cytoflow.operations.bead_calibration¶
The bead_calibration
module contains two classes:
BeadCalibrationOp
– calibrates the raw measurements in a
Experiment
using fluorescent particles.
BeadCalibrationDiagnostic
– a diagnostic view to make sure
that BeadCalibrationOp
correctly estimated its parameters.
- class cytoflow.operations.bead_calibration.BeadCalibrationOp[source]¶
Bases:
traits.has_traits.HasStrictTraits
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_file
to an FCS file containing events collected using the same cytometer settings as the data you’re calibrating. Specify which beads you ran by settingbeads
to match one of the values ofBeadCalibrationOp.BEADS
; and setunits
to which channels you want calibrated and in which units. Then, callestimate
and check the peak-finding withBeadCalibrationDiagnostic.plot
. If the peak-finding is wacky, try adjustingbead_peak_quantile
andbead_brightness_threshold
. When the peaks are successfully identified, callapply
to scale your experimental data set.If you can’t make the peak finding work, please submit a bug report!
This procedure works best when the beads file is very clean data. It does not do its own gating (maybe a future addition?) In the meantime, I recommend gating the acquisition on the FSC/SSC channels in order to get rid of debris, cells, and other noise.
Finally, because you can’t have a negative number of fluorescent molecules (MEFLs, etc) (as well as for math reasons), this module filters out negative values.
- units¶
A dictionary specifying the channels you want calibrated (keys) and the units you want them calibrated in (values). The units must be keys of the
beads
attribute.- Type
Dict(Str, Str)
- beads_file¶
A file containing the FCS events from the beads.
- Type
File
- beads¶
The beads’ characteristics. Keys are calibrated units (ie, MEFL or MEAP) and values are ordered lists of known fluorophore levels. Common values for this dict are included in
BeadCalibrationOp.BEADS
.- Type
Dict(Str, List(Float))
- bead_peak_quantile¶
The quantile threshold used to choose bead peaks.
- Type
Int (default = 80)
- bead_brightness_threshold¶
How bright must a bead peak be to be considered?
- Type
Float (default = 100)
- bead_brightness_cutoff¶
If a bead peak is above this, then don’t consider it. Takes care of clipping saturated detection. Defaults to 70% of the detector range.
- Type
Float
- bead_histogram_bins¶
The number of bins to use in computing the bead histogram. Tweak this if the peak find is having difficulty, or if you have a small number of events
- Type
Int (default = 512)
- force_linear¶
A linear fit in log space doesn’t always go through the origin, which means that the calibration function isn’t strictly a multiplicative scaling operation. Set
force_linear
to force the such behavior. Keep an eye on the diagnostic plot, though, to see how much error you’re introducing!- Type
Bool (default = False)
Notes
The peak finding is rather sophisticated.
For each channel, a 256-bin histogram is computed on the log-transformed bead data, and then the histogram is smoothed with a Savitzky-Golay filter (with a window length of 5 and a polynomial order of 1).
Next, a wavelet-based peak-finding algorithm is used: it convolves the smoothed histogram with a series of wavelets and looks for relative maxima at various length-scales. The parameters of the smoothing algorithm were arrived at empircally, using beads collected at a wide range of PMT voltages.
Finally, the peaks are filtered by height (the histogram bin has a quantile greater than
bead_peak_quantile
) and intensity (brighter thanbead_brightness_threshold
).How to convert from a series of peaks to mean equivalent fluorochrome? If there’s one peak, we assume that it’s the brightest peak. If there are two peaks, we assume they’re the brightest two. If there are
n >=3
peaks, we check all the contiguousn
-subsets of the bead intensities and find the one whose linear regression (in log space!) has the smallest norm (square-root sum-of-squared-residuals.)There’s a slight subtlety in the fact that we’re performing the linear regression in log-space: if the relationship in log10-space is
Y=aX + b
, then the same relationship in linear space isx = 10**X
,y = 10**y
, andy = (10**b) * (x ** a)
.Note
Adding a new set of beads is easy! Please don’t add them directly to
BEADS
, though – instead, add them tobeads.csv
, then run thecytoflow.scripts.parse_beads
script to convert it into a 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
>>> bead_op = flow.BeadCalibrationOp() >>> beads = 'RCP-30-5A Lot AA01, AA02, AA03, AA04, AB01, AB02, AC01 & GAA01-R' >>> bead_op.beads = flow.BeadCalibrationOp.BEADS[beads] >>> bead_op.units = {"Pacific Blue-A" : "MEBFP", ... "FITC-A" : "MEFL", ... "PE-Tx-Red-YG-A" : "MEPTR"} >>> >>> bead_op.beads_file = "tasbe/beads.fcs"
Estimate the model parameters
>>> bead_op.estimate(ex)
Plot the diagnostic plot
>>> bead_op.default_view().plot(ex)
Apply the operation to the experiment
>>> ex = bead_op.apply(ex)
- estimate(experiment)[source]¶
Estimate the calibration coefficients from the beads file.
- Parameters
experiment (
Experiment
) – The experiment used to compute the calibration.
- apply(experiment)[source]¶
Applies the bleedthrough correction to an experiment.
- Parameters
experiment (
Experiment
) – the experiment to which this operation is applied- Returns
A new experiment with the specified channels calibrated in physical units. The calibrated channels also have new metadata:
- bead_calibration_fnCallable (
pandas.Series
–>pandas.Series
) The function to calibrate raw data to bead units
- bead_calibration_fnCallable (
- bead_unitsStr
The units this channel was calibrated to
- Return type
- default_view(**kwargs)[source]¶
Returns a diagnostic plot to see if the peak finding is working.
- Returns
An diagnostic view, call
BeadCalibrationDiagnostic.plot
to see the diagnostic plots- Return type
- BEADS = {'ACP 30-2K': {'MEAP': [7880.0, 17400.0, 53100.0, 130000.0, 208000.0]}, 'RCP-30-5 Lot AA01, AB01, AB02, AC01 & AD01': {'MEAP': [6720.0, 17962.0, 30866.0, 51704.0, 146080.0], 'MECY': [12901.0, 36837.0, 76621.0, 261671.0, 1069858.0], 'MEFL': [6028.0, 17493.0, 35674.0, 126907.0, 290983.0], 'MEPE': [4974.0, 13118.0, 26757.0, 94930.0, 250470.0], 'MEPTR': [2198.0, 6063.0, 12887.0, 51686.0, 170219.0]}, 'RCP-30-5 Lot AM02, AM01, AL01, AH01, AG01, AF01 & AD03': {'MEA700': [7850.64102564103, 26574.358974359, 87058.3333333333, 232771.153846154, 428898.076923077], 'MEA750': [643.319414830418, 1682.85038466727, 4905.43254465399, 15637.5278759487, 44664.1560269625], 'MEAP': [2395.0, 8273.0, 27652.0, 75669.0, 145428.0], 'MECY5.5': [8737.0, 28177.0, 93996.0, 334087.0, 1023447.0], 'MEFL': [4447.0, 14227.0, 46322.0, 133924.0, 276897.0], 'MEKO': [4100.1862606147, 13503.2020463521, 45019.6494865316, 152691.355293162, 391037.895005993], 'MEPB': [902.826150264251, 2543.25777035562, 7577.3103315121, 19902.1552759773, 35490.1854343577], 'MEPCY7': [4447.52977431211, 12826.6344100731, 41676.365575392, 149440.701418692, 474797.252391984], 'MEPE': [3236.0, 10754.0, 34842.0, 104483.0, 245894.0], 'METR': [1486.0, 5112.0, 17664.0, 60371.0, 179787.0]}, 'RCP-30-5A (Euroflow) Lot EAK01, EAG01, EAE01 & EAF01': {'MEAP': [1366.0, 4706.0, 14822.0, 58161.0, 140920.0, 204810.0, 280646.0], 'MEAPCY7': [12540.2912310804, 27790.424415523, 57114.7530172427, 137792.795419592, 245420.419831163, 312870.988997371, 387104.388350457], 'MEAXL700': [1180.89572037678, 3930.96580785077, 11270.6100091203, 45502.2217551306, 109122.081384077, 151781.075700287, 237988.013854553], 'MEBFP': [2584.06901535744, 5291.27272439487, 11909.3205931143, 38804.9157590269, 107470.790614424, 359515.748179449, 736906.777253776], 'MECSB': [3827.07306877147, 6410.85503814999, 12405.91715676, 37097.3178176766, 92487.7710023634, 267142.304767532, 499972.639106986], 'MECY': [1276.0, 3603.0, 9520.0, 35518.0, 102755.0, 328185.0, 1052496.0], 'MEFL': [806.0, 2159.0, 5640.0, 19900.0, 52630.0, 172155.0, 345870.0], 'MEPCY7': [9726.6114174626, 25173.4200339912, 57085.1373522142, 136728.333019744, 324682.702797253], 'MEPE': [409.0, 1250.0, 3428.0, 12229.0, 34294.0, 113118.0, 256134.0], 'MEPTR': [171.0, 538.0, 1514.0, 5659.0, 16972.0, 64615.0, 183897.0]}, 'RCP-30-5A (Euroflow) Lot EAM02 & EAM01': {'MEAP': [736.0, 1892.0, 4804.0, 14248.0, 42425.0, 113026.0, 227044.0], 'MEAPCY7': [558.0, 1417.0, 3224.0, 8309.0, 20779.0, 48391.0, 89183.0], 'MEAXL700': [682.0, 1276.0, 2352.0, 4724.0, 9284.0, 17217.0, 26930.0], 'MEBFP': [1295.0, 2398.0, 4884.0, 13920.0, 34027.0, 95282.0, 172500.0], 'MECSB': [480.0, 698.0, 1192.0, 2947.0, 6546.0, 15893.0, 27382.0], 'MECY': [998.0, 3064.0, 8614.0, 28030.0, 90459.0, 298273.0, 849431.0], 'MEFL': [789.0, 1896.0, 4872.0, 15619.0, 47116.0, 143912.0, 333068.0], 'MEPCY7': [106.0, 343.0, 1088.0, 4215.0, 15949.0, 62905.0, 208319.0], 'MEPE': [507.0, 1204.0, 3171.0, 10440.0, 34385.0, 114122.0, 311207.0], 'MEPTR': [187.0, 543.0, 1536.0, 5423.0, 17825.0, 63989.0, 207649.0]}, 'RCP-30-5A Lot AA01, AA02, AA03, AA04, AB01, AB02, AC01 & GAA01-R': {'MEAP': [578.0, 2433.0, 6720.0, 17962.0, 30866.0, 51704.0, 146080.0], 'MEAPCY7': [718.0, 1920.0, 5133.0, 9324.0, 14210.0, 26735.0], 'MEBFP': [700.0, 1705.0, 4262.0, 17546.0, 35669.0, 133387.0, 412089.0], 'MECSB': [179.0, 400.0, 993.0, 3203.0, 6083.0, 17777.0, 36331.0], 'MECY': [1437.0, 4693.0, 12901.0, 36837.0, 76621.0, 261671.0, 1069858.0], 'MEFL': [692.0, 2192.0, 6028.0, 17493.0, 35674.0, 126907.0, 290983.0], 'MEPCY7': [32907.0, 107787.0, 503797.0], 'MEPE': [505.0, 1777.0, 4974.0, 13118.0, 26757.0, 94930.0, 250470.0], 'MEPTR': [207.0, 750.0, 2198.0, 6063.0, 12887.0, 51686.0, 170219.0]}, 'RCP-30-5A Lot AC02, AC03 & AD01': {'MEAP': [1184.0, 4024.0, 8892.0, 20919.0, 35336.0, 62371.0, 160356.0], 'MEAPCY7': [1638.44517911143, 4232.87970031999, 8021.74368319802, 14091.8060342384, 27002.3850136509], 'MEAmC': [689.818391446723, 1645.66379392412, 4353.99728581043, 17956.9358902402, 37196.3751279619, 136964.361513719, 422642.751819192], 'MECY': [1434.98342378079, 4725.12552939372, 12977.4579084514, 34975.0986132135, 71893.2990690699, 258366.215367105, 1120607.11147369], 'MEFL': [694.316757280561, 2095.54714141499, 6077.97998121964, 18079.7185767491, 37488.3221945023, 127548.70589779, 292408.003430039], 'MEPB': [179.490842861769, 399.130271822164, 1004.33041842402, 3326.09220035309, 6280.9781554728, 18181.900886873, 37446.4126347345], 'MEPCY7': [14858.8422415397, 31336.9778664833, 107223.701409309, 519777.268051615], 'MEPE': [525.988079665053, 1735.72870920068, 5023.48980798513, 13251.1367386049, 27327.3892526052, 96552.680798141, 259880.668965796], 'MEPTR': [218.12305864236, 737.206689077331, 2197.57129248996, 6081.95974182049, 13048.0691337032, 52446.8891318169, 177982.883907379]}, 'RCP-30-5A Lot AG01': {'MEAP': [292.0, 903.0, 2944.0, 10279.0, 31830.0, 88779.0, 136890.0], 'MEAPCY7': [152.481010512631, 358.004365649928, 966.611772258365, 2861.65093025875, 8041.50258137422, 21487.9458259072, 34373.1492632902], 'MEBFP': [783.479435075178, 1649.6663503655, 4198.58208277468, 14660.9866605248, 45084.832628766, 155778.308324188, 386263.847966924], 'MECSB': [165.674334973794, 340.486972724961, 826.600919891466, 2624.32033982357, 7136.97835687739, 19016.8923138331, 32485.972305376], 'MECY': [1301.0, 3260.0, 8681.0, 30542.0, 94737.0, 355044.0, 1041442.0], 'MEFL': [646.0, 1704.0, 4827.0, 15991.0, 47609.0, 135896.0, 273006.0], 'MEPCY7': [43612.1316610686, 157277.99967019, 471882.579572875], 'MEPE': [418.0, 1188.0, 3445.0, 11858.0, 35821.0, 108150.0, 248022.0], 'MEPTR': [182.0, 512.0, 1503.0, 5542.0, 17662.0, 61847.0, 179707.0]}, 'RCP-30-5A Lot AK01, AJ01, AH02, AH01, AF02, AF01, AD04 & AE01': {'MEAP': [373.0, 1079.0, 3633.0, 9896.0, 28189.0, 79831.0, 151008.0], 'MEAPCY7': [2863.86529976503, 7644.40047827793, 19081.4267726604, 37257.7414357138], 'MEBFP': [861.176890115253, 1997.18594899185, 5775.55800127844, 15232.7589688612, 45388.9855190994, 152561.805143073, 396759.154027137], 'MECSB': [216.0, 464.0, 1232.0, 2940.0, 7669.0, 19812.0, 35474.0], 'MECY': [1614.0, 4035.0, 12025.0, 31896.0, 95682.0, 353225.0, 1077421.0], 'MEFL': [792.0, 2079.0, 6588.0, 16471.0, 47497.0, 137049.0, 271647.0], 'MEPCY7': [14916.4569850334, 42336.4964302585, 153840.442723689, 494262.78101307], 'MEPE': [531.0, 1504.0, 4819.0, 12506.0, 36159.0, 109588.0, 250892.0], 'MEPTR': [233.0, 669.0, 2179.0, 5929.0, 18219.0, 63944.0, 188785.0]}, 'RCP-30-5A Lot AN04, AN03, AN02, AN01, AM02, AM01, AL01, AK04, AK03 & AK02': {'MEAP': [341.010388310164, 1027.34896530879, 3155.71287209302, 7750.10141500535, 23446.4537774744, 68701.80510944, 116813.097393489], 'MEAPCY7': [173.309661734951, 427.442877227215, 1097.43242546677, 2399.15279284361, 6359.25563563231, 17474.9563255425, 30725.4485529926], 'MEBFP': [843.503722117931, 1957.71825828363, 5421.80193415564, 13522.433084656, 42717.4973739119, 153501.022826764, 420359.287816952], 'MECSB': [205.139224587675, 470.418789207962, 1211.03409137091, 2739.85605412079, 7516.43849705557, 20121.7589207813, 35572.7129888405], 'MECY': [1414.42033101552, 3808.80637667958, 10852.1944856379, 27904.3884607569, 85866.2647607231, 324106.419847251, 1040895.428772], 'MEFL': [771.204227758779, 2106.46973727296, 6262.29508551021, 15182.5413019226, 45291.7071432442, 136257.847794468, 291041.740879689], 'MEPCY7': [12752.0445894082, 39056.5340076057, 142957.954887933, 448890.055464371], 'MEPE': [487.398484275159, 1473.64215674594, 4516.24975517653, 11260.0753555562, 34341.0801281963, 107608.01291543, 260461.299924314], 'MEPTR': [204.868534691815, 643.202193579403, 2021.09484018683, 5278.32442121266, 17017.8228394271, 62450.9816067639, 198932.678535898]}, 'RCP-30-5A Lot Z02 and Z03': {'MEAP': [6600.0, 11135.0, 20320.0, 68250.0, 134075.0], 'MECY': [1684.0, 3603.0, 10436.0, 29791.0, 70042.0, 310480.0, 830853.0], 'MEFL': [601.0, 1645.0, 4920.0, 15169.0, 39664.0, 149723.0, 309976.0], 'MEPE': [404.0, 1096.0, 3752.0, 11972.0, 29596.0, 126945.0, 292721.0], 'MEPTR': [175.0, 480.0, 1687.0, 5549.0, 14005.0, 66220.0, 180787.0]}, 'RCP-60-5': {'MEBFP': [2864.0329353713, 8443.49646470612, 26220.2573429104, 100989.554710812, 303460.407560259], 'MECSB': [751.643759068972, 1920.57650587408, 5279.84831730671, 17646.2346728647, 46326.3118984758], 'MEFL': [4353.33008297943, 13939.3805748209, 43401.6051922607, 159034.493056801, 359570.84295444], 'MEPCY': [15.8150373621659, 5086.64305323489, 16533.7622690629, 53254.5341431493, 213548.514439041, 535345.766430253], 'MEPE': [3177.87432453532, 9831.93042961122, 31667.5628810337, 126234.183762106, 304230.63179907], 'MEPTR': [1249.10167677766, 4450.58520313724, 15543.94283828, 67795.5145283527, 149369.723878365]}, 'URCP 38-2K': {'MEAP': [1400.0, 8400.0, 24000.0, 57000.0, 101500.0], 'MEAPCY7': [1755.0, 13655.0, 43800.0, 117260.0, 257610.0], 'MEAlexa700': [7720.0, 65300.0, 210450.0, 563470.0, 1274350.0], 'MEBFP': [608.0, 4104.0, 11561.0, 30735.0, 72366.0], 'MEBV421': [211.0, 1267.0, 3519.0, 8917.0, 20718.0], 'MEBV500': [1750.0, 6320.0, 13155.0, 28040.0, 52715.0], 'MEBV605': [2300.0, 8685.0, 21000.0, 58960.0, 158765.0], 'MECSB': [211.0, 1267.0, 3519.0, 8917.0, 20718.0], 'MEFL': [3635.0, 31180.0, 93455.0, 237290.0, 437385.0], 'MEPCY5': [630.0, 10900.0, 53125.0, 250350.0, 1109525.0], 'MEPCY7': [16460.0, 62930.0, 289710.0, 1265380.0], 'MEPE': [2870.0, 23850.0, 67430.0, 163085.0, 319420.0], 'MEPTR': [7480.0, 62600.0, 184935.0, 508840.0, 1149085.0], 'MEPerCP': [6800.0, 34000.0, 85330.0, 216650.0, 534585.0], 'MEPerCPCy5.5': [3115.0, 20615.0, 75070.0, 309220.0, 1272450.0]}, 'URCP 38-2K Lot AN01, AM01, AL02, AL01, AK03, AK02, AK01, AJ02 & AJ03': {'MEAP': [1224.0, 6275.0, 16016.0, 49490.0, 109302.0], 'MEAPCY7': [1494.0, 9444.0, 27262.0, 101046.0, 258585.0], 'MEAlexa700': [6591.02998645881, 42548.5504851513, 125788.849777232, 475002.69573088, 1269504.83599914], 'MEBUV395': [871.141855176918, 3857.76891199076, 8428.28640168851, 16978.9108417844, 29323.3959547754], 'MEBUV737': [183.259605936699, 785.83204702247, 2025.88773461442, 7453.30284333274, 29429.229169638], 'MEBV421': [543.0, 2418.0, 5646.0, 12601.0, 28608.0], 'MEBV510': [1175.0, 5189.0, 12663.0, 30220.0, 72302.0], 'MEBV605': [883.0, 3331.6464149406, 8126.37672213155, 21926.3325629935, 63287.45416728], 'MEBV650': [3000.93657721926, 7266.96915687983, 20931.195845994, 62364.6257039747], 'MEBV711': [706.371218651242, 2806.25617659897, 6536.3741423501, 19293.0554727062, 56753.3744602146], 'MEBV786': [706.748702299005, 2758.23102388779, 6388.95396508851, 19061.9810254142, 56137.0077072925], 'MECY7': [14926.0, 53996.0, 282559.0, 1368162.0], 'MEFL': [3884.0, 33300.0, 97805.0, 253325.0, 484433.0], 'MEPCY5 (488 ex)': [1192.0, 15866.0, 62567.0, 299858.0, 1305867.0], 'MEPCY5 (561 ex)': [15579.0, 258556.0, 1074152.0, 4387781.0, 13943895.0], 'MEPCy5.5': [6371.10927410355, 31258.2726388408, 75288.3558534389, 211044.540217265, 542552.430980202], 'MEPE': [3107.83774255919, 24809.3002510258, 70842.9661903017, 181769.458300597, 347816.312804139], 'MEPTR': [6845.0, 59229.0, 175449.0, 487544.0, 1082135.0], 'MEPerCPCy5.5': [603.044436159273, 2993.43100035362, 7241.2334144918, 20027.1938003096, 54740.5383527368]}, 'URCP 50-2K': {'MEAP': [6780.0, 56850.0, 160850.0, 403930.0, 919070.0], 'MEAPCY7': [1480.0, 13305.0, 38640.0, 106285.0, 417030.0], 'MEFL': [2615.0, 22590.0, 63305.0, 155800.0, 328880.0], 'MEPCY5': [1270.0, 11790.0, 37800.0, 127280.0, 618430.0], 'MEPCY7': [1555.0, 10910.0, 37500.0, 149310.0, 1060350.0], 'MEPE': [2205.0, 19085.0, 54450.0, 134910.0, 248895.0], 'MEPTR': [1390.0, 12155.0, 35370.0, 92185.0, 199280.0], 'MEPerCP': [1840.0, 16485.0, 54070.0, 195200.0, 1074110.0], 'MEPerCPCy5.5': [1280.0, 11675.0, 37440.0, 127460.0, 623165.0]}, 'URCP 50-2K Lot AM01 & AJ01': {'MEAP': [11452.646449399, 84842.0267436591, 203505.318422001, 604708.533266664, 1290472.19989895], 'MEAPCY7': [2537.13182116939, 22526.7252158067, 58567.0220162963, 202718.67988687, 521885.134400135], 'MEAlexa700': [20616.5600284507, 185848.147292231, 486731.646398276, 1702570.50723759, 4437433.03758529], 'MEBV421': [553.069779590127, 2688.24002627859, 6206.37168246614, 15217.7386666591, 31977.7923579754], 'MEBV510': [1025.26689799175, 4383.09920065957, 15056.4249502571, 38999.7688815165, 83332.4222376615], 'MEBV605': [709.488157879778, 3805.19098506487, 8979.50618284471, 26351.2615487229, 45928.1493603154], 'MEBV650': [1019.75926894535, 5239.75611798151, 11479.5593728535, 31915.4253433031, 70341.7021485763], 'MEBV711': [1354.17337049447, 7066.55939540903, 14960.9218266887, 41313.9874398959, 100837.800463451], 'MEBV786': [706.748702299005, 2758.23102388779, 6388.95396508851, 19061.9810254142, 56137.0077072925], 'MECY7': [1389.33665669744, 17806.9766820921, 57589.2401205632, 292894.463825277, 1205021.89058945], 'MEFL': [2601.82488607447, 23545.8436109714, 59292.4242759641, 165160.426302325, 331838.359003713], 'MEPCY5 (488 ex)': [1144.7161092547, 15196.6416305133, 46123.587062421, 171320.367389561, 452836.401230128], 'MEPCY5 (561 ex)': [1144.7161092547, 15196.6416305133, 46123.587062421, 171320.367389561, 452836.401230128], 'MEPCy5.5': [11628.3996442711, 65451.0769345489, 142185.562107704, 401557.948615379, 979320.213365762], 'MEPE': [2106.44797555202, 17768.3884525601, 45248.196768689, 123615.682766542, 234032.785605637], 'MEPTR': [1226.55300211598, 11850.2867438131, 30690.2606448733, 86022.0614784648, 166798.756993696], 'MEPerCPCy5.5': [1350.20092756121, 13792.2877652179, 40033.6068115353, 171229.100849295, 659334.053913482]}}¶
A dictionary containing the calibrated beads that Cytoflow currently knows about. The available bead sets are:
Spherotech ACP 30-2K
Spherotech RCP-30-5A Lot AN04, AN03, AN02, AN01, AM02, AM01, AL01, AK04, AK03 & AK02**
Spherotech RCP-30-5A (Euroflow) Lot EAM02 & EAM01
Sphreotech RCP-30-5A (Euroflow) Lot EAK01, EAG01, EAE01 & EAF01
Spherotech RCP-30-5A Lot AK01, AJ01, AH02, AH01, AF02, AF01, AD04 & AE01
Spherotech RCP-30-5A Lot AG01
Spherotech RCP-30-5A Lot AA01, AA02, AA03, AA04, AB01, AB02, AC01 & GAA01-R
Spherotech RCP-30-5A Lot AC02, AC03 & AD01
Spherotech RCP-30-5A Lot Z02 and Z03
Spherotech RCP-30-5 Lot AA01, AB01, AB02, AC01 & AD01
Spherotech RCP-30-5 Lot AM02, AM01, AL01, AH01, AG01, AF01 & AD03
Spherotech RCP-60-5
Spherotech URCP 38-2K
Spherotech URCP 38-2K Lot AN01, AM01, AL02, AL01, AK03, AK02, AK01, AJ02 & AJ03
Spherotech URCP 50-2K Lot AM01 & AJ01
Spherotech URCP 50-2K
The Spherotech fluorophores labels and the laser / filter sets (that I know about) are:
MECSB (Cascade Blue, 405 –> 450/50)
MEBFP (BFP, 405 –> 530/40)
MEFL (Fluroscein, 488 –> 530/40)
MEPE (Phycoerythrin, 488 –> 575/25)
MEPTR (PE-Texas Red, 488 –> 613/20)
MECY (Cy5, 488 –> 680/30)
MEPCY7 (PE-Cy7, 488 –> 750 LP)
MEAP (APC, 633 –> 665/20)
MEAPCY7 (APC-Cy7, 635 –> 750 LP)
- class cytoflow.operations.bead_calibration.BeadCalibrationDiagnostic[source]¶
Bases:
traits.has_traits.HasStrictTraits
A diagnostic view for
BeadCalibrationOp
.Plots the smoothed histogram of the bead data; the peak locations; a scatter plot of the raw bead fluorescence values vs the calibrated unit values; and a line plot of the model that was computed. Make sure that the relationship is linear; if it’s not, it likely isn’t a good calibration!
- op¶
The operation instance whose parameters we’re plotting. Set automatically if you created the instance using
BeadCalibrationOp.default_view
.- Type
Instance(
BeadCalibrationOp
)
- plot(experiment)[source]¶
Plots the diagnostic view.
- Parameters
experiment (
Experiment
) – The experiment used to create the diagnostic plot.