Catalog

ASAP is committed to accelerating the pace of discovery and informing a path to a cure for Parkinson’s disease through collaboration, research-enabling resources, and data sharing. We’ve created this catalog to showcase the research outputs and tools developed by ASAP-funded programs.

Code

surmeierlab/EZT2022SA: EZTNotebooks

This repository contains five Jupyter Notebooks (Python 3.0) created or modified for specific use with action potential analysis for the Zampese, et.al. 2022 Science Advances paper.

Article

Dopamine neuron activity encodes the length of upcoming contralateral movement sequences

The relationship between the activity of dopaminergic neurons (DANs) and the length of movement sequences is unknown. The authors imaged the activity of SNc DANs in mice. Results indicate that movement-initiation DANs encode more than a general motivation signal and invigorate aspects of contralateral movements. View original preprint.

Dataset

Source data for Mendonça et al 2024

Source data and code from dopamine neuron activity encode the length of upcoming contralateral movement sequences by Mendonça et al 2024.

Code

RectiPy software package

Recurrent neural network training in Python (RectiPy) is a software package developed by Richard Gast that allows for lightweight implementations of recurrent neural networks (RNNs) based on ordinary or delayed differential equations. Here, the team provides a tool that allows for the implementation of biologically informed spiking neural networks and optimizes the parameters of these networks via gradient descent.

Dataset

Source data for “Ca2+ channels couple spiking to mitochondrial metabolism in substantia nigra dopaminergic neurons”

Source data for publication: “Ca2+ channels couple spiking to mitochondrial metabolism in substantia nigra dopaminergic neurons.”

Article

Motor learning selectively strengthens cortical and striatal synapses of motor engram neurons

Publication: Learning and consolidating new motor skills require plasticity in the motor cortex and striatum, two key motor regions of the brain. However, how neurons undergo synaptic changes and become recruited during motor learning to form a memory remains unknown. Here the authors identify M1 engram neurons important for memory.

Article

Neural heterogeneity controls computations in spiking neural networks

Published: The authors want to understand how neural heterogeneity affect macroscopic neural dynamics and contribute to neurodynamic functions. Here, the authors study the macroscopic dynamics of networks of heterogeneous Izhikevich neurons. Their analysis suggests that the level of heterogeneity of inhibitory populations controls resonance and hysteresis properties of systems of coupled excitatory and inhibitory neurons. View original preprint.
 

Article

Feed-forward metabotropic signaling by Cav1 Ca2+ channels supports pacemaking in pedunculopontine cholinergic neurons

Published: Like a handful of other neuronal types in the brain, cholinergic neurons (CNs) in the pedunculopontine nucleus (PPN) are lost in the course of Parkinson’s disease (PD). PPN CNs have a distinctive physiological phenotype that shares some, but not all, of the features of other neurons that are selectively vulnerable in PD. View original preprint.

Code

Day2023 R code and analysis

Datasets for all figures 1-8 in: GABAergic regulation of striatal spiny projection neuron excitability depends upon their activity state.
Image is taken from Fig 1B inset and illustrates RiboTag-eGFP in SPNs of the striatum.

Dataset

Day2023 supplementary dataset

Datasets for all supplementary figures S1-4 in GABAergic regulation of striatal spiny projection neuron excitability depends upon their activity state (2023).

Dataset

Day2023 dataset

Datasets for all figures 1-8 in: GABAergic regulation of striatal spiny projection neuron excitability depends upon their activity state
Image is taken from Fig 1B inset and illustrates RiboTag-eGFP in SPNs of the striatum.

Article

Dynamic behaviour restructuring mediates dopamine-dependent credit assignment

Published: Reinforcement mechanism promotes not only reinforcement, but gradual refinement of the entire behavioral repertoire to assign credit to specific actions and action sequences that lead to dopamine release.

Article

Macroscopic dynamics of neural networks with heterogeneous spiking thresholds

Published: The authors develop a new computational model to represent different neuron types and spiking dynamics. The model is comprised of biophysical state variables and parameters, incorporates realistic spike resetting conditions, and accounts for heterogeneity in neural spiking thresholds. These features allow for a broad applicability of the model as well as for a direct comparison to experimental data. View original preprint.

Dataset

Motor learning selectively strengthens cortical and striatal synapses of motor engram neurons Dataset

This upload includes 1) ImageJ macros / scripts for minor automated cell counting for brain slides with immunostaining and 2) MATLAB functions / scripts for minor automated spine location cluster analysis (nearest neighbor distance / index).