20251211 Analysis (Cytation 3)

!pip install nucleus-cdk==0.5.0rc2 | tail -n2

# Surface a failed install here, rather than as a confusing ModuleNotFoundError
# in the import cell below.
import importlib.metadata as md
assert md.version("nucleus-cdk") == "0.5.0rc2", f"got {md.version('nucleus-cdk')}"

%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()

# Specify file paths
data_file = "20251211-cytation3-pure-timecourse-gfp-EXPERIMENT-biotek-cdk.txt"
platemap_file = "20251211-ClpXP-Cy3-2.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()

g = pr.plot_curves(data=data)