Nucleus Developer Notes

Analysis: 20250616

!pip install nucleus-cdk==0.5.0rc2 | tail -n2
Requirement already satisfied: asttokens in /opt/homebrew/anaconda3/lib/python3.12/site-packages (from stack-data->ipython>=6.1.0->ipywidgets==8.*->jupyter-bokeh<5.0.0,>=4.0.5->nucleus-cdk==0.5.0rc2) (2.0.5)
Requirement already satisfied: pure-eval in /opt/homebrew/anaconda3/lib/python3.12/site-packages (from stack-data->ipython>=6.1.0->ipywidgets==8.*->jupyter-bokeh<5.0.0,>=4.0.5->nucleus-cdk==0.5.0rc2) (0.2.2)

from cdk.analysis.cytosol import platereader as pr
import matplotlib.pyplot as plt
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/20250616-160504-cytation5-pure-timecourse-gfp-ppk-cp-biotek-cdk.txt", "20250616-PPK CP-CK platemap.csv")

Basic Plots

Kinetics

Kinetic time traces of every well on the plate

p = pr.plot_curves(data, palette="colorblind")
p.savefig("plot1-timeseries")
<Figure size 825.5x500 with 1 Axes>

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.

p1= pr.plot_steadystate(data, palette="colorblind")
plt.xlabel("Condition")
p1.savefig("plot2-endpoint")
<Figure size 600x400 with 1 Axes>

Kinetics Analysis

These functions calculate key kinetic parameters of the time series.

pr.plot_kinetics(data)
PROVIDING AVERAGED KINETICS
(<seaborn.axisgrid.FacetGrid at 0x14b8af9d0>, Velocity \ Time Name Read PURE w/CP + PPK + Polyp 18mM Mg 2+ GFP-Gext 0 days 01:37:02.985893445 PURE w/CP 8mM Mg 2+ GFP-Gext 0 days 01:30:11.183020599 PURE w/PPK + Polyp 18mM Mg 2+ GFP-Gext 0 days 01:16:15.056125978 PURExpress NC (-DNA) GFP-Gext 0 days 08:22:11.208282580 PURExpress PC GFP-Gext 0 days 01:35:03.233243742 \ Data Max Name Read PURE w/CP + PPK + Polyp 18mM Mg 2+ GFP-Gext 1142988.56 1380549.46 PURE w/CP 8mM Mg 2+ GFP-Gext 584893.79 793465.68 PURE w/PPK + Polyp 18mM Mg 2+ GFP-Gext 135845.79 143510.00 PURExpress NC (-DNA) GFP-Gext 1363.52 167.92 PURExpress PC GFP-Gext 850639.37 967516.28 Lag \ Time Name Read PURE w/CP + PPK + Polyp 18mM Mg 2+ GFP-Gext 0 days 00:47:22.392950327 PURE w/CP 8mM Mg 2+ GFP-Gext 0 days 00:45:55.787595782 PURE w/PPK + Polyp 18mM Mg 2+ GFP-Gext 0 days 00:19:21.788669307 PURExpress NC (-DNA) GFP-Gext 0 days 00:13:49.447245369 PURExpress PC GFP-Gext 0 days 00:42:16.995848500 \ Data Name Read PURE w/CP + PPK + Polyp 18mM Mg 2+ GFP-Gext 270166.30 PURE w/CP 8mM Mg 2+ GFP-Gext 137313.14 PURE w/PPK + Polyp 18mM Mg 2+ GFP-Gext 32170.94 PURExpress NC (-DNA) GFP-Gext 322.44 PURExpress PC GFP-Gext 200602.45 Steady State \ Time Name Read PURE w/CP + PPK + Polyp 18mM Mg 2+ GFP-Gext 0 days 02:50:11.072913668 PURE w/CP 8mM Mg 2+ GFP-Gext 0 days 02:35:20.507916682 PURE w/PPK + Polyp 18mM Mg 2+ GFP-Gext 0 days 02:40:00.134997899 PURExpress NC (-DNA) GFP-Gext 0 days 20:21:09.831959821 PURExpress PC GFP-Gext 0 days 02:52:44.629645062 \ Data Name Read PURE w/CP + PPK + Polyp 18mM Mg 2+ GFP-Gext 2171678.26 PURE w/CP 8mM Mg 2+ GFP-Gext 1111298.20 PURE w/PPK + Polyp 18mM Mg 2+ GFP-Gext 258106.99 PURExpress NC (-DNA) GFP-Gext 2590.69 PURExpress PC GFP-Gext 1616214.80 Fit \ params Name Read PURE w/CP + PPK + Polyp 18mM Mg 2+ GFP-Gext [2285977.111810936, 2.4160489944570442, 1.6174... PURE w/CP 8mM Mg 2+ GFP-Gext [1169787.5764115045, 2.712290228560942, 1.5031... PURE w/PPK + Polyp 18mM Mg 2+ GFP-Gext [271691.5708766907, 2.1120079231950206, 1.2708... PURExpress NC (-DNA) GFP-Gext [2727.047352489795, 0.2459395018310663, 8.3697... PURExpress PC GFP-Gext [1701278.733888923, 2.274204732121089, 1.58423... R^2 drift Name Read PURE w/CP + PPK + Polyp 18mM Mg 2+ GFP-Gext 1.00 -2951.38 PURE w/CP 8mM Mg 2+ GFP-Gext 0.99 -2785.05 PURE w/PPK + Polyp 18mM Mg 2+ GFP-Gext 0.97 -671.76 PURExpress NC (-DNA) GFP-Gext 1.00 -8.07 PURExpress PC GFP-Gext 0.99 -3113.84 )
<Figure size 1800x800 with 5 Axes>

We can also calculate the kinetics and display the parameters as a table.

pr.kinetic_analysis(data)
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Analysis: 20250613