paninski-lab / funimag

Compression, denoising and demixing of functional imaging recordings

Functional Imaging Compression, Denoising and Demixing

We introduce a pipeline to compress, denoise, and demix* several types of functional imaging recordings including:

* Calcium Imaging (1p, 2p, 3p)
* Voltage Imaging (1p)
* Widefield

Installation

After installing the dependencies, install from the master branch as:

.. code-block:: shell

git clone https://github.com/paninski-lab/FunImag.git funimag
cd funimag
pip install -e .

Note: We currently only support Linux OS (tested on Ubuntu 16.04 and 18.04).

Demos

• Denoising and demixing demos with a sample data from CaImAn.

  * [Denoising demo]()
  * [Demixing demo]()
  

Dependencies

• TREFIDE

Running tests

In progress

Reference

If you use this code please cite the paper:

E. Kelly Buchanan, Ian Kinsella, Ding Zhou, Rong Zhu, Pengcheng Zhou, Felipe Gerhard, John Ferrante, Ying Ma, Sharon Kim, Mohammed Shaik, Yajie Liang, Rongwen Lu, Jacob Reimer, Paul Fahey, Taliah Muhammad, Graham Dempsey, Elizabeth Hillman, Na Ji, Andreas Tolias, Liam Paninski bioRxiv 334706; doi: https://doi.org/10.1101/334706