Skip to main content

No project description provided

Project description

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()

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

binarize2pcalcium-0.1.24.tar.gz (32.5 kB view hashes)

Uploaded Source

Built Distribution

binarize2pcalcium-0.1.24-py3-none-any.whl (32.6 kB view hashes)

Uploaded Python 3

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page