ExperimentQuantifyCells
ExperimentQuantifyCells[Samples]⟹Protocol
generates a Protocol object that measures the cell concentration in the provided Samples with various methods. The methods that are currently supported include measuring the absorbance at 600 nm (OD600) of the Samples with AbsorbanceIntensity measurement and measuring the turbidity of the Samples with Nephelometry measurement.
ExperimentQuantifyCells measures the cell concentration in the provided samples with various methods. The methods that are currently supported include measuring the absorbance at 600 nm (OD600) of the samples via AbsorbanceIntensity, and measuring the turbidity of the samples via Nephelometry. The absorbance, or turbidity of the solution is proportional to the cell density in the solution, and can be converted to number of cells per mL using a pre-defined standard curve.
Experimental Principles
Figure 1.1: A general procedural overview of a QuantifyCells experiment. Step 1: Samples are prepared and transferred into instrument-compatible cuvette/plate(s) if it is not in one already. Step 2: The prepared samples are sent into different instruments in the order listed in the Methods option. Step 3: The collected experimental data is converted into cell concentration using any available standard curves or coefficients.
Figure 1.2: Procedural overview of a QuantifyCells experiment using a Cary3500 Spectrophotometer. Step 1: Samples are prepared and transferred into instrument-compatible cuvettes. Step 2: Prepared samples are optionally held at a specified temperature. Step 3: The absorbance value is collected for the specified wavelength for each of the samples (up to 7 samples and 1 blank simultaneously). Step 4: The collected absorbance is converted into cell concentration using any available standard curves or coefficients.
Figure 1.3: Procedural overview of a QuantifyCells experiment using the PHERAstar FS, FLUOstar Omega, or CLARIOstar plate readers. Step 1: Samples are prepared and transferred into a reader-compatible shallow well plate. Step 2: The assay plate is optionally held at a specified temperature inside the plate reader chamber. Step 3: The assay plate is shaken. Step 4: The absorbance value is collected for the specified wavelength for each of the samples. Step 5: The collected absorbance is converted into cell concentration using any available standard curves or coefficients.
Figure 1.4: Procedural overview of a QuantifyCells experiment using a NEPHELOstar Plus plate reader. Step 1: Samples are prepared and transferred into a reader-compatible shallow well plate. Step 2: The assay plate is optionally held at a specified temperature inside the nephelometer chamber. Step 3: The assay plate is shaken. Step 4: The turbidity value is collected for each of the samples. Step 5: The collected turbidity is converted into cell concentration using any available standard curves or coefficients.
Instrumentation
Cary 3500
Figure 2.1: The Cary 3500 is a UV/Vis spectrometer with the capacity to interrogate seven samples and one reference sample simultaneously. The temperature for each pair of sample cuvettes is controlled by Peltier modules for a total of 4 independent temperature zones that can range from -10 Celsius to 100 Celsius. Currently ExperimentUVMelting supports a single temperature profile for all temperature zones. Thermal profiles can be programmed into the instrument to interrogate samples at multiple temperatures. Sample temperature can either be recorded from the cuvette block temperature or by immersion probes. The light source is a xenon flash lamp. The light beam from the lamp is split into different wavelengths ranging from 190 nm to 900 nm and the desired wavelength is isolated using a monochromator. The incident light beam then passes into the sample module where it is split into 8 beams by a fiber optic beam splitter. Each beam excites one sample cuvette and the emitted light is then collected by the instrument detector.
CLARIOstar
Figure 2.2: The CLARIOstar is primarily a monochromator-based plate reader and can thus support arbitrary combinations of excitation and emission wavelengths. Up to five wavelength pairs can be read in a single run. The CLARIOstar also has specialty excitation and emission filters which be used for particularly sensitive assays, including TR-FRET.
The plate chamber can be heated up to 45°C and it can mix the plate at up to 700 RPM before and/or during the run.
The reader has two 300μL syringe pump injectors which can be used for 0.5 - 300 μL injections of two unique samples at up to 4 time points during the run.
There are two primary kinetics read modes. It can perform all readings, injections and mixing for a single well before moving onto the next well or it can read in cycles, reading all the assay wells in the plate again and again until the RunTime has been reached. The second mode is generally recommended for assays except those that use very fast kinetics.
CLARIOstar Plus with ACU
Figure 2.3: The CLARIOstar Plus is primarily a monochromator-based plate reader and can thus support arbitrary combinations of excitation and emission wavelengths. Up to five wavelength pairs can be read in a single run. The CLARIOstar Plus also has specialty excitation and emission filters which be used for particularly sensitive assays, including TR-FRET. The plate chamber can be heated up to 65°C and it can mix the plate at up to 700 RPM before and/or during the run. It has an atmospheric control unit that can control the amount of carbon dioxide and oxygen (0.1-20%) in the plate reader chamber throughout the run. The reader has two 300μL syringe pump injectors which can be used for 0.5 - 300 μL injections of two unique samples at up to 4 time points during the run. There are two primary kinetics read modes. It can perform all readings, injections and mixing for a single well before moving onto the next well or it can read in cycles, reading all the assay wells in the plate again and again until the RunTime has been reached. The second mode is generally recommended for assays except those that use very fast kinetics.
FLUOstar Omega
Figure 2.4: The Omega is a filter-based instrument. It has two independently spinning filter wheels which can be used to support an arbitrary combination of excitation and emission wavelengths. It has eight filter slots in each wheel and all 8 of these filters can be used in a single experiment - though reading will be sequential.
The plate chamber can be headed up to 45°C and it can mix the plate at up to 700 RPM before and/or during the run.
The reader has two 300μL syringe pump injectors which can be used for 0.5 - 300 μL injections of two unique samples at up to 4 time points during the run.
There are two primary kinetics read modes. It can perform all readings, injections and mixing for a single well before moving onto the next well or it can read in cycles, reading all the assay wells in the plate again and again until the RunTime has been reached. The second mode is recommended for most assays, except those that use very fast kinetics.
PHERAstar FS
Figure 2.5: The PHERAstar uses optic modules to package excitation and emission filters into a single package. This means wavelength combinations are restricted to those which already exist in the optic module. Up to five excitation/emission pairs can be recorded in a single experiment. Additionally, the PHERAstar supports dual emission so it's possible to record emission data at 2 different wavelengths simultaneously.
The plate chamber can be heated up to 45°C and it can mix the plate at up to 700 RPM before and/or during the run.
The reader has two 300μL syringe pump injectors which can be used for 0.5 - 300 μL injections of two unique samples at up to four time points during the run.
There are two primary kinetics read modes. It can perform all readings, injections and mixing for a single well before moving onto the next well or it can read in cycles, reading all the assay wells in the plate again and again until the RunTime has been reached. The second mode is recommended for most assays, except those that use very fast kinetics.
NEPHELOstar Plus
Figure 2.6: 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
Methods
The experimental instrumentation used to measure the cell concentration in the input cell samples. Instrumentation options include: 1) Absorbance, where the absorbance (at the provided Wavelength) of the cell sample is measured using a spectrophotometer or plate reader and then converted to QuantificationUnit using either the AbsorbanceStandardCurve or AbsorbanceStandardCoefficient; 2) Nephelometry, where the scattered light attenuation of the cell sample at 653 nm is measured using a nephelometer and then converted to QuantificationUnit using either the NephelometryStandardCurve or NephelometryStandardCoefficient. The order of methods dictates the order of operations when the protocol is executed in the lab.
Default Calculation: Automatically set to Absorbance if any Absorbance options are provided or Instruments is set to a Spectrophotometer or PlateReader. Automatically set to Nephelometry if any Nephelometry options are provided or Instruments is set to a Nephelometer. Otherwise, if QuantificationUnit is set, Methods is automatically set to the instrumentation capable of generating raw experimental results in that unit. If the QuantificationUnit cannot be directly generated by any instrumentation, Methods is automatically set to the instrumentation whose native output can be converted to the QuantificationUnit using the specified StandardCurve/StandardCoefficient, or using the standard curve found from cell models in the Composition of the input samples. Otherwise, Methods is automatically set to Absorbance.
Instruments
The instrument used to measure the absorbance (at the provided Wavelength) or nephelometry (scattered light attenuation) for the input cell samples.
Default Calculation: Automatically set to include a spectrophotometer or plate reader model if Methods include Absorbance. Automatically set to include a nephelometer model if Methods include Nephelometry. Please see the documentation of ExperimentAbsorbanceIntensity and ExperimentNephelometry for more details on the how the instrument option is determined given the input cell samples and corresponding Absorbance/Nephelometry options.
Pattern Description: An object of type or subtype Model[Instrument, PlateReader], Object[Instrument, PlateReader], Model[Instrument, Spectrophotometer], Object[Instrument, Spectrophotometer], Model[Instrument, Nephelometer], or Object[Instrument, Nephelometer]
Programmatic Pattern: ObjectP[{Model[Instrument, PlateReader], Object[Instrument, PlateReader], Model[Instrument, Spectrophotometer], Object[Instrument, Spectrophotometer], Model[Instrument, Nephelometer], Object[Instrument, Nephelometer]}] | Automatic
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.
WorkCell
The automated workstation with a collection of integrated instruments on which this unit operation will be will be performed if Preparation -> Robotic.
NumberOfReplicates
The number of times each of the input samples is analyzed using identical experimental parameters. If Absorbance/NephelometryAliquot is set to True, this specifies the number of replicate aliquots to prepare from each input cell sample under the same aliquot conditions.
RecoupSample
Indicates if the aliquots from the corresponding input cell samples used for quantification measurement are returned to those input cell samples after the protocol is completed.
MultiMethodAliquots
Indicates if a single aliquot is taken from the input cell samples and reused in all quantification measurements (Shared) or if each measurement takes a new aliquot from the input cell samples (Individual).
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.
Pattern Description: {AmbientStorage, EnclosedAmbientStorage, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, YeastShakingIncubation, BacterialIncubation, BacterialShakingIncubation, MammalianIncubation, ViralIncubation, CrystalIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, UVVisLightTesting} or Disposal or Null.
Analysis
QuantificationUnit
The preferred unit of cell concentration to update the composition of the input sample after the quantification measurement. If the specified unit cannot be directly measured with the specified quantification Methods, Absorbance/NephelometryStandardCurve or Absorbance/NephelometryStandardCoefficient will be used to convert the raw experimental result. If the Absorbance/NephelometryStandardCurve or Absorbance/NephelometryStandardCoefficient information is neither provided nor available from the input samples' cell compositions, the unit that is directly measured with the specified quantification Methods will be used to update the composition. The final concentration used to update the composition is the mean value of any raw experimental results and any converted values from the raw experimental result in the unit of QuantificationUnit. If the QuantificationUnit is neither convertible nor directly measured by the quantification Methods, the composition of the input sample will not be updated. If the input sample contains more than one cell type, its composition will not be updated given that the quantification Methods only measure one overall quantity of all contents in the sample.
Default Calculation: Automatically set to "EmeraldCell/Milliliter" if a standard curve or standard coefficient is provided in StandardCurve/StandardCoefficient options or found from the input cell samples' cell Composition to convert the raw experimental result from Methods to "EmeraldCell/Milliliter". Otherwise, automatically set to "OD600".
AbsorbanceStandardCurve
The standard curve used to convert the raw experimental result, expressed in units of OD600 or AbsorbanceUnit, to the specified QuantificationUnit.
Default Calculation: Automatically set to the standard curve that is found from the input cell sample's cell Composition that can convert raw OD600 or AbsorbanceUnit to the target QuantificationUnit. Otherwise, automatically set to Null.
AbsorbanceStandardCoefficient
The factor used to multiply the raw experimental result in units of OD600 or AbsorbanceUnit to the specified QuantificationUnit, assuming a linear relationship.
NephelometryStandardCurve
The standard curve used to convert the raw experimental result, expressed in the unit of RelativeNephelometricUnit, to the specified QuantificationUnit.
Default Calculation: Automatically set to the standard curve that is found from the input cell sample's cell Composition that can convert raw RelativeNephelometricUnit to the target QuantificationUnit. Otherwise, automatically set to Null.
NephelometryStandardCoefficient
The factor used to multiply the raw experimental result in units of RelativeNephelometricUnit to the specified QuantificationUnit, assuming a linear relationship.
Aliquoting
AbsorbanceAliquot
Indicates if an aliquot is taken from the input cell sample or the aliquot from the previous quantification measurements (if any), and is used for the subsequent Absorbance measurement. If NumberOfReplicates is specified this indicates that the input samples will also be aliquoted that number of times.
AbsorbanceAssayBuffer
The solution that is added to the aliquot taken from the input cell sample or the aliquot from the previous quantification measurements (if any). The volume of this solution added is the difference between the AbsorbanceAliquotAmount and the AbsorbanceAssayVolume.
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: ((Null | (ObjectP[{Model[Sample], Object[Sample]}] | _String)) | Automatic) | Null
AbsorbanceAliquotAmount
The amount of the sample that is transferred from the input cell sample or the aliquot from the previous quantification measurements (if any) into the new aliquot.
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.
AbsorbanceAssayVolume
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 4. milliliters or Null.
AbsorbanceAliquotContainer
The desired type of container that is used to house the aliquot sample prior to the Absorbance measurement, with indices indicating grouping of samples in the same plates, if desired.
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: Container or Container with Index or list of one or more Container or Container with Index entries or Null.
Programmatic Pattern: (((ObjectP[{Model[Container], Object[Container]}] | _String) | {GreaterEqualP[1, 1], ObjectP[{Model[Container], Object[Container]}] | _String} | {((ObjectP[{Model[Container], Object[Container]}] | _String) | {GreaterEqualP[1, 1], ObjectP[{Model[Container], Object[Container]}] | _String})..}) | Automatic) | Null
AbsorbanceDestinationWell
The desired position in the corresponding AbsorbanceAliquotContainer in which the aliquot sample will be placed.
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: ((Null | (WellPositionP | {((Automatic | Null) | WellPositionP)..})) | Automatic) | Null
AbsorbanceAliquotSampleStorageCondition
The non-default conditions under which any unused aliquot sample generated for Absorbance measurement is stored after the protocol is completed.
NephelometryAliquot
Indicates if an aliquot is taken from the input cell sample or the aliquot from the previous quantification measurements (if any), and is used for the subsequent Nephelometry measurement. If NumberOfReplicates is specified this indicates that the input samples will also be aliquoted that number of times.
NephelometryAssayBuffer
The solution that is added to the aliquot taken from the input cell sample or the aliquot from the previous quantification measurements (if any). The volume of this solution added is the difference between the NephelometryAliquotAmount and the NephelometryAssayVolume.
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: ((Null | (ObjectP[{Model[Sample], Object[Sample]}] | _String)) | Automatic) | Null
NephelometryAliquotAmount
The amount of the sample that is transferred from the input cell sample or the aliquot from the previous quantification measurements (if any) into the new aliquot.
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.
NephelometryAssayVolume
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 4. milliliters or Null.
NephelometryAliquotContainer
The desired type of container that is used to house the aliquot sample prior to the Nephelometry measurement, with indices indicating grouping of samples in the same plates, if desired.
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: Container or Container with Index or list of one or more Container or Container with Index entries or Null.
Programmatic Pattern: (((ObjectP[{Model[Container], Object[Container]}] | _String) | {GreaterEqualP[1, 1], ObjectP[{Model[Container], Object[Container]}] | _String} | {((ObjectP[{Model[Container], Object[Container]}] | _String) | {GreaterEqualP[1, 1], ObjectP[{Model[Container], Object[Container]}] | _String})..}) | Automatic) | Null
NephelometryDestinationWell
The desired position in the corresponding NephelometryAliquotContainer in which the aliquot sample will be placed.
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: ((Null | (WellPositionP | {((Automatic | Null) | WellPositionP)..})) | Automatic) | Null
NephelometryAliquotSampleStorageCondition
The non-default conditions under which any unused aliquot sample generated for Nephelometry measurement is stored after the protocol is completed.
Blanks
AbsorbanceBlankMeasurement
Indicates if blank samples are prepared and measured prior to Absorbance measurement. The absorbance (at the provided Wavelength) of the blank samples are measured and background subtracted to account for any background signals.
AbsorbanceBlank
The source used to generate a blank sample used to account for the background signal prior to the Absorbance measurement of the cell samples of interest.
Default Calculation: Automatically set to Null if BlankMeasurement is False. Otherwise, automatically set to the value of Solvent in SamplesIn. If Solvent not specfied, set to Model[Sample, "Milli-Q water"].
Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.
Programmatic Pattern: ((Null | (ObjectP[{Model[Sample], Object[Sample]}] | _String)) | Automatic) | Null
AbsorbanceBlankVolume
The volume of the blank that is transferred out and used for blank measurements prior to the Absorbance measurement. If AbsorbanceBlank is specified, AbsorbanceBlankVolume of Null indicates that the blanks are read inside their current containers. If AbsorbanceBlank is specified, AbsorbanceBlankVolume of a specific volume indicates the blanks are transferred to a container with the same model as the measurement container that holds the input cell samples or their aliquots for the Absorbance measurement.
Default Calculation: If BlankMeasurement is True, automatically set to the value of AssayVolume if that was specified, or maximum volume of the container otherwise.
Pattern Description: Greater than or equal to 1 microliter and less than or equal to 4000 microliters or Null.
NephelometryBlankMeasurement
Indicates if blank samples are prepared and measured prior to Nephelometry measurement. The scattered light attenuation of the blank samples are measured and background subtracted to account for any background signals.
NephelometryBlank
The source used to generate a blank sample used to account for the background signal prior to the Nephelometry measurement of the cell samples of interest.
Default Calculation: Automatically set to Null if BlankMeasurement is False. Otherwise, automatically set to the value of Solvent in SamplesIn. If Solvent not specfied, set to Model[Sample, "Milli-Q water"].
Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.
Programmatic Pattern: ((Null | (ObjectP[{Model[Sample], Object[Sample]}] | _String)) | Automatic) | Null
NephelometryBlankVolume
The volume of the blank that is transferred out and used for blank measurements prior to the Nephelometry measurement. If NephelometryBlank is specified, NephelometryBlankVolume of Null indicates that the blanks are read inside their current containers. If NephelometryBlank is specified, NephelometryBlankVolume of a specific volume indicates the blanks are transferred to a container with the same model as the measurement container that holds the input cell samples or their aliquots for the Nephelometry measurement.
Default Calculation: If BlankMeasurement is True, automatically set to the value of AssayVolume if that was specified, or maximum volume of the container otherwise.
Pattern Description: Greater than or equal to 1 microliter and less than or equal to 4000 microliters or Null.
Absorbance Measurement
AbsorbanceAcquisitionTemperature
Indicates the temperature the cell samples are held at during data acquisition within the absorbance instrument.
Default Calculation: Sets to Ambient if an instrument is capable of manipulating the temperature of the samples.
Pattern Description: Ambient or greater than or equal to 25 degrees Celsius and less than or equal to 45 degrees Celsius or Null.
AbsorbanceEquilibrationTime
The length of time for which the cell samples are held at the requested temperature within the absorbance instrument before data acquisition.
Default Calculation: If an instrument is capable setting the temperature of the samples, sets to 0 second when Temperature is set to Ambient. Otherwise, it is set to 5 minutes.
AbsorbanceTargetCarbonDioxideLevel
Pattern Description: Greater than or equal to 0.1 percent and less than or equal to 20 percent or Null.
AbsorbanceTargetOxygenLevel
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.
Pattern Description: Greater than or equal to 0.1 percent and less than or equal to 20 percent or Null.
AbsorbanceAtmosphereEquilibrationTime
The length of time for which the samples equilibrate at the requested oxygen and carbon dioxide level before being read.
Default Calculation: Automatically set to 5 Minute if TargetCarbonDioxideLevel or TargetOxygenLevel is specified. Otherwise, set to Null.
NumberOfReadings
The number of times to acquire data from each input cell sample or its aliquot that is loaded into the instrument during the Absorbance measurement. Each data acquisition is performed on the same cell sample without reloading the instrument.
Default Calculation: If an instrument capable of adjusting NumberOfReadings is selected, resolves to 100. Otherwise resolves to Null
Pattern Description: Greater than or equal to 1 and less than or equal to 200 in increments of 1 or Null.
AbsorbanceMethod
Indicates the type of container to be used to measure the absorbance of the input cell samples or its aliquot. PlateReader utilize an open well container that transverses light from top to bottom. Cuvette uses a square container with transparent sides to transverse light from the front to back at a fixed path length. Microfluidic uses small channels to load samples which are then gravity-driven towards chambers where light transverse from top to bottom and measured at a fixed path length.
Default Calculation: If any of the SamplesIn provided has a volume less than 500 Micro Liter, set to microfluidic. Otherwise, if there are less 8 samples, set to Cuvette. If none of options are true, set to PlateReader
SpectralBandwidth
When using the Cuvette Method, indicates the physical size of the slit from which light passes out from the monochromator. The narrower the bandwidth, the greater the resolution in measurements.
Default Calculation: When using the Cuvette Method, automatically set 1.0 Nanometer. If using plate reader, set to Null.
Pattern Description: Greater than or equal to 0.5 nanometers and less than or equal to 5 nanometers or Null.
Wavelength
The specific wavelength which should be used to measure absorbance of the input cell samples or its aliquot.
Default Calculation: Automatically resolves to the shortest wavelength specified in the input samples' ExtinctionCoefficients field, and 260 Nanometer if that field is not populated.
Pattern Description: Greater than or equal to 200 nanometers and less than or equal to 1000 nanometers or Null.
Nephelometry Measurement
NephelometryAcquisitionTemperature
Indicates the temperature the cell samples are held at during data acquisition within the nephelometer instrument.
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 or Null.
NephelometryEquilibrationTime
The length of time for which the cell samples are held at the requested temperature within the nephelometer instrument before data acquisition.
Default Calculation: Automatically set to 0 second when Temperature is set to Ambient, or 5 minutes when Temperature is above Ambient.
NephelometryTargetCarbonDioxideLevel
Pattern Description: Greater than or equal to 0.1 percent and less than or equal to 20 percent or Null.
NephelometryTargetOxygenLevel
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.
Pattern Description: Greater than or equal to 0.1 percent and less than or equal to 20 percent or Null.
NephelometryAtmosphereEquilibrationTime
The length of time for which the samples equilibrate at the requested oxygen and carbon dioxide level before being read.
Default Calculation: Automatically set to 5 Minute if TargetCarbonDioxideLevel or TargetOxygenLevel is specified. Otherwise, set to Null.
BeamAperture
The diameter of the opening allowing the source laser light to pass through to the cell 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.
Pattern Description: Greater than or equal to 1.5 millimeters and less than or equal to 3.5 millimeters or Null.
BeamIntensity
The percentage of the total amount of the laser source light passed through to reach the cell 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.
Pattern Description: Greater than or equal to 0 percent and less than or equal to 100 percent or Null.
IntegrationTime
The amount of time that scattered light is measured. Increasing the IntegrationTime leads to higher signal and noise intensity.
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.
Protocol Options
Organizational Information
Template
A template protocol whose methodology should be reproduced in running this experiment. Option values will be inherited from the template protocol, but can be individually overridden by directly specifying values for those options to this Experiment function.
Pattern Description: An object of type or subtype Object[Protocol] or an object of type or subtype of Object[Protocol] with UnresolvedOptions, ResolvedOptions specified or Null.
Programmatic Pattern: (ObjectP[Object[Protocol]] | FieldReferenceP[Object[Protocol], {UnresolvedOptions, ResolvedOptions}]) | Null
Name
Example Results
- The results of this protocol contain information about the raw experimental result, linked raw method data source, calculated concentration in the unit of QuantificationUnit in the input sample
protocol = ExperimentQuantifyCells[
Object[Sample, "id:mnk9jOk4GOrl"],
Methods -> {Absorbance, Nephelometry},
MultiMethodAliquots -> Shared,
AbsorbanceMethod -> PlateReader,
Confirm -> True
]
Example Calls
Data Processing
Warnings and Errors
Messages (22)
AliquotOptionMismatch (1)
AlternativeStandardCurveAvailable (2)
Throw a warning if the specified standard curve can not convert the raw experimental result to the target quantification unit becuase it fails the instrument and wavelength check for Absorbance method, but we found an alternative:
Throw a warning if the specified standard curve can not convert the raw experimental result to the target quantification unit but we found an alternative:
ConflictingMethodOptions (3)
Methods and method-specific options are compatible. If a method is specified, its required method-specific options cannot be specified as Null:
Methods and method-specific options are compatible. If in conflict with the specifid methods, method-specific standard curve and standard coefficient options also trigger the error:
Methods and method-specific options are compatible. If Methods is specified to not include a method, the required method-specific options of this excluded method cannot be specified as not Null:
DuplicatedMethods (1)
MissingQuantificationUnit (1)
NoQuantifyCellsMethodToUse (1)
NoStandardCurveCoefficientAvailable (1)
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):
RecoupContamination (1)
RedundantStandardCurve (1)
Possible Issues
Quantifying Concentration
Only SamplesIn with 1 valid cell analyte in their composition are automatically updated with the cell concentration in the unit of QuantificationUnit. If SamplesIn contains more than 1 analytes, please inspect the data object and manually update SamplesIn using DefineComposition. The concentration is averaged over all experimental data collected from the same input sample during the execution of the protocol.
Standard Curve
Even though the standard curve is provided in the option (e.g., AbsorbanceStandardCurve, NephelometryStandardCurve), if a warning is suggesting that it is considered unusable, it will not be used to convert the experimental concentration to the target quantification unit. It can be considered unusable if: 1) the StandardDataUnits do not match the raw experimental unit and the quantification unit; 2) for Absorbance method, the Instrument used obtain the standard curve is not the same object or model as the one used in the ExperimentQuantifyCells call; 3) for Absorbance method, the Wavelengths used to obtain the standard curve are not the same as the Wavelength used in the ExperimentQuantifyCells call.
Standard Coefficient
Last modified on Wed 17 Sep 2025 15:46:23