cytoflow.operations.autofluorescence¶
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class
cytoflow.operations.autofluorescence.
AutofluorescenceOp
[source]¶ Bases:
traits.has_traits.HasStrictTraits
Apply autofluorescence correction to a set of fluorescence channels.
The
estimate()
function loads a separate FCS file (not part of the inputExperiment
) and computes the untransformed median and standard deviation of the blank cells. Then,apply()
subtracts the median from the experiment data.To use, set the
blank_file
property to point to an FCS file with unstained or nonfluorescing cells in it; set thechannels
property to a list of channels to correct.apply()
also adds theaf_median
andaf_stdev
metadata to the corrected channels, representing the median and standard deviation of the measured blank distributions.-
channels
¶ The channels to correct.
Type: List(Str)
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blank_file
¶ The filename of a file with “blank” cells (not fluorescent). Used to
estimate()
the autofluorescence.Type: File
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blank_file_conditions
¶ Occasionally, you’ll need to specify the experimental conditions that the blank tube was collected under (to apply the operations in the history.) Specify them here.
Type: Dict
Examples
Create a small experiment:
>>> import cytoflow as flow >>> import_op = flow.ImportOp() >>> import_op.tubes = [flow.Tube(file = "tasbe/rby.fcs")] >>> ex = import_op.apply()
Create and parameterize the operation
>>> af_op = flow.AutofluorescenceOp() >>> af_op.channels = ["Pacific Blue-A", "FITC-A", "PE-Tx-Red-YG-A"] >>> af_op.blank_file = "tasbe/blank.fcs"
Estimate the model parameters
>>> af_op.estimate(ex)
Plot the diagnostic plot
>>> af_op.default_view().plot(ex)
Apply the operation to the experiment
>>> ex2 = af_op.apply(ex)
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estimate
(experiment, subset=None)[source]¶ Estimate the autofluorescence from
blank_file
in channels specified inchannels
.Parameters: - experiment (Experiment) – The experiment to which this operation is applied
- subset (str (default = “”)) – An expression that specifies the events used to compute the autofluorescence
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apply
(experiment)[source]¶ Applies the autofluorescence correction to channels in an experiment.
Parameters: experiment (Experiment) – the experiment to which this op is applied Returns: a new experiment with the autofluorescence median subtracted. The corrected channels have the following metadata added to them: - af_median : Float The median of the non-fluorescent distribution
- af_stdev : Float The standard deviation of the non-fluorescent distribution
Return type: Experiment
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class
cytoflow.operations.autofluorescence.
AutofluorescenceDiagnosticView
[source]¶ Bases:
traits.has_traits.HasStrictTraits
Plots a histogram of each channel, and its median in red. Serves as a diagnostic for the autofluorescence correction.
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op
¶ The
AutofluorescenceOp
whose parameters we’re viewing. Set automatically if you created the instance usingAutofluorescenceOp.default_view()
.Type: Instance(AutofluorescenceOp)
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