yacare

A companion to CaImAn for calcium imaging analysis. There are some questions that come up frequently in caiman's gitter forum, and many useful tools embedded in caiman that are not illustrated in the demos. The goal of yacare is to tackle these topics in standalone Jupyter notebooks. It mainly assumes you have a working caiman virtual environment.

Yacare is named after the South American yacare caiman, pictured above.

If you want to contribute, or want to see a topic covered, please open an issue. For caiman support, see the gitter forum.

Notebooks

• normalize_1p_traces.ipynb
• visualize_ridge_plot.ipynb

To do

• Multisession registration
• How to manually remove units
• Plotting denoised movies
• Seed plot for cnmfe

Acknowledgments

• Developed with support from NIH Bioinformatics and the Neurobehavioral Core at NIEHS.
• The caiman developers and community for providing such useful tools and feedback.
• Yacare caiman image is from Wikimedia.