Contents
Analysis: 20250610
!pip install nucleus-cdk | tail -n2import matplotlib.pyplot as plt
from cdk.analysis.cytosol import platereader as pr
import warnings
warnings.filterwarnings('ignore')
pr.plot_setup()data, platemap = pr.load_platereader_data("./data/20250610-161953-cytation5-pure-timecourse-gfp-ppk-controls-2-biotek-cdk.txt", "20250610-ppk-energy-solution-platemap.csv")data index Time Well Data Row Column Read Experiment \
0 0 0 days 00:00:25 A1 237 A 1 GFP-Gext PPK Energy
1 1 0 days 00:05:25 A1 267 A 1 GFP-Gext PPK Energy
2 2 0 days 00:10:25 A1 269 A 1 GFP-Gext PPK Energy
3 3 0 days 00:15:25 A1 452 A 1 GFP-Gext PPK Energy
4 4 0 days 00:20:25 A1 821 A 1 GFP-Gext PPK Energy
.. ... ... ... ... .. ... ... ...
877 2396 0 days 03:40:25 G7 1324868 G 7 GFP-Gext PPK Energy
878 2397 0 days 03:45:25 G7 1329150 G 7 GFP-Gext PPK Energy
879 2398 0 days 03:50:25 G7 1332282 G 7 GFP-Gext PPK Energy
880 2399 0 days 03:55:25 G7 1332115 G 7 GFP-Gext PPK Energy
881 2400 0 days 04:00:25 G7 1329940 G 7 GFP-Gext PPK Energy
Name CP
0 ES + CP 1
1 ES + CP 1
2 ES + CP 1
3 ES + CP 1
4 ES + CP 1
.. ... ..
877 PURE Positive 1
878 PURE Positive 1
879 PURE Positive 1
880 PURE Positive 1
881 PURE Positive 1
[882 rows x 10 columns]g = pr.plot_curves(data, palette="colorblind")
g.savefig("plot1")
s = pr.plot_steadystate(data, palette="colorblind")
plt.xlabel('Condition')
s.savefig("plot2")
pr.plot_kinetics(data)Failed to solve: Optimal parameters not found: Number of calls to function has reached maxfev = 800.
pr.kinetic_analysis(data)Failed to solve: Optimal parameters not found: Number of calls to function has reached maxfev = 800.
Velocity \
Time Data Max
Well Name Read
A1 ES + CP GFP-Gext 0 days 01:10:25 59946.00 34.61
A4 ES + CP GFP-Gext 0 days 03:35:25 314329.00 88.22
A7 ES + CP GFP-Gext 0 days 02:10:25 329881.00 130.61
D1 ES - CP GFP-Gext NaT NaN NaN
D4 ES - CP GFP-Gext 0 days 03:00:25 532.00 0.11
D7 ES - CP GFP-Gext 0 days 02:20:25 594.00 0.18
G1 PURE Positive GFP-Gext 0 days 00:55:25 354492.00 355.16
G4 PURE Positive GFP-Gext 0 days 00:55:25 358932.00 353.82
G7 PURE Positive GFP-Gext 0 days 00:55:25 327951.00 317.07
Lag \
Time Data
Well Name Read
A1 ES + CP GFP-Gext 0 days 00:41:32.790406473 22383.54
A4 ES + CP GFP-Gext 0 days 02:36:02.121698719 256649.57
A7 ES + CP GFP-Gext 0 days 01:28:19.305183370 165537.06
D1 ES - CP GFP-Gext NaT NaN
D4 ES - CP GFP-Gext 0 days 01:42:10.882352941 439.83
D7 ES - CP GFP-Gext 0 days 01:24:22.735849057 463.10
G1 PURE Positive GFP-Gext 0 days 00:38:46.871474561 165899.50
G4 PURE Positive GFP-Gext 0 days 00:38:30.561532592 160776.11
G7 PURE Positive GFP-Gext 0 days 00:38:10.693530414 149323.26
Steady State Fit \
Time Data L k
Well Name Read
A1 ES + CP GFP-Gext 0 days 03:55:25 256728.00 255842.37 0.00
A4 ES + CP GFP-Gext 0 days 04:00:25 320024.00 305057.60 0.00
A7 ES + CP GFP-Gext 0 days 03:10:25 413670.00 423904.96 0.00
D1 ES - CP GFP-Gext NaT NaN NaN NaN
D4 ES - CP GFP-Gext 0 days 03:30:25 551.00 2956.01 0.00
D7 ES - CP GFP-Gext 0 days 03:50:25 736.00 1502.65 0.00
G1 PURE Positive GFP-Gext 0 days 03:30:25 1520984.00 1484831.24 0.00
G4 PURE Positive GFP-Gext 0 days 03:10:25 1469930.00 1435243.58 0.00
G7 PURE Positive GFP-Gext 0 days 03:55:25 1332115.00 1307814.30 0.00
x0
Well Name Read
A1 ES + CP GFP-Gext 6456.30
A4 ES + CP GFP-Gext 6392.94
A7 ES + CP GFP-Gext 5976.62
D1 ES - CP GFP-Gext NaN
D4 ES - CP GFP-Gext 44468.08
D7 ES - CP GFP-Gext 13956.26
G1 PURE Positive GFP-Gext 4827.50
G4 PURE Positive GFP-Gext 4752.33
G7 PURE Positive GFP-Gext 4772.97 