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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()
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