Data Analysis

SqueakR: An Experiment Interface for 'DeepSqueak' Bioacoustics Research

SqueakR is an open-source R package, available on CRAN, which streamlines bioacoustics research through automated data processing and visualizations for rodent vocalizations exported from DeepSqueak. These functions are harnessed through the ‘SqueakR’ Shiny Dashboard, available as a function within the package, which can be used to visualize experimental results and analyses, as well as conduct statistical significance test between call features across groups.

A Flexible Platform for Monitoring Cerebellum-Dependent Sensory Associative Learning

Climbing fiber inputs to Purkinje cells provide instructive signals critical for cerebellum-dependent associative learning. Studying these signals in head-fixed mice facilitates the use of imaging, electrophysiological, and optogenetic methods. Here, a low cost behavioral platform (~$1000) was developed that allows tracking of associative learning in head-fixed mice that locomote freely on a running wheel.

BrainJ

BrainJ enables high-throughput analysis of serial tissue sections imaged using confocal or widefield techniques. Developed in Fiji, our approach leverages freely available tools for machine learning pixel classification for cell detection and mesoscale mapping of axons and dendrites.

FastSurfer

FastSurfer is a fast and extensively validated deep-learning pipeline for the fully automated processing of structural human brain MRIs. As such, it provides FreeSurfer conform outputs, enables efficient big-data analysis for large cohort studies, and time-critical clinical applications such as structure localization during image acquisition or rapid extraction of quantitative measures for precision medicine.

Mesmerize

Mesmerize is a platform for the annotation and analysis of neuronal calcium imaging data. Mesmerize encompasses the entire process of calcium imaging analysis from raw data to interactive visualizations. Mesmerize allows you to create FAIR-functionally linked datasets that are easy to share.

TopMouseTracker

TopMouseTacker is a Python library based on OpenCV made for object tracking in videos. It uses a color camera and depth camera to infer the position of objects in the arena.

CaImAn: open source scalable algorithms for calcium and voltage imaging data

Advances in fluorescence microscopy enable monitoring larger brain areas in-vivo with finer time resolution. The resulting data rates require reproducible analysis pipelines that are reliable, fully automated, and scalable to datasets generated over the course of months.

CASCADE: Calibrated inference of spiking from calcium ΔF/F data using deep networks

CASCADE translates calcium imaging ΔF/F traces into spiking probabilities or discrete spikes. CASCADE is based on deep networks and runs on Python (Linux/Windows/Mac); it can be used either as a web application (Colaboratory notebook), or locally on a CPU or GPU.

DANNCE

DANNCE (3-Dimensional Aligned Neural Network for Computational Ethology) is a convolutional neural network (CNN) that calculates the 3D positions of user-defined anatomical landmarks on behaving animals from videos taken at multiple angles.

Pingouin

Pingouin is an open-source statistical package written in Python 3 and based mostly on Pandas and NumPy. Some of its main features are listed below. For a full list of available functions, please refer to the API documentation.