20251212-Analysis
!pip install nucleus-cdk==0.5.0rc2 | tail -n2Requirement 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)
Setup¶
%load_ext autoreload
%autoreload 2
import pandas as pd
import seaborn as sns
import matplotlib.pyplot as plt
# Import the cdk platereader module
from cdk.analysis.cytosol import platereader as pr
import warnings
warnings.filterwarnings('ignore')
# Set up plotting
pr.plot_setup()Load Data¶
# Specify file paths
data_file = "20251212-cytation3-pure-timecourse-gfp-EXPERIMENT-biotek-cdk.txt"
platemap_file = "20251212-ClpXP.csv"
# Load data
data, platemap = pr.load_platereader_data(
data_file=data_file,
platemap_file=platemap_file,
platereader="biotek-cdk" # Options: "cytation", "envision", "biotek-cdk"
)
# Checkout first few rows
data.head()Loading...
Plot Raw Curves¶
g = pr.plot_curves(data=data)