cellutils

Utility functions for High throughput microscopy machine learning pipelines

Installation

TODO:include requirements.txt file

git clone git@github.com:halliganbs/cellutils.git

cd cellutils

pip install .

Utils

• make_well - Converts Object level measurements to well level means
• split_metadata - Splits filename into metadata columns
• zpad - Pads zeros into well ids ie. A1 -> A01
• zprime - Calculates ZPrime of a plate
• get_data_cols - Sorts out measurement columns
• char_range - Generates a letters in an iterable range
• add_controls - Adds control rows to platemap file
• synergy_convert - Converts HPD300 despense platemap/viability score into synergy format for processing
• find_number_components - Calculates optimal number of components needed to meet provided variance threshold (defaults to 90%)

Distance

• euclidean - Calculates euclidean distance for each row
• mahalanobis - Calculates mahalobis distance for the plate

Plotting

• plot_plate - Plots well level plate
• plot_reg_facet - Plots facet grid of regression plots
• synergy_plot - Plots synergy score plot with option Bliss Synergy

Score

• score_plate - Scores a database file using a provided model and column names