Techniques & Tools
Our group actively develops and disseminates software with applications to neuroscience research. We primarily develop tools using Matlab. Here we provide links to open source tools that we use, developed in the lab and elsewhere.
Techniques
This is a major technique used by the lab to understand coding of information in individual cells and neural populations across time.
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.
Our lab uses immunostaining, brain clearing, and viral approaches to understand 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.
Our lab uses fiber photometry to explore the activity of genetically-defined populations and projections.
Our lab has a method to non-invasively track multiple behavioral and somatic parameters that response to environmental changes.
Stujenske Lab Resources
This is a github package containing the code for Monte Carlo and heat diffusion simulations as published in Stujenske et al., 2014, Cell Reports.
Includes TiffViewer, which can load a HUGE tiff stack in a matter of SECONDS.
This is a fork of another repo. Used with Tiff Read & Write repo, can convert .oir files to tiffs quickly.
Other Resources
