Techniques & Tools

Two photon calcium imaging Imaging activity in genetically-identified and spatially-localized neurons in vivo

This is a major technique used by the lab to understand coding of information in individual cells and neural populations across time.

Electrophysiology In vivo extracellular recordings

This is another major technique for tracking activity in neural populations. We use micro-LED silicon probes and CMOS-based high density probes, among other approaches.

Anatomy Understanding cell types and connections

Our lab uses immunostaining, brain clearing, and viral approaches to understand cells and circuits.

Optogenetics Manipulating cells and circuits

Our lab uses optogenetics to activate or silence cells and circuits, while monitoring the effects using electrophysiology. See “modeling for optogenetics” below.

Fiber photometry Tracking genetically defined populations

Our lab uses fiber photometry to explore the activity of genetically-defined populations and projections.

Behavior and physiology Tracking behavioral and physiological metrics of internal state response simultaneously

Our lab has a method to non-invasively track multiple behavioral and somatic parameters that response to environmental changes.

Modeling for Optogenetics Predict light and heat spread from optic fibers

This is a github package containing the code for Monte Carlo and heat diffusion simulations as published in Stujenske et al., 2014, Cell Reports.

Tiff Read & Write Suite of tools for fast reading and writing of uncompressed tiffs in Matlab.

Includes TiffViewer, which can load a HUGE tiff stack in a matter of SECONDS.

ReadOIR Read Olympus .oir files in Matlab and/or convert to tiff.

This is a fork of another repo. Used with Tiff Read & Write repo, can convert .oir files to tiffs quickly.

Suite2p Calcium imaging package

Cell detection based on correlated activity.

Blender 3D design software

This is a very versatile software that we use for designing 3D prints.

Kilosort Spike sorting software

We use this for spike sorting from electrophysiological recordings.

Phy Visualizing electrophysiological data

We use this for cell selection after kilosort.