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calciumbayes

Data Mining Final (STAT 4240)

caltracer

MATLAB based software for viewing and analyzing Calcium indicator data.

common-input

Trying to solve the common input problem for functional connectivity inference.

fast-oopsi

a repository containing everything relevant to our fast non-negative deconvolution work

iit

Code for computing the integrated information (big phi) of a system and other relevant quantities and structures.

joint_calcium_ephys_mapping

This is a small-scale demo of using Bayesian event inference methods to detect postsynaptic currents.

masa_stim

Making Masa's stimulation code.

moog.github.io

Modular Object-Oriented Games (MOOG): Python-based game engine for reinforcement learning, psychology, and neurophysiology.

neuroglm

Fitting and analysis of trial-based neural spike responses with Generalized Linear Model (GLM).

oasis

Deconvolution of calcium imaging data

oasis_matlab

odessa-beta

A MATLAB sketch of a simple framework for controlling experiments. The essential object is a sequence of actions in time. Any programmatic way of creating a sequence of actions - including adaptive, closed-loop, or totally predetermined sequences. Action objects, in general, will be split into two classes: io and processing. We want to create a simple core of objects can be extended by users and therefore interface with most hardware or software. Data related objects include general types that are exchanged with hardware, i.e. input and output signals, and hardware interfaces like DAQ and channel objects. From a user's perspective, we want to make it (relatively) easy to orchestrate experiments that require controlling a lot of hardware and/or online analysis. Ideally, we can abstract a protocol as a sequence of nodes, and the user will interface with a node-based gui, i.e. a flow-diagram. As a user, I am expected - at least for now - to understand how to write my own modules. As a library of modules is developed, the software may become easier to use. But for the developer's sake and for hopeful flexibility, we only want to write some abstract classes. The rule of thumb will be to resist writing anything too specific.

open-ephys-data-format

A Record Engine plugin that saves data in the original Open Ephys data format

plugin-gui

Software for processing, recording, and visualizing multichannel electrophysiology data

psc-detection

A Bayesian/probabilistic approach to modelling postsynaptic currents in whole-cell voltage-clamp traces. PSCs can then be detected from noisy data using Gibbs Sampling.

psc-detection-dist

Distribution of code implementing the Bayesian PSC detection algorithm described in Merel et al, J. Neuro. Meths., 2016.

reveal.js

The HTML Presentation Framework

rhythm-oni-plugin

Source plugin for Open Ephys Acquisition Board with custom FPGA (available Dec 2022)

smc-oopsi

code to implement our sequential monte carlo (smc) algorithm to perform optimal optical spike inference (oopsi) for individual neurons

sync-conda-env

sync conda environment pre-commit hook

thunder

Large-scale neural data analysis with Spark

ttl-panels

TTL toggle and display panels to help with debugging