read_data

This module contains functions that help read quantitative phenotyping data (mainly tierpsy features) and the corresponding experimental metadata and format them in the format used by the downstream modules: two dataframes with matching index, one containing features and one containing metadata information.

Contents

hydra_metadata

Functions to read feature summaries and metadata from an experiment performed on the new multi-camera rig (hydra). These functions read the standardised files containing the tierpsy features and the metadata and create matching feat and meta dataframes that can be used for downstream analysis.

Functions available to the user:

• read_hydra_metadata
• build_matching_feat_meta
• align_bluelight_conditions

compile_features_summaries

This script contains functions that can be used to compile indivudual features_summaries and filenames_summaries (assuming tierpsy format) and create one features_summaries and one filenames_summaries file containing all the results.

Functions for the user:

• compile_tierpsy_summaries Helper functions potentially useful to the user:
• find_fname_summaries
• check_summary_type

get_feat_summaries

Functions to read the tierpsy feature stats (that correspond to plate feature summaries) directly from the featuresN files. This is an alternative way to feature summaries files, instead of recalculating them using the summarizer. Since they are not recalculated, the process is faster than it is with the summarizer. However, it is not recommended as the features stats stored in the featuresN files might have been calculated with an older version of tierpsy which might contain more bugs than the most recent version. It is recommended to use the summarizer for feature extraction.

Functions for the user:

• read_feat_stats
• get_all_feat_summaries
• write_all_feat_summaries_to_file

get_timeseries

Functions to read timeseries data from featuresN files within a root directory.

Main functions for the user:

• get_timeseries
• read_timeseries

[cyclops_metadata]

Contains one function that generates feat and meta dataframes for a specific experiment screened on the cyclops rig.

[phenix_metadata]

Contains functions to read feature summaries and metadata for the syngenta experiments performed on phenix. These functions are not generalisable to other experiments but can be used as templated for reading data from old screens.