The Carmel Lab utilizes a systems neuroscience approach to studying damage to the motor system and associated motor recovery. This means different aspects of physiology, anatomy and behavior are examined and brought together in analyses to obtain a more lucid picture of the motor system.

For this purpose we have developed some in-house tools and techniques to enable analysis using our systems neuroscience approach. In this page, we list the tools and techniques by category.


Tissue Morph: This is a spinal cord slice image registration software. This tool registers cross-sectional slices of the spinal cord to idealized template images using affine and nonlinear transformations. This enables experimentalists to perform image based comparisons of slices that have been infused with different dye techniques.

Viral Injection Techniques: Viral tracers can be more effective than traditional anterograde tracers in labeling the corticospinal tract. Read more about techniques and benefits of the viral tracers.


Motometrics: This is a software that allows experimentalists to analyze Motor evoked Potentials (MEPs) that are obtained from measuring EMG from muscles after stimulating the motor system. Motometrics can quantify MEPs and generate relevant recruitment curves for analysis.


Autoscala: A software and hardware system for automated behavior capture and analysis. This tool was specifically built to automate analysis for the rat ladder task, a skilled walking task that is sensitive to injury and recovery of the motor system.

Dexterity: Dexterity is MATLAB software that enables quick analysis of data from automated manipulation tasks. Through a graphical user interface, files are loaded and data are automatically identified and analyzed. These data can be annotated or graphed directly. Analysis is saved, and the graph and corresponding data can be exported. For additional analysis, Dexterity provides easy access to custom scripts created by other users.