Plotting interspike intervals (ISI) and spikes from fast-scan cyclic voltammetric (FSCV) electrochemical and electrophysiological recordings
By Emma Sherrell onCode for plotting interspike intervals (ISI) and spikes from fast-scan cyclic voltammetric (FSCV) electrochemical (EChem) and electrophysiological (EPhys) recordings.
Task data for plotting interspike intervals (ISI) and spikes from fast-scan cyclic voltammetric (FSCV) electrochemical and electrophysiological recordings
By Emma Sherrell onData for plotting interspike intervals (ISI) and spikes from fast-scan cyclic voltammetric (FSCV) electrochemical (EChem) and electrophysiological (EPhys) recordings.
3D printed MR-compatible stereotaxic frame for NHPs
By Emma Sherrell onA compact MRI-compatible stereotaxis suitable for a variety of NHP species (Macaca mulatta, Macaca fascicularis, and Cebus apella) that allows multimodal alignment through technique-specific fiducial markers.
pyRASP
By Emma Sherrell onThe package "pyRASP" (written in support of https://www.biorxiv.org/content/10.1101/2023.12.18.572148v2) is a set of Python classes that can be run from scripts, interactive notebooks, and so on to analyze microscopy data. An example notebook is provided, showing user analyses.
Richert/Heterogeneous_SNNs: v1.0.0: Scripts to replicate the results of Gast et al. PNAS 2024
By Julia Julia Leonard onThis release includes configuration files and scripts to replicate the main results presented in Gast et al. PNAS 2024, including Python scripts for the simulation, bifurcation analysis, and training of networks of Izhikevich neurons with heterogeneous spike thresholds.
RNAseq FASTQ: Effect of age and trisomy on transcriptional profile in cortex of Dp16 mice
By Emma Sherrell onCortex was isolated from control and Dp16 mice at 5 months of age and 14-16 months of age, and RNA was isolated and sequenced (5 mice per group, for a total of 20 mice).
ImageJ FIJI code to semi-automatize the morphological analysis of microglia in histological sections
By savannah onImageJ FIJI code to semi-automatize the morphological analysis of microglia in histological sections.
TX2P – Transcript to protein
By savannah onTX2P allows for automated integration of mass spectometry data in long-read RNA-sequencing workflow. It does so by predicting open reading frames for each transcripts within an input GTF/GFF file, translates it into peptide sequences and then searches for those predicted proteins in mass spec datasets using MetaMorpheus.
State-dependent GABAergic regulation of striatal spiny projection neuron excitability: NEURON + Python model of striatal projection neurons
By Emma Sherrell onThis repository contains a NEURON + Python model of striatal projection neurons (or SPNs) designed to simulate the interaction between GABAergic and glutamatergic synaptic inputs.
RectiPy software package
By Emma Sherrell onRecurrent 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.
surmeierlab/EZT2022SA: EZTNotebooks
By Emma Sherrell onThis 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.
Day2023 R code and analysis
By Emma Sherrell onDatasets 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.
Evaluation of a novel method for spectral analysis of neurophysiology data
By Emma Sherrell onThis code implements a novel method for correcting a distortion effect that is present in the power spectra of neuronal spike trains. This method is compared to an alternative, inter-spike interval shuffling procedure that has been conventionally employed for this purpose in the past.
Population fraction of Parkinson’s disease attributable to preventable risk factors
By Emma Sherrell onThe complete R-based Posit project reproduces the analyses and output in the article, "Population fraction of Parkinson's disease attributable to preventable risk factors."
Metagenomics of Parkinson’s disease implicates the gut microbiome in multiple disease mechanisms
By Emma Sherrell onThe code provided here is the same "Supplementary Code" that is provided in the supplement of the manuscript. Individual level raw shotgun sequences and metadata are available on NCBI Sequence Read Archive (SRA) under BioProject ID PRJNA834801.
Boles_et-al_DSS_time-series
By Emma Sherrell onProcessed and normalized counts after the removal of low-quality genes and samples. These data are separated into colon ("colon_clean_VST_counts.csv") and brain ("brain_clean_VST_counts.csv"). The sample key can be found in the metadata at the GEO entry page. This repository contains the code that was used to generate these cleaned counts from the raw counts.
LBD-case-case-GWAS
By Emma Sherrell onCode used in the analysis from the manuscript Wu et al., Investigation of the genetic aetiology of Lewy body diseases with and without dementia (2023).
Manual Tracking/measure_ECM.ijm
By savannah onA script to generate circular ROIs in each frame of a timelapse, using a previously generated track as reference. Used to measure fluorescence intensity (i.e., extracellular matrix content) along a microglia track. To be used as a continuation of 2_tracking.ijm.
Manual Tracking/tracking.ijm
By savannah onA script to store in ImageJ’s ROImanager the tracks generated using Manual Tracking plugin, for later use (drawing tracks, frame-by-frame analysis). To be used as a continuation of 1_image_prep.ijm.
Manual Tracking/image_prep.ijm
By savannah onA script to register 2-channel timelapse images using HyperStackReg, using only 1 of the channels to compute transformation. The script also enhances contrast and prepares the image for manual tracking.