Tools and resources

Brain atlasing

Waxholm Space Atlas of the Sprague Dawley Rat Brain

Image of a rats brain

Open access volumetric atlas offering comprehensive anatomical delineations of the rat brain based on structural contrast in isotropic magnetic resonance (39 μm) and diffusion tensor (78 μm) images acquired ex vivo from an 80 day old male Sprague Dawley rat at the Duke Center for In Vivo Microscopy.

Spatial reference is provided by the Waxholm Space coordinate system. The location of bregma and lambda are identified as anchors towards stereotaxic space.

Application areas include localization of signal in non-structural images e.g. functional or pharmacological MRI and PET, or assignation of location to features extracted from microscopic images from histological sections.

Computational neuroscience


LFPy logo

LFPy is a Python package for calculation of extracellular potentials from biophysically detailed (multicompartmental) neuron models and networks of such neurons. It relies on the NEURON simulator.


ViSAPy logo

ViSAPy (Virtual Spiking Activity in Python) is a tool for model-based generation of biophysically-realistic benchmarking data for evaluation of automatic spike-sorting algorithms.


ViMEAPy logo

Virtual MEA measurements in Python (ViMEAPy) is a Python toolbox for calculating and analysing the extracellular potential measured in an in vitro slice setting, where a slice of neural tissue is immersed in saline on top of a Microelectrode Array (MEA).


Uncertainpy logo

Uncertainpy is a Python toolbox for uncertainty quantification and sensitivity analysis of computational models of the types used in neuroscience.


Logo pyLGNpyLGN is a simulator of spatiotemporal cell responses to visual stimuli in the early part of the visual system, that is, the retina, lateral geniculate nucleus (LGN) and primary visual cortex. The simulator is based on a mechanistic, firing-rate model that incorporates the influence of thalamocortical loops, in addition to the feedforward connections.


The Experimental Directory Structure (Exdir) is a proposed, open file format specification for experimental pipelines. Exdir uses the same abstractions as HDF5 and is compatible with the HDF5 Abstract Data Model, but stores data and metadata in directories instead of in a single file.

Published Sep. 12, 2018 10:46 AM - Last modified Oct. 23, 2018 1:05 PM