Repository for the article "Distributed chromatic processing at the interface between retina and brain in the larval zebrafish", Guggiana et al. 2021, Curr. Bio.

2-Photon Imaging Data Registration/Alignment Across Recording Days. Created for Apostolides Lab, rotation 2, Fall 2020.

CalciumImaging analysis matlab pipeline for suite2p outputs

Calcium signal processing algorithm for automated analysis of intracellular calcium responses

Scripts for extraction and analysis of widefield calcium data from awake behaving mice.

Toolbox for fast, variational 1D alignment

Code to analyze calcium imaging data in Algamal et al. 2022, doi: https://doi.org/10.1101/2022.04.27.489759

3D files for an active commutator, endoscope encasing, etc

Complete Matlab pipeline for matching in vivo recorded cells post hoc in histology

Matlab scripts for analyzing calcium imaging data presented in "Neural Coding of Leg Proprioception in Drosophila" (Mamiya, Gurung, and Tuthill (2018) Neuron: DOI:https://doi.org/10.1016/j.neuron.2018.09.009)

Suite of MATLAB algorithms (recommended to be used with App Designer GUI) for the analysis and coincidence detection of local field sharp wave ripples (SWRs), local field oscillations (theta, gamma, etc.), spikes (SWR coincidence and spike-phase coupling), post-synaptic currents (PSCs), and calcium transients. Written in MATLAB 2022a Update 4

Signal Processing Toolbox for Calcium Imaging Data

Basic toolbox for analysis of in vivo 2-photon data. Originally written at Glenn Turner's lab, CSHL, when I was working with flies.

Scripts to create prominence plots from widefield calcium imaging data. Steinmetz et al., 2017 eneuro

PVBS (Prairie View Browsing Solution) - General-purpose GUI for electrophysiology (patch clamp) and calcium imaging

interactive analysis of two-photon calcium imaging data

Matlab functions to convert calcium imaging data and associated intracellular electrophysiology data to Neurodata Without Borders (NWB) file format

Collection of LabView & Matlab tools for simultaneous calcium & fMRI measurements

This repository is a streamlined Miniscope Analysis pipeline that utilizes open source projects to motion correct, extract curate and align Miniscope data.