binarize2pcalcium

Binarize2PCalcium
=================

Binarize2PCalcium is a Python package for processing calcium imaging data.

Features
--------

- Support for data preprocessing.
- Visualization tools for calcium imaging data.

Installation
------------

You can install Binarize2PCalcium using pip:

.. code-block:: bash

   pip install binarize2pcalcium

Usage
-----

To use Binarize2PCalcium, import the package in your Python code:

.. code-block:: python

   from binarize2pcalcium import binarize2pcalcium as binca

   animal_id = 'DON-011733'
   session = '20230203'

   c = binca.Calcium(data_dir, animal_id)

   c.session = session 
   c.session_name = session

   c.data_type = '2p'
   c.remove_bad_cells = False
   c.verbose = False  # outputs additional information during processing
   c.recompute_binarization = True  # recomputes binarization and other processing steps; False: loads from previous saved locations

   # set flags to save matlab and python data
   c.save_python = True  # save output as .npz file 
   c.save_matlab = False  # save output as .mat file

   # manual thresholds for spike detection
   c.dff_min = 0.05  # min %DFF for [ca] burst to be considered a spike (default 5%) overwrites percentile threshold parameter
   c.percentile_threshold = 0.9999  # this is pretty fixed, we don't change it; we want [ca] bursts that are well outside the "physics-caused" noise
   c.maximum_std_of_signal = 0.08  # if std of signal is greater than this, then we have a noisy signal and we don't want to binarize it
								   # - this is a very important flag! come see me if you don't understand it

   #
   c.binarize_data()