Posts

A Flexible Platform for Monitoring Cerebellum-Dependent Sensory Associative Learning

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

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

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.

MINI2P

MINI2P

MINI2P is an open-source miniature 2-photon microscope brain explorer for fast high-resolution calcium imaging in freely-moving mice. In brief Development of a miniature 2-photon miniscope for large-scale calcium imaging in freely moving mice allows stable simultaneous recording of more than a thousand cells across multiple planes of densely active cortical regions in a wide spectrum of behavioral tasks without impediment of the animal’s behavior.

Optogenetics TTL driver

Optogenetics TTL driver

This simple optogenetics stimulation driver is based on the Arduino Uno, and produces millisecond-accurate timing to control a single laser or LED. The dials allow easy control of pulse on-time and frequency, with a simple switch to turn the flashing on or off.

HistoEnder

HistoEnder

Automated microscope slide stainers are typically very expensive, and unless the lab performs heavy histological work it is hard to justify buying a €2000-€10000 machine. As a result, histology and pathology labs around the world lose thousands of working hours for following a procedure that could be easily automated.

Mesmerize

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.

Raspberry Pi controlled precise treat dispenser

Raspberry Pi controlled precise treat dispenser

Some forms of canine cognition research require a dispenser that can accurately dispense precise quantities of treats. When using off-the-shelf or retrofitted dispensers, there is no guarantee that a precise number of treats will be dispensed.

TopMouseTracker

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

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.