Metadata-Version: 2.1
Name: biteen_utilities
Version: 0.1.2
Summary: Tools for working with single-molecule localization data.
Author: Daniel Foust
Author-email: djfoust@umich.edu
Classifier: Programming Language :: Python :: 3
Classifier: Operating System :: OS Independent
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: h5py
Requires-Dist: hdf5storage
Requires-Dist: matplotlib
Requires-Dist: matplotlib_scalebar
Requires-Dist: napari[all]
Requires-Dist: napari_animation
Requires-Dist: nd2
Requires-Dist: numpy
Requires-Dist: pandas
Requires-Dist: scikit-image
Requires-Dist: scipy
Requires-Dist: tifffile

# 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
