Calibrate arbitrary channels to molecules-of-fluorophore using fluorescent beads (eg, the Spherotech RCP-30-5A rainbow beads.)
Computes a log-linear calibration function that maps arbitrary fluorescence units to physical units (ie molecules equivalent fluorophore, or MEF).
To use, set Beads to the beads you calibrated with (check the lot!) and Beads File to an FCS file containing events collected using the same cytometer settings as the data you’re calibrating. Then, click Add a channel to add the channels to calibrate, and set both the channel name and the units you want calibrate to. Click Estimate, and make sure you check the diagnostic plot to see that the correct peaks were found.
If it didn’t find all the peaks (or found too many), try tweaking Peak Quantile, Peak Threshold and Peak Cutoff. If you can’t make the peak finding work by tweaking , please submit a bug report!
The beads you’re calibrating with. Make sure to check the lot number!
- Beads file
A file containing the FCS events from the beads.
A list of the channels you want calibrated and the units you want them calibrated in.
- Peak Quantile
Peaks must be at least this quantile high to be considered. Default = 80.
- Peak Threshold
Don’t search for peaks below this brightness. Default = 100.
- class cytoflowgui.op_plugins.bead_calibration.UnitHandler(*args: Any, **kwargs: Any)¶
- class cytoflowgui.op_plugins.bead_calibration.BeadCalibrationHandler(*args: Any, **kwargs: Any)¶
- channels = <traits.traits.ForwardProperty object>¶
- beads_name_choices = <traits.trait_factory.TraitFactory object>¶
- beads_units = <traits.traits.ForwardProperty object>¶
- class cytoflowgui.op_plugins.bead_calibration.BeadCalibrationViewHandler(*args: Any, **kwargs: Any)¶
- class cytoflowgui.op_plugins.bead_calibration.BeadCalibrationPlugin¶
- operation_id = 'edu.mit.synbio.cytoflow.operations.beads_calibrate'¶
- view_id = 'edu.mit.synbio.cytoflow.view.beadcalibrationdiagnosticview'¶
- short_name = 'Bead Calibration'¶
- get_handler(model, context)¶