FluoView_FRAP_Parser

A tool to parse and analyze FRAP data generated by Olympus' FluoView software.

This is useful for quickly turning around FRAP data from FluoView. I change bits and pieces of it each time I use it so it is far from polished. It ingests the .csvs that are produced by FluoView, handles the variations in formatting, and returns a pandas dataframe along with some basic statistics about the series of recovery data that it has parsed.

Arguments

--cutoff-value

Each replicate is trimmed to the shortest replicate in the data set. Increasing the cutoff value from the default (0) allows the user to specify the number of replicates to ignore when trimming the data.

For example, if six replicates were acquired but one was halted early for whatever reason, increasing this value to 1 will ignore the short replicate and trim the data to the second shortest replicate.

--path

Set the path to the directory that contains the .csv files to be parsed.

--append-dir

Creates a new series in the final dataframe containing the directory from which the data were retrieved. This is useful when appending data from multiple sets of replicates into a larger dataset later.

--bin-size

Edit the width of the window that is used to bin replicates into discrete time points.

--normalization-frames

Change the number of frames that are pulled from the head of the data and used to set the baseline pre-bleach fluorescence intensity.

--stats {short, full}

Print some statistics about the parsed fluorescence recovery data.

• short prints a brief summary of the data to stdout.
• long prints the data from "short" and also dumps an html file containing the final dataframe into the current directory.

--purge-outliers

Remove replicates whose τ_1/2 has a Z-score beyond a certain threshold (2; currently hardcoded because this feature isn't very useful).