This code implements the Zero-Inflated Gamma encoding and decoding model for post-deconvolved calcium imaging traces.
A Jupyter Notebook tutorial is available in the code folder. There're more examples in the examples in paper folder.
The code is written in Python 3.6. In addition to standard scientific Python libraries (numpy, scipy, matplotlib), the code expects: Tensorflow (=1.9.0).
The code doesn't support for Tensorflow 2 so far. Cumol (thanks!) mentioned in the Issues that you can try fixing it by replacing the line import tensorflow as tf in the relevant code files as:
import tensorflow.compat.v1 as tf
tf.disable_v2_behavior()
To download this code, run git clone https://github.com/zhd96/zig.git
The real datasets analyzed in the paper1 can be downloaded at https://drive.google.com/drive/folders/1roTjSoEpBGNjJEaL89c_16svp6vYOp0_?usp=sharing.
There is a sample simulated data in the data folder. The code to generate the simulated datasets analyzed in the paper1 is in the code folder.
If you use this code, please cite the paper:
- Wei, X.X., Zhou, D., Grosmark, A., Ajabi, Z., Sparks, F., Zhou, P., Brandon, M., Losonczy, A. and Paninski, L., 2019. A zero-inflated gamma model for post-deconvolved calcium imaging traces. bioRxiv, p.637652. https://www.biorxiv.org/content/10.1101/637652v1