Analysis pipeline for high-speed, high-resolution microscopy datasets.
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Updated
Aug 19, 2024 - MATLAB
Analysis pipeline for high-speed, high-resolution microscopy datasets.
Flow-Registration toolbox for 2P motion compensation
Drawing ROIs with a non-graphical user interface
CIAtah (pronounced cheetah): a software package for calcium imaging analysis of one- and two-photon imaging datasets. Documentation: https://git.io/ciatah_docs. Formerly known as calciumImagingAnalysis (ciapkg).
PVBS (Prairie View Browsing Solution) - General-purpose GUI for electrophysiology (patch clamp) and calcium imaging
This is MATLAB script created and used via the Trinkaus-Randall Lab at Boston University for the analysis of epithelial cellular calcium signaling during wound healing.
Custom code (Python or Matlab) to compute centripetal propagation from astrocytic calcium recordings using pixel-wise correlation functions
Signal Processing Toolbox for Calcium Imaging Data
This repository contains code for morphology-free analysis of functional fluorescence microscopy. The focal algorithm, Graph-Filtered Time-trace (GraFT) Dictionary Learning, is published in Charles et al. 2022 in the IEEE Transactions of Image Processing.
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
Complete Matlab pipeline for large scale calcium imaging data analysis
Matlab functions to convert calcium imaging data and associated intracellular electrophysiology data to Neurodata Without Borders (NWB) file format
CalciumImaging analysis matlab pipeline for suite2p outputs
Matlab routines for online non-rigid motion correction of calcium imaging data
Code to analyze calcium imaging data in Algamal et al. 2022, doi: https://doi.org/10.1101/2022.04.27.489759
This repository is a streamlined Miniscope Analysis pipeline that utilizes open source projects to motion correct, extract curate and align Miniscope data.
An open-source automated surgical instrument for microendoscope implantation
Calcium signal processing algorithm for automated analysis of intracellular calcium responses
3D files for an active commutator, endoscope encasing, etc
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