spectra at a single point of the well. Spiral: Collects spectra at each point along a spiral pattern. FilledSpiral: Collects spectra at each point along a spiral pattern with the specified area coverage. FilledSquare: Collects spectra in a designated square area by sampling along an S-pattern. Grid: Collects spectra along specified grid lines. Rings: Collects spectra at sparse points on nested rings. Custom: Collects spectra at the requested coordinates.
    Figure 3.1: Specific motion patterns can be indicated using the available SamplingPattern set and associated options for each pattern. By mapping over the sample, it is possible to compose images of the sample based on the Raman spectra collected at each point. Patterns are restricted to the well in which the sample is located, though it is possible to specify the z-dimension in the Grid and Coordinates patterns to analyze the sample at a variety of depths.
    Default Value: SinglePoint
    Pattern Description: SinglePoint, Spiral, FilledSpiral, FilledSquare, Grid, Rings, or Coordinates.
    Programmatic Pattern: SinglePoint | Spiral | FilledSpiral | FilledSquare | Grid | Rings | Coordinates
    Index Matches to: experiment samples

    SamplingTime

    For each member of SamplesIn, specifies the amount of time to complete the requested Spiral or Grid SamplingPattern.
    Default Value: Automatic
    Default Calculation: The value of SamplingTime is based on the SamplingPattern. For SamplingPattern -> (Spiral or FilledSquare) this will be set to 600 Second.
    Pattern Description: Greater than or equal to 1 second and less than or equal to 9999 seconds or Null.
    Programmatic Pattern: (RangeP[1*Second, 9999*Second] | Automatic) | Null
    Index Matches to: experiment samples

    SpiralInnerDiameter

    For each member of SamplesIn, specifies the inner diameter of the Spiral or FilledSpiral SamplingPattern.
    Default Value: Automatic
    Default Calculation: If the SamplingPattern is set Spiral or Filled Spiral, SpiralInnerDiameter will be set to 50 Micrometer if SpiralOuterDiameter is Automatic or greater than 100 Micrometer, and 1 Micrometer is SpiralOuterDiameter is less than 100 Micrometer.
    Pattern Description: Greater than or equal to 10 micrometers and less than or equal to 250000 micrometers or Null.
    Programmatic Pattern: (RangeP[10*Micrometer, 250000*Micrometer] | Automatic) | Null
    Index Matches to: experiment samples

    SpiralOuterDiameter

    For each member of SamplesIn, specifies the outer diameter of the Spiral or FilledSpiral SamplingPattern.
    Default Value: Automatic
    Default Calculation: If the SamplingPattern is set Spiral or FilledSpiral, SpiralOuterDiameter will be set to 200 Micrometer if SpiralInnerDiameter is Automatic or less than 100 Micrometer, and SpiralInnerDiameter + 200 Micrometer otherwise.
    Pattern Description: Greater than or equal to 10 micrometers and less than or equal to 250000 micrometers or Null.
    Programmatic Pattern: (RangeP[10*Micrometer, 250000*Micrometer] | Automatic) | Null
    Index Matches to: experiment samples

    SpiralFillArea

    For each member of SamplesIn, specifies the percentage of the total area inside the FilledSpiral pattern from which spectra are collected. Note that when percentages greater than 100 Percent are specified, the pattern will include overlapping measurements.
    Default Value: Automatic
    Default Calculation: If the SamplingPattern is set to FilledSpiral, SpiralFillArea will be set to 50 Percent.
    Pattern Description: Greater than or equal to 1 percent and less than or equal to 999 percent or Null.
    Programmatic Pattern: (RangeP[1*Percent, 999*Percent] | Automatic) | Null
    Index Matches to: experiment samples

    SpiralResolution

    For each member of SamplesIn, specifies the distance between adjacent sampling points in the FilledSpiral or Spiral pattern.
    Default Value: Automatic
    Default Calculation: If the SamplingPattern is set to Spiral or FilledSpiral, SpiralResolution will be set to 10 Micrometer.
    Pattern Description: Greater than or equal to 1 micrometer and less than or equal to 250000 micrometers or Null.
    Programmatic Pattern: (RangeP[1*Micrometer, 250000*Micrometer] | Automatic) | Null
    Index Matches to: experiment samples

    SamplingXDimension

    For each member of SamplesIn, specifies the size of the Grid or FilledSquare SamplingPattern in the X direction.
    Default Value: Automatic
    Default Calculation: If the SamplingPattern is set to Grid or FilledSquare, SamplingXDimension will be set to 200 Micrometer.
    Pattern Description: Greater than or equal to 1 micrometer and less than or equal to 250000 micrometers or Null.
    Programmatic Pattern: (RangeP[1*Micrometer, 250000*Micrometer] | Automatic) | Null
    Index Matches to: experiment samples

    SamplingYDimension

    For each member of SamplesIn, specifies the size of the Grid or FilledSquare SamplingPattern in the Y direction.
    Default Value: Automatic
    Default Calculation: If the SamplingPattern is set to Grid or FilledSquare, SamplingYDimension will be set to 200 Micrometer.
    Pattern Description: Greater than or equal to 1 micrometer and less than or equal to 250000 micrometers or Null.
    Programmatic Pattern: (RangeP[1*Micrometer, 250000*Micrometer] | Automatic) | Null
    Index Matches to: experiment samples

    SamplingZDimension

    For each member of SamplesIn, specifies the size of the Grid SamplingPattern in the Z direction.
    Default Value: Automatic
    Default Calculation: When SamplingPattern -> Grid, this will be set to 0 Micrometer, indicating that no z steps will be taken.
    Pattern Description: Greater than or equal to 1 micrometer and less than or equal to 2500 micrometers or Null.
    Programmatic Pattern: (RangeP[1*Micrometer, 2500*Micrometer] | Automatic) | Null
    Index Matches to: experiment samples

    SamplingXStepSize

    For each member of SamplesIn, specifies the spacing between adjacent points of the Grid SamplingPattern in the X direction.
    Default Value: Automatic
    Default Calculation: If the SamplingPattern is set to Grid, SamplingXStepSize will be set to 20 Micrometer.
    Pattern Description: Greater than or equal to 1 micrometer and less than or equal to 250000 micrometers or Null.
    Programmatic Pattern: (RangeP[1*Micrometer, 250000*Micrometer] | Automatic) | Null
    Index Matches to: experiment samples

    SamplingYStepSize

    For each member of SamplesIn, specifies the spacing between adjacent points of the Grid SamplingPattern in the Y direction.
    Default Value: Automatic
    Default Calculation: If the SamplingPattern is set to Grid, SamplingYStepSize will be set to 20 Micrometer.
    Pattern Description: Greater than or equal to 1 micrometer and less than or equal to 250000 micrometers or Null.
    Programmatic Pattern: (RangeP[1*Micrometer, 250000*Micrometer] | Automatic) | Null
    Index Matches to: experiment samples

    SamplingZStepSize

    For each member of SamplesIn, specifies the spacing between adjacent points of the Grid SamplingPattern in the Z direction.
    Default Value: Automatic
    Default Calculation: When SamplingPattern -> Grid, this will be set to 0 Micrometer, indicating that no step will be taken.
    Pattern Description: Greater than or equal to 1 micrometer and less than or equal to 2500 micrometers or Null.
    Programmatic Pattern: (RangeP[1*Micrometer, 2500*Micrometer] | Automatic) | Null
    Index Matches to: experiment samples

    FilledSquareNumberOfTurns

    For each member of SamplesIn, specifies the number of parallel lines within the FilledSquare pattern along which spectra are recorded.
    Default Value: Automatic
    Default Calculation: If the SamplingPattern is set to FilledSquare, FilledSquareNumberOfTurns is set to 10.
    Pattern Description: Greater than or equal to 1 and less than or equal to 999 in increments of 1 or Null.
    Programmatic Pattern: (RangeP[1, 999, 1] | Automatic) | Null
    Index Matches to: experiment samples

    RingSpacing

    For each member of SamplesIn, specifies the difference in radius of consecutive nested rings for the Rings SamplingPattern. This value also designates the radius of the innermost ring.
    Default Value: Automatic
    Default Calculation: If the SamplingPattern is set to Rings, RingSpacing will be set to 100 Micrometer.
    Pattern Description: Greater than or equal to 1 micrometer and less than or equal to 250000 micrometers or Null.
    Programmatic Pattern: (RangeP[1*Micrometer, 250000*Micrometer] | Automatic) | Null
    Index Matches to: experiment samples

    NumberOfRings

    For each member of SamplesIn, specifies the number of evenly spaced rings in the Rings SamplingPattern.
    Default Value: Automatic
    Default Calculation: If the SamplingPattern is set to Rings, NumberOfRings will be set to 5.
    Pattern Description: Greater than or equal to 1 and less than or equal to 99 in increments of 1 or Null.
    Programmatic Pattern: (RangeP[1, 99, 1] | Automatic) | Null
    Index Matches to: experiment samples

    NumberOfSamplingPoints

    For each member of SamplesIn, specifies the total number of distinct measurement points generated along the circumference of the rings specified by NumberOfRings and RingSpacing.
    Default Value: Automatic
    Default Calculation: If the SamplingPattern is set to Rings, NumberOfPoints will be set to 30.
    Pattern Description: Greater than or equal to 1 and less than or equal to 999 in increments of 1 or Null.
    Programmatic Pattern: (RangeP[1, 999, 1] | Automatic) | Null
    Index Matches to: experiment samples

    NumberOfShots

    For each member of SamplesIn, specifies the number of redundant times the sample is illuminated with the excitation laser at each point in the SinglePoint, Grid, Rings, or Coordinates SamplingPattern.
    Default Value: Automatic
    Default Calculation: If SamplingPattern -> (SinglePoint, Grid, Rings, or Coordinates), NumberOfShots will be set to 5.
    Pattern Description: Greater than or equal to 1 and less than or equal to 9999 in increments of 1 or Null.
    Programmatic Pattern: (RangeP[1, 9999, 1] | Automatic) | Null
    Index Matches to: experiment samples

    SamplingCoordinates

    For each member of SamplesIn, specifies positions at which to record spectra. The coordinates are referenced to the center of the well, which has coordinates of (0,0,0).
    Default Value: Automatic
    Default Calculation: If the SamplingPattern is set to Custom, SamplingCoordinates will be set to randomly sample 20 points in the well with the Z-dimension of 0.
    Pattern Description: List of one or more {X Dimension, Y Dimension, Z Dimension} entries or Null.
    Programmatic Pattern: ({{RangeP[-125*Millimeter, 125*Millimeter], RangeP[-85*Millimeter, 85*Millimeter], RangeP[-10*Millimeter, 10*Millimeter]}..} | Automatic) | Null
    Index Matches to: experiment samples

    Protocol

    NumberOfReplicates

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

    Model Input

    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 when the input model has a product associated with both Amount and DefaultContainerModel populated, automatically set to the DefaultContainerModel value in the product. Otherwise set to Model[Container, Vessel, "2mL Tube"].
    Pattern Description: An object of type or subtype Model[Container] or Null.
    Programmatic Pattern: (ObjectP[Model[Container]] | Automatic) | Null
    Index Matches to: experiment samples

    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 1 Milliliter.
    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

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} 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

    Raman Spectroscopy

    Measure the average Raman spectrum of a solid sample:
    Measure the average Raman spectrum of multiple samples:

    Principle Component Analysis

    Map the distribution of distinct components of a solid or liquid sample:

    Tablet Analysis

    Map the distribution of distinct components within tablet cut along a specified axis or analyzed whole:

Preferred Input Containers

    The plate and tablet holder used in this experiment can be loaded from a variety of container types. For solids, it is best to use a container suitable for solid sample transfers.

Data Processing

    Plot spectra as a function of position, the position pattern, or the average of all collected spectra for a given sample:

Warnings and Errors

    Messages  (52)

    ExcessiveRamanSamplingTime  (1)

    If the sampling pattern parameters result in excessively long sampling times, an error is thrown:

    IncompatibleRamanSampleTypes  (1)

    All samples must have SampleType -> Liquid or Powder, or all have SampleType -> Tablet:

    IncorrectRamanSampleType  (1)

    If the SampleType is in conflict with the physical state of the sample after TabletProcessing and Sample Preparation, an error will be thrown:

    InstrumentPrecision  (1)

    If an option is given with higher precision than the instrument can achieve, the value is rounded to the instrument precision and a warning is displayed:

    InvalidRamanBlankFormFactor  (1)

    Blank must be in liquid or solid form, not Tablets:

    InvalidRamanTabletProcessingRequested  (1)

    If the SampleType -> Liquid but the sample is a tablet, an error will be thrown:

    LongRamanSamplingTime  (1)

    If the sampling pattern parameters result in a long sampling time, a warning is thrown:

    MissingNumberOfShots  (1)

    When SamplingPattern -> Rings, Grid, Coordinates, or SinglePoint, NumberOfShots must not be Null:

    MissingRamanAdjustmentEmissionWavelength  (1)

    If an adjustment is performed, AdjustmentEmissionWavelength must not be Null:

    MissingRamanAdjustmentSample  (1)

    If an adjustment is performed, AdjustmentSample must not be Null:

    MissingRamanAdjustmentTarget  (1)

    If an adjustment is performed used AdjustmentTarget must not be Null:

    MissingRamanMicroscopeImageExposureTime  (1)

    If InvertedMicroscopeImage -> True, the MicroscopeImageExposureTime must not be Null :

    MissingRamanMicroscopeImageLightIntensity  (1)

    If InvertedMicroscopeImage -> True, the MicroscopeImageLightIntensity must not be Null :

    MissingRamanSamplingCoordinates  (1)

    When SamplingPattern -> Coordinates, SamplingCoordinates must not be Null:

    MissingRamanSamplingDimension  (1)

    When SamplingPattern -> Grid, SamplingXDimension must not be Null:

    MissingRamanSamplingStepSize  (1)

    When SamplingPattern -> Grid, SamplingXStepSize must not be Null:

    MissingRamanSamplingTime  (1)

    When SamplingPattern -> FilledSpiral, SamplingTime must not be Null:

    MissingRamanTabletProcessing  (1)

    If the sample is a tablet and the TabletProcessing parameters are not specified or automatic, an error will be thrown:

    NoRamanAdjustmentEmissionWavelengthRequired  (1)

    If no adjustment is performed, AdjustmentEmissionWavelength should not be informed:

    NoRamanAdjustmentSampleRequired  (1)

    If no adjustment is performed, AdjustmentSample should not be informed:

    NoRamanAdjustmentTargetRequired  (1)

    If no adjustment is performed, AdjustmentTarget should not be informed:

    NoRamanObjective  (1)

    If FloodLight is False, ObjectiveMagnification must be specified:

    ObjectDoesNotExist  (4)

    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):

    RamanAdjustmentSamplesNotPresent  (1)

    AdjustmentSamples must be a member of SamplesIn or Blank:

    RamanMaxSpeedExceeded  (1)

    If the specified parameters require the sample stage to move a t a speed beyond its capabilities, an error is thrown:

    RamanMissingFilledSquareNumberOfTurns  (1)

    When SamplingPattern -> FilledSquare, FilledSquareNumberOfTurns must not be Null:

    RamanMissingNumberOfRings  (1)

    When SamplingPattern -> Rings, NumberOfRings must not be Null:

    RamanMissingNumberOfSamplingPoints  (1)

    When SamplingPattern -> Rings, NumberOfSamplingPoints must not be Null:

    RamanMissingSpiralFillArea  (1)

    When SamplingPattern -> FilledSpiral, SpiralFillArea must not be Null:

    RamanMissingSpiralInnerDiameter  (1)

    When SamplingPattern -> Spiral or FilledSpiral, SpiralInnerDiameter must not be Null:

    RamanMissingSpiralOuterDiameter  (1)

    When SamplingPattern -> Spiral or FilledSpiral, SpiralOuterDiameter must not be Null:

    RamanMissingSpiralResolution  (1)

    When SamplingPattern -> FilledSpiral, SpiralResolution must not be Null:

    RamanNotEnoughSample  (1)

    If the is not a sufficient amount of sample to perform the experiment, an error will be thrown:

    RamanObjectiveMisMatch  (1)

    If FloodLight is True, ObjectiveMagnification can only be set if InvertedMicroscopeImage is also True:

    RamanSampleTypeRequiresDissolution  (1)

    If the SampleType -> Liquid but the State of the sample is Solid, an error will be thrown:

    RamanSampleWithoutBlank  (1)

    The user will be warned if Liquid/Solid samples do not have any blank specified:

    RamanSamplingCoordinatesPrecision  (1)

    If an option is given with higher precision than the instrument can achieve, the value is rounded to the instrument precision and a warning is displayed:

    RamanSamplingPatternOutOfBounds  (1)

    If the specified parameters result in points which lie outside the well region, an error is thrown:

    RamanSwappedInnerOuterDiameter  (1)

    If the inner spiral diameter is larger than the outer spiral diameter, an error is thrown:

    RamanSwappedXDimensionStepSize  (1)

    If the SamplingXDimension is Smaller than the SamplingXStepSize, an error is thrown:

    RamanSwappedYDimensionStepSize  (1)

    If the SamplingYDimension is Smaller than the SamplingYStepSize, an error is thrown:

    RamanSwappedZDimensionStepSize  (1)

    If the SamplingZDimension is Smaller than the SamplingZStepSize, an error is thrown:

    RamanTabletProcessingInconsistancy  (1)

    If the SampleType -> Solid for a tablet sample but TabletProcessing is not Grind or Automatic, an error will be thrown:

    TabletWithRamanBlankSample  (1)

    The Blank option is not supported for tablet inputs:

    TooManyRamanSampleInputs  (1)

    If there are too many samples to be measured in a single plate for the specified SampleType, and error will be thrown:

    UnusedRamanMicroscopeImageExposureTime  (1)

    If MicroscopeImageExposureTime is set but InvertedMicroscopeImage -> False, an error is thrown:

    UnusedRamanMicroscopeImageLightIntensity  (1)

    If MicroscopeImageLightIntensity is set but InvertedMicroscopeImage -> False, an error is thrown:

    UnusedRamanSamplingPatternParameterOption  (1)

    If parameters are specified which are not required for the selected SamplingPattern, an error will be thrown:

    UnusedRamanTabletProcessing  (1)

    If TabletProcessing is specified but the sample is not a tablet, an error will be shown:

Possible Issues

    Uneven Surface

    Uneven surfaces on processed tablets may not result in reliable spectra depending when sampling at a fixed z-dimension. Use TabletProcessing -> Crush to measure the tablet as a powder or select a SamplingPattern that allows adjustment along the Z-axis, such as Coordinates or Grid to analyze the sample composition at multiple depths.

    Background Fluorescence

    Strongly fluorescent samples will be often result in broad background features which overwhelm the weaker Raman scattering. Post processing techniques can generally be used to remove these features. If the fluorescence arises from an impurity or solvent used to dilute the sample, consider purifying the sample or utilizing a different solvent.

    Weak Signal

    Set LaserPower and ExposureTime to Optimize to manually adjust the power and exposure settings for your sample. Increase the LaserPower or Exposure manually, keeping in mind that high power can lead to sample damage and detector saturation will impact spectral resolution. Conversely, LaserPower under 20% might not generate any signal.

    Sample Damage

    Sample damage may be evidenced by a broadening of sample peaks over the course of the measurement or changes in the Raman spectrum between repeated measurements. Decrease the LaserPower and increase Exposure to compensate. If the sample is darkly colored it is possible that laser damage is inevitable in which case it is best to use a SamplingPattern to prevent repeated measurement of damaged areas. A solution of the sample may also help to prevent heating and damage.

    Background Overwhelms Signal

    Background signal from the solvent, matrix, or glass sample plate may convolute weak Raman scattering peaks. If this is problematic, consider setting a Blank sample.

    Cosmic Radiation

    If sharp, intense peaks appear sporadically in the spectra, they are likely a result of cosmic radiation. Use a sampling pattern with NumberOfShots > 2 and set CosmicCorrection -> True to correct for these abberations.
Last modified on Mon 8 Sep 2025 11:11:17

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