Software

GuPPy, a Python toolbox for the analysis of fiber photometry data

Fiber photometry (FP) is an adaptable method for recording in vivo neural activity in freely behaving animals. It has become a popular tool in neuroscience due to its ease of use, low cost, the ability to combine FP with freely moving behavior, among other advantages.

ACQ4

ACQ4 is a python-based platform for experimental neurophysiology developed at the Allen Institute for Brain Science and the University of North Carolina, Chapel Hill. It includes support for patch-clamp electrophysiology, multiphoton imaging, scanning laser photostimulation, and many other experimental techniques.

Automated morphometric analysis with SMorph software reveals plasticity induced by antidepressant therapy in hippocampal astrocytes

Nervous system development and plasticity involves changes in cellular morphology, making morphological analysis a valuable exercise in the study of nervous system development, function and disease. Morphological analysis is a time-consuming exercise requiring meticulous manual tracing of cellular contours and extensions.

PUMA 3D Printed Open Source Microscope

PUMA is 3D printed open source portable modular microscope with augmented reality, fluorescence, phase contrast, epi-illumination, epi- and trans-polarisation and other features. You can either build it fully DIY or purchase the basic scope ready made and upgrade it as required (see below for details).

Diffusion MRI Q-ball CSA-ODF and Hough Tractography

This is a diffusion-weighted MRI processing Matlab toolbox (including binaries), which can be used to: • Compute the Q-Ball Imaging Orientation Distribution Function in Constant Solid Angle (CSA-ODF) (Aganj et al, MRM 2010).

Stalefish

Stalefish is a tool to analyse gene expression from ISH or other histology slice images. From your 2D brain slice images you can build a 3D expression surface from a brain structure such as the isocortex or the hippocampus.

Autopilot

Autopilot is a Python framework for performing complex, hardware-intensive behavioral experiments with swarms of networked Raspberry Pis. As a tool, it provides researchers with a toolkit of flexible modules to design experiments without rigid programming & API limitations.

NeuroDesk

Neuroimaging researchers require a diverse collection of bespoke command-line and graphical tools to analyse data and answer research questions. Installing and maintaining a neuroimaging software setup is challenging and often results in un-reproducible environments.

Clinica

Clinica is a software platform for clinical research studies involving patients with neurological and psychiatric diseases and the acquisition of multimodal data (neuroimaging, clinical and cognitive evaluations, genetics…), most often with longitudinal follow-up.

Load confound

Load a sensible subset of the fMRI confounds generated with fMRIprep in python (Esteban et al., 2018). The predefined denoising strategies are all adapted from Ciric et al. 2017. Check the docstring of each strategy for more info and a list of parameters.