Resources

Materials aiding our research

Software

NeuroML

NeuroML is a modular, declarative, and simulator-independent standard for specifying computational neuroscience models. The community-driven ecosystem of NeuroML models and tools is growing every year.

SciDash: SciUnit and NeuronUnit

SciUnit is a framework for test-driven validation of scientific models. NeuronUnit provides a set of pre-built tests that can be used to assess how well a neuroscience model corresponds to experimental data.

NeuroML Database

NeuroML Database provides access to 1,500+ NeuroML models. Each model features extensive characterizations of electrophysiology, morhology, and computational complexity.

BlenderNEURON

BlenderNEURON allows the visualization of NEURON models and their simulation results in Blender, the open-source, professional 3D modeling software.

SwarmSight

SwarmsSight is a video analysis software with two modules: one for assessing changes in motion in video scenes and another for tracking the positions of insect antennae.

PyLMeasure: A Python Wrapper for LMeasure

PyLMeasure provides a Python interface to the popular neuronal morphology analysis software L-Measure.

hoc2swc: A HOC to SWC converter

hoc2swc is a Python package that converts a model instantiated in NEURON simulator to the popular SWC morphology format. Tools like L-Measure that support the SWC format can then be used to analyze and visualize neuron model morphology.

NSF COA: Auto-generate your COA forms for NSF grant applications

Tired of filling out your Collaborators and Other Affiliations form by hand? Have papers with dozens of co-authors? Let us do the work for you.

Calimag: A calcium imaging conversion pipeline to convert raw data to the NWB standard file format.

MoSeq: Machine vision for behavior analysis

MoSeq is a technique that uses 3D machine vision and unsupervised machine learning to automatically discover the underlying modular structure of mouse behavior in the lab. Please email dattalab@hms.harvard.edu with your full contact information and a valid GitHub account name, and we can help you get started.

 

A BRAIN Initiative Research Team

Funded by NINDS U19NS112953

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