biteen-utilities 0.1.1

Tools for working with single-molecule localization data.

biteen-utilities

A repository for common coding tasks in the Biteen Lab.

Methods:

biteen_io.py:

Reading, writing, and converting between different file types.

• convert .nd2 to .tif
• convert .nd2 to .npy
• extract ROIs from cellpose .npy into 2d numpy array
• convert cellpose .npy to .mat (SMALL-LABS format)
• convert SMALL-LABS output (*_fits.mat, *_guesses.mat) to pandas DataFrame
• convert SMALL-LABS output (*_fits.mat, *_guesses.mat) to .csv
• convert pandas DataFrame to SMALL-LABS format .mat
• convert SMALL-LABS output to Spot-On format
• convert pandas DataFrame to Spot-On format

biteen_pandas.py:

Working with tabular data stored in pandas DataFrames.

• calculate individual step data from localizations
• filter localization data by number of localizations in each track
• calculate median step size for each track

biteen_plots.py

Plotting single-molecule data.

• Plot localizations overlayed on image data, e.g. phase contrast
• Plot trajectories overlayed on image data, e.g. phase contrast

Future

• dpsp related format conversions
• drift correction with RCC
• using napari
• MSD
• using NOBIAS output
• heatmaps
• rotation to align with cell axes