Decoding for calcium imaging

[ZhaomingPsych]

Hi everyone, I have some questions regarding the shuffle method, tuning curves, and decoding in your library:

1. Shuffle Method: Is the TsDataFrame suitable for the shuffle method? Can TsDataFrame be transformed into a TsGroup?
2. Tuning Curves: It appears that Tsd cannot be used as an input for tuning curves, despite the documentation indicating that it should be possible.
3. Decoding: Can TsDataFrame be used as an input for the decoding process?

Thank you for your assistance.

[gviejo]

Hey,

1. Currently the shuffle methods works only for timestamps object (Ts) or TsGroup. In what case would you want to shuffle a TsdFrame? In any case, you can transform a Tsd into a TsGroup but not a TsdFrame.
2. Which function did you try to use?
3. Not yet. It's in the roadmap. Feel free to describe your use case here.

[ZhaomingPsych]

Thank you for your reply!

1. You're right! I transformed TsDataframe to Tsd, and now it works!
2. compute_1d_tuning_curves_continuous
3. Currently, I am trying to analyze place fields from two-photon calcium imaging using pynapple. Our goal is to decode the mouse's position from the calcium imaging data. Do you have any suggestions?

[gviejo]

For 3. it's in the roadmap to add more capabilities for decoding with calcium imaging data but it's not ready yet. I would just try to train a machine learning model from scikit-learn if you want to do some decoding. I can leave this issue open until new decoding functions are implemented.