OptoFP 2P Imaging Analysis and Modeling

This repository contains code used to analyze 2‑photon calcium imaging data during a mouse reach‑to‑consume task with and without optogenetic muscle stimulation. batch2Ana_Fezf2_Population_Final_20260204.ipynb used to generate population‑level data analysis figures.

This repository also contains analysis code and notebooks for fitting and evaluating a neural–behavior coupling model for the reach-to-consume task. The notebooks reproduce the main computational modeling results and figures in the paper.
all_session_summary_plot.ipynb, session4_plot.ipynb, and no_pertubation_test.ipynb generate figures related to the computational model.

Notebook

• batch2Ana_Fezf2_Population_Final_20260204.ipynb

  • Population analysis for Fezf2 ET neurons during a reach‑to‑consume task with/without optogenetic muscle stimulation.

• session4_plot.ipynb

  • Single-session computational model fitting and reproduction of figures used in the paper.

• all_session_summary_plot.ipynb

  • Multi-session computational model analysis. This notebook aggregates results across all sessions and generates summary figures used for population-level evaluation in the paper.

• no_pertubation_test.ipynb

  • Model comparison across variants, including:

    • Intrinsic-only dynamics (no external kinematic input);
    • Intrinsic + unperturbed kinematic feedback;
    • Full model with perturbation-dependent feedback gating.

Requirements

Python packages used directly in the notebook:

• numpy
• scipy
• pandas
• pickle
• matplotlib
• scikit-learn
• pingouin

Local modules required (must be importable from the repo root):

• AdvancedAnalysis_2P.py
• BasicProcessing_2P.py
• regression_utils.py

Data Files (required)

For general data analysis, please place these in the repo root (same folder as the notebook), unless you update paths inside the notebook:

• Fezf2_OptoFP_2P_Spks_Sum.pkl
• Fezf2_Sortinfo.pkl

The data files for running computational modeling has been put in the directory /modeling_data, these data is directly extracted from Fezf2_OptoFP_2P_Spks_Sum.pkl with no other preprocessing.

Run

jupyter lab

Open the desired .ipynb file and run all cells.

Outputs

The notebook batch2Ana_Fezf2_Population_Final_20260204.ipynb writes PDF figures to the working directory, including:

• Fezf2_Session_LDA_Blocks_Lineplot_Summary_Spks.pdf
• All_Fezf2_PCA_Neural_Trajectory_Spk_activity_2D_All_Neurons.pdf
• All_Fezf2_PCA_Neural_Trajectory_Spk_activity_3D_All_Neurons.pdf
• Fezf2_PCA_Neural_Trajectory_Spk_activity_Off_Plane_Proj_All_Neurons.pdf
• Fezf2_PCA_Neural_Trajectory_Spk_activity_Off_Plane_Vel_All_Neurons.pdf

Citation

If you use this dataset, please cite the associated manuscript or preprint:

Distorted Proprioceptive Feedback Reshapes Descending Cortical Dynamics
Yi Li, X. Hermione Xu, Shiyang Pan, Xu An, Patrick J. Mulcahey, Zixuan Qiu, Shengli Zhao, Nuo Li, John Pearson, Z. Josh Huang
bioRxiv 2025.11.11.687832; doi: 10.1101/2025.11.11.687832

Contact

Please contact Dr. Yi Li (liyi.start@gmail.com) for questions about the dataset.