Contents
Analysis: 20260612
!pip install nucleus-cdk | tail -n2from cdk.analysis.cytosol import platereader as pr
import matplotlib.pyplot as plt
import seaborn as sns
import warnings
# Filter warnings
warnings.filterwarnings('ignore')
# Initialize plotting
pr.plot_setup()Load the data¶
Provide a CSV file containing the data, and a platemap. This function returns both the data with the plate map mapped to it, and the platemap by itself, which is useful for certain tasks.
data, platemap = pr.load_platereader_data("./data/20250612-cytation3-pure-timecourse-gfp-ppk-biotek-cdk.txt", "20250612-PPK.csv")Basic Plots¶
Kinetics¶
Kinetic time traces of every well on the plate
pr.plot_plate(data);
g = pr.plot_curves(data[data["Read"]=="GFP-F-G35"], units="Well", estimator=None, height=12)
g.savefig("plot4")
Steady state¶
Bar graph of steady-state endpoint of each sample. Steady state is calculated as the maximum fluorescence value over a 3-sample rolling average on the data.
steadystate = data.merge(pr.find_steady_state(data[data["Read"]=="GFP-F-G35"]).reset_index(), on="Well", how="left")
steadystate.loc[steadystate["Column"]==13, "Column"] = 14
sns.barplot(data=steadystate, x="Name", y="Data_steadystate", hue="Column")<Axes: xlabel='Name', ylabel='Data_steadystate'>
ss= pr.plot_steadystate(data[data["Read"]=="GFP-F-G35"])
plt.xlabel('Condition')
ss.savefig("plot5")
Kinetics Analysis¶
These functions calculate key kinetic parameters of the time series.
pr.plot_kinetics(data[data["Read"] == "GFP-F-G35"])Failed to solve: Optimal parameters not found: Number of calls to function has reached maxfev = 800.
Failed to solve: Optimal parameters not found: Number of calls to function has reached maxfev = 800.
Failed to solve: Optimal parameters not found: Number of calls to function has reached maxfev = 800.
Failed to solve: Optimal parameters not found: Number of calls to function has reached maxfev = 800.
Failed to solve: Optimal parameters not found: Number of calls to function has reached maxfev = 800.
Failed to solve: Optimal parameters not found: Number of calls to function has reached maxfev = 800.
Failed to solve: Optimal parameters not found: Number of calls to function has reached maxfev = 800.
Failed to solve: Optimal parameters not found: Number of calls to function has reached maxfev = 800.
Failed to solve: Optimal parameters not found: Number of calls to function has reached maxfev = 800.
We can also calculate the kinetics and display the parameters as a table.
pr.kinetic_analysis(data)Failed to solve: Optimal parameters not found: Number of calls to function has reached maxfev = 800.
Failed to solve: Optimal parameters not found: Number of calls to function has reached maxfev = 800.
Failed to solve: Optimal parameters not found: Number of calls to function has reached maxfev = 800.
Failed to solve: Optimal parameters not found: Number of calls to function has reached maxfev = 800.
Failed to solve: Optimal parameters not found: Number of calls to function has reached maxfev = 800.
Failed to solve: Optimal parameters not found: Number of calls to function has reached maxfev = 800.
Failed to solve: Optimal parameters not found: Number of calls to function has reached maxfev = 800.
Failed to solve: Optimal parameters not found: Number of calls to function has reached maxfev = 800.
Failed to solve: Optimal parameters not found: Number of calls to function has reached maxfev = 800.
Failed to solve: Optimal parameters not found: Number of calls to function has reached maxfev = 800.
Failed to solve: Optimal parameters not found: Number of calls to function has reached maxfev = 800.
Failed to solve: Optimal parameters not found: Number of calls to function has reached maxfev = 800.
Failed to solve: Optimal parameters not found: Number of calls to function has reached maxfev = 800.
Failed to solve: Optimal parameters not found: Number of calls to function has reached maxfev = 800.
Failed to solve: Optimal parameters not found: Number of calls to function has reached maxfev = 800.
Velocity \
Time Data Max
Well Name Read
A19 CP + PolyP + 8 mM Mg GFP-F-G35 0 days 03:30:00 54.00 0.01
A21 CP + PolyP + 8 mM Mg GFP-F-G35 0 days 00:20:00 45.00 0.00
A23 CP + PolyP + 8 mM Mg GFP-F-G35 NaT NaN NaN
C19 PolyP + PPK + 8 mM Mg GFP-F-G35 NaT NaN NaN
C21 PolyP + PPK + 8 mM Mg GFP-F-G35 NaT NaN NaN
C23 PolyP + PPK + 8 mM Mg GFP-F-G35 NaT NaN NaN
E19 PolyP + PPK + 10 mM Mg GFP-F-G35 0 days 00:05:00 43.00 0.00
E21 PolyP + PPK + 10 mM Mg GFP-F-G35 NaT NaN NaN
E23 PolyP + PPK + 10 mM Mg GFP-F-G35 NaT NaN NaN
G19 PolyP + PPK + 12 mM Mg GFP-F-G35 NaT NaN NaN
G21 PolyP + PPK + 12 mM Mg GFP-F-G35 NaT NaN NaN
G23 PolyP + PPK + 12 mM Mg GFP-F-G35 NaT NaN NaN
I19 PolyP + PPK + 14 mM Mg GFP-F-G35 0 days 02:05:00 4125.00 1.23
I21 PolyP + PPK + 14 mM Mg GFP-F-G35 0 days 02:05:00 4535.00 1.32
I23 PolyP + PPK + 14 mM Mg GFP-F-G35 0 days 01:50:00 7667.00 2.09
A19 CP + PolyP + 8 mM Mg GFP-M-G100 NaT NaN NaN
A21 CP + PolyP + 8 mM Mg GFP-M-G100 0 days 03:10:38 18.00 0.04
A23 CP + PolyP + 8 mM Mg GFP-M-G100 NaT NaN NaN
C19 PolyP + PPK + 8 mM Mg GFP-M-G100 0 days 01:10:38 18.00 0.03
C21 PolyP + PPK + 8 mM Mg GFP-M-G100 NaT NaN NaN
C23 PolyP + PPK + 8 mM Mg GFP-M-G100 0 days 01:50:38 22.00 0.05
E19 PolyP + PPK + 10 mM Mg GFP-M-G100 0 days 00:25:38 13.00 0.03
E21 PolyP + PPK + 10 mM Mg GFP-M-G100 NaT NaN NaN
E23 PolyP + PPK + 10 mM Mg GFP-M-G100 NaT NaN NaN
G19 PolyP + PPK + 12 mM Mg GFP-M-G100 0 days 00:35:38 17.00 0.02
G21 PolyP + PPK + 12 mM Mg GFP-M-G100 0 days 02:15:38 20.00 0.04
G23 PolyP + PPK + 12 mM Mg GFP-M-G100 NaT NaN NaN
I19 PolyP + PPK + 14 mM Mg GFP-M-G100 0 days 02:05:38 1361.00 0.46
I21 PolyP + PPK + 14 mM Mg GFP-M-G100 0 days 02:15:38 1768.00 0.49
I23 PolyP + PPK + 14 mM Mg GFP-M-G100 0 days 01:55:38 2793.00 0.73
Lag \
Time Data
Well Name Read
A19 CP + PolyP + 8 mM Mg GFP-F-G35 0 days 01:15:00 0.00
A21 CP + PolyP + 8 mM Mg GFP-F-G35 -1 days +20:35:00 24.75
A23 CP + PolyP + 8 mM Mg GFP-F-G35 NaT NaN
C19 PolyP + PPK + 8 mM Mg GFP-F-G35 NaT NaN
C21 PolyP + PPK + 8 mM Mg GFP-F-G35 NaT NaN
C23 PolyP + PPK + 8 mM Mg GFP-F-G35 NaT NaN
E19 PolyP + PPK + 10 mM Mg GFP-F-G35 -1 days +20:30:00 0.00
E21 PolyP + PPK + 10 mM Mg GFP-F-G35 NaT NaN
E23 PolyP + PPK + 10 mM Mg GFP-F-G35 NaT NaN
G19 PolyP + PPK + 12 mM Mg GFP-F-G35 NaT NaN
G21 PolyP + PPK + 12 mM Mg GFP-F-G35 NaT NaN
G23 PolyP + PPK + 12 mM Mg GFP-F-G35 NaT NaN
I19 PolyP + PPK + 14 mM Mg GFP-F-G35 0 days 01:09:06.341463415 1170.02
I21 PolyP + PPK + 14 mM Mg GFP-F-G35 0 days 01:07:35.696202532 1275.20
I23 PolyP + PPK + 14 mM Mg GFP-F-G35 0 days 00:48:57.420382166 0.00
A19 CP + PolyP + 8 mM Mg GFP-M-G100 NaT NaN
A21 CP + PolyP + 8 mM Mg GFP-M-G100 0 days 03:03:42.615384615 14.45
A23 CP + PolyP + 8 mM Mg GFP-M-G100 NaT NaN
C19 PolyP + PPK + 8 mM Mg GFP-M-G100 0 days 01:01:38 12.31
C21 PolyP + PPK + 8 mM Mg GFP-M-G100 NaT NaN
C23 PolyP + PPK + 8 mM Mg GFP-M-G100 0 days 01:43:45.500000 14.24
E19 PolyP + PPK + 10 mM Mg GFP-M-G100 0 days 00:17:30.500000 12.15
E21 PolyP + PPK + 10 mM Mg GFP-M-G100 NaT NaN
E23 PolyP + PPK + 10 mM Mg GFP-M-G100 NaT NaN
G19 PolyP + PPK + 12 mM Mg GFP-M-G100 0 days 00:18:38 13.48
G21 PolyP + PPK + 12 mM Mg GFP-M-G100 0 days 02:07:56.461538462 17.45
G23 PolyP + PPK + 12 mM Mg GFP-M-G100 NaT NaN
I19 PolyP + PPK + 14 mM Mg GFP-M-G100 0 days 01:16:19.304347826 463.62
I21 PolyP + PPK + 14 mM Mg GFP-M-G100 0 days 01:15:29.836734694 453.28
I23 PolyP + PPK + 14 mM Mg GFP-M-G100 0 days 00:52:09.363636364 594.70
Steady State Fit \
Time Data L
Well Name Read
A19 CP + PolyP + 8 mM Mg GFP-F-G35 0 days 03:40:00 54.00 0.00
A21 CP + PolyP + 8 mM Mg GFP-F-G35 0 days 01:50:00 49.00 54.19
A23 CP + PolyP + 8 mM Mg GFP-F-G35 NaT NaN NaN
C19 PolyP + PPK + 8 mM Mg GFP-F-G35 NaT NaN NaN
C21 PolyP + PPK + 8 mM Mg GFP-F-G35 NaT NaN NaN
C23 PolyP + PPK + 8 mM Mg GFP-F-G35 NaT NaN NaN
E19 PolyP + PPK + 10 mM Mg GFP-F-G35 0 days 00:15:00 44.00 44.46
E21 PolyP + PPK + 10 mM Mg GFP-F-G35 NaT NaN NaN
E23 PolyP + PPK + 10 mM Mg GFP-F-G35 NaT NaN NaN
G19 PolyP + PPK + 12 mM Mg GFP-F-G35 NaT NaN NaN
G21 PolyP + PPK + 12 mM Mg GFP-F-G35 NaT NaN NaN
G23 PolyP + PPK + 12 mM Mg GFP-F-G35 NaT NaN NaN
I19 PolyP + PPK + 14 mM Mg GFP-F-G35 0 days 05:25:00 10072.00 9658.32
I21 PolyP + PPK + 14 mM Mg GFP-F-G35 0 days 05:45:00 10921.00 10441.53
I23 PolyP + PPK + 14 mM Mg GFP-F-G35 0 days 05:00:00 15987.00 0.00
A19 CP + PolyP + 8 mM Mg GFP-M-G100 NaT NaN NaN
A21 CP + PolyP + 8 mM Mg GFP-M-G100 0 days 04:05:38 16.00 46.00
A23 CP + PolyP + 8 mM Mg GFP-M-G100 NaT NaN NaN
C19 PolyP + PPK + 8 mM Mg GFP-M-G100 0 days 02:05:38 12.00 27.16
C21 PolyP + PPK + 8 mM Mg GFP-M-G100 NaT NaN NaN
C23 PolyP + PPK + 8 mM Mg GFP-M-G100 0 days 02:15:38 12.00 14.25
E19 PolyP + PPK + 10 mM Mg GFP-M-G100 0 days 01:50:38 16.00 15.98
E21 PolyP + PPK + 10 mM Mg GFP-M-G100 NaT NaN NaN
E23 PolyP + PPK + 10 mM Mg GFP-M-G100 NaT NaN NaN
G19 PolyP + PPK + 12 mM Mg GFP-M-G100 0 days 01:20:38 13.00 13.55
G21 PolyP + PPK + 12 mM Mg GFP-M-G100 0 days 02:55:38 18.00 20.58
G23 PolyP + PPK + 12 mM Mg GFP-M-G100 NaT NaN NaN
I19 PolyP + PPK + 14 mM Mg GFP-M-G100 0 days 05:45:38 3416.00 3269.77
I21 PolyP + PPK + 14 mM Mg GFP-M-G100 0 days 04:30:38 3348.00 3290.10
I23 PolyP + PPK + 14 mM Mg GFP-M-G100 0 days 04:30:38 5395.00 5209.24
k x0
Well Name Read
A19 CP + PolyP + 8 mM Mg GFP-F-G35 0.00 0.00
A21 CP + PolyP + 8 mM Mg GFP-F-G35 0.00 -10961.36
A23 CP + PolyP + 8 mM Mg GFP-F-G35 NaN NaN
C19 PolyP + PPK + 8 mM Mg GFP-F-G35 NaN NaN
C21 PolyP + PPK + 8 mM Mg GFP-F-G35 NaN NaN
C23 PolyP + PPK + 8 mM Mg GFP-F-G35 NaN NaN
E19 PolyP + PPK + 10 mM Mg GFP-F-G35 0.00 -1270.79
E21 PolyP + PPK + 10 mM Mg GFP-F-G35 NaN NaN
E23 PolyP + PPK + 10 mM Mg GFP-F-G35 NaN NaN
G19 PolyP + PPK + 12 mM Mg GFP-F-G35 NaN NaN
G21 PolyP + PPK + 12 mM Mg GFP-F-G35 NaN NaN
G23 PolyP + PPK + 12 mM Mg GFP-F-G35 NaN NaN
I19 PolyP + PPK + 14 mM Mg GFP-F-G35 0.00 8365.69
I21 PolyP + PPK + 14 mM Mg GFP-F-G35 0.00 8324.93
I23 PolyP + PPK + 14 mM Mg GFP-F-G35 0.00 0.00
A19 CP + PolyP + 8 mM Mg GFP-M-G100 NaN NaN
A21 CP + PolyP + 8 mM Mg GFP-M-G100 -0.00 -297621.96
A23 CP + PolyP + 8 mM Mg GFP-M-G100 NaN NaN
C19 PolyP + PPK + 8 mM Mg GFP-M-G100 0.00 7049.86
C21 PolyP + PPK + 8 mM Mg GFP-M-G100 NaN NaN
C23 PolyP + PPK + 8 mM Mg GFP-M-G100 0.00 -820.99
E19 PolyP + PPK + 10 mM Mg GFP-M-G100 0.00 -1761.18
E21 PolyP + PPK + 10 mM Mg GFP-M-G100 NaN NaN
E23 PolyP + PPK + 10 mM Mg GFP-M-G100 NaN NaN
G19 PolyP + PPK + 12 mM Mg GFP-M-G100 -0.00 7532.27
G21 PolyP + PPK + 12 mM Mg GFP-M-G100 0.00 -6640.19
G23 PolyP + PPK + 12 mM Mg GFP-M-G100 NaN NaN
I19 PolyP + PPK + 14 mM Mg GFP-M-G100 0.00 8588.16
I21 PolyP + PPK + 14 mM Mg GFP-M-G100 0.00 8024.84
I23 PolyP + PPK + 14 mM Mg GFP-M-G100 0.00 6834.15 