Software, Datasets, Methods Papers, & More


Ephus, WaveSurfer, & ScanImage – We have been involved in helping to develop and support these highly flexible software packages for general-purpose data acquisition, electrophysiology, and laser scanning microscopy, developed and maintained in Karel Svoboda’s laboratory and Vidrio Technologies.


Length density analysis routines – A package of tools for analyzing digitally reconstructed neuronal morphology in terms of axonal and dendritic length density. The source code can be downloaded via this link (via eLife).


A dataset of digitally reconstructed dendritic arbors of mouse corticospinal neurons, by Ben Suter, has been deposited with NeuroMorpho.


Methods papers: About photostimulation-based circuit mapping, and Ephus software.


Laminar connectivity matrix datasets are available at SenseLab – a web site supporting multiple databases for computational modeling and related neuroinformatics tools, maintained by the lab of Gordon M. Shepherd, professor of neuroscience at Yale (neuroscientists sometimes confuse us).



Mouse corticospinal motor cortex

Shepherd Lab

Department of Physiology & NUIN

Feinberg School of Medicine

Northwestern University

303 East Chicago Avenue

Chicago, IL 60611

© 2015 Gordon Shepherd Lab. All rights reserved.

Corticospinal neurons (Suter & Shepherd 2015)