Complementary cortical and thalamic contributions to cell-type-specific striatal activity dynamics during movement

Coordinated motor behavior emerges from information flow across brain regions. How long-range inputs influence cell-type-specific activity within motor circuits remains unclear. The dorsolateral striatum (DLS) contains direct- and indirect-pathway medium spiny neurons (dMSNs and iMSNs) that exhibit distinct roles in movement control, and receives converging cortical and thalamic inputs. We performed 2-photon imaging from dMSNs, iMSNs, and their cortical and thalamic inputs identified by monosynaptic rabies tracing, as mice executed a skilled locomotion task. We used recurrent neural network (RNN) classifiers and hierarchical clustering analyses to reveal functionally heterogeneous subpopulations in each population. We found that dMSNs were preferentially active at movement onset and offset, and iMSNs during execution. Cortical and thalamic inputs were preferentially active during onset/offset and execution, respectively. dMSN- and iMSN-projecting neurons in each region showed similar tr..., , # Complementary cortical and thalamic contributions to cell-type-specific striatal activity dynamics during movement

Dryad DOI: https://doi.org/10.5061/dryad.np5hqc07j

This repository contains the full analysis pipeline for the paper:

Gjoni E., Sristi R. D., Liu H., Dror S., Lin X., O’Neil K., Arroyo O. M.,\
Hong S. W., Kim H., Liu J., Blumenstock S., Lim B., Mishne G., & Komiyama T. (2025).\
**Complementary cortical and thalamic contributions to cell-type-specific striatal activity dynamics during movement.**

The code reproduces Figures 1–4 from the manuscript.

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## Data Requirements

Before running any notebooks, download and unzip the following datasets:

* Neural activity data\
Unzip `neural_activity_data.zip` into `data/`
* Paw-position (DeepLabCut) data\
Unzip `paw_position_data.zip` into `data/`
* Trained TEA-Net models\
Unzip `TrainedModels.zip` into `data/`

Detailed descriptions of each dataset are provided below.

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## Repository Structure

* `data/`
* `neu...,