20250930 Analysis
!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')}"
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
import os
from cdk.analysis.cytosol import platereader as pr
import warnings
warnings.filterwarnings('ignore')
# Initialize plotting
pr.plot_setup()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)
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_file = "synergy-2-pure-timecourse-gfp_20250929-ClpXP-3_.txt"
platemap_file = "20250930-ClpXP-new.csv"
data, platemap = pr.load_platereader_data(data_file, platemap_file, platereader = "biotek-cdk")No data loaded: section potentially unrecognized:
No data loaded: section potentially unrecognized:
No data loaded: section potentially unrecognized:
No data loaded: section potentially unrecognized: Procedure Details
No data loaded: section potentially unrecognized: Layout
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24
A Well ID
B Well ID
C Well ID
D SPL1 SPL2 SPL3 SPL4 Well ID
E Well ID
F Well ID
G Well ID
H Well ID
I Well ID
J Well ID
K Well ID
L Well ID
M Well ID
N Well ID
O Well ID
P Well ID
No data loaded: section potentially unrecognized: Time T° GFP-G35
No data loaded: section potentially unrecognized: Time T° GFP-G70
No data loaded: section potentially unrecognized: Time T° GFP-G100
No data loaded: section potentially unrecognized: Well ID SPL1 SPL2 SPL3 SPL4
Well D1 D2 D3 D4
Max V [GFP-G35
No data loaded: section potentially unrecognized: Protocol PURE Timeseries
Experiment File Name
No data loaded: section potentially unrecognized: Plate Type Greiner 384 SV NoBind Automap
Well Selection Runtime
Eject plate on completion
Set Temperature Temperature
No data loaded: section potentially unrecognized: Time T° GFP-G35
No data loaded: section potentially unrecognized: Time T° GFP-G70
data.Read.unique()
data = data[data.Read == "GFP-G35"]Basic Analysis¶
Curves¶
Curves of RFU over time, by named sample.
pr.plot_curves(data);