Open Neuroscience

Aggregator & curation of open source neuroscience projects


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WholeBrain

WholeBrain is a software to create anatomical maps. With a code base in C/C++ with wrappers to R and JavaScript/WASM. The purpose of WholeBrain is to provide a user-friendly and efficient way for scientist with minimal knowledge of computers to create anatomical maps and integrate this information with behavioral and physiological data for sharing on the web.

brainrender

brainrender is a python package for the visualization of three dimensional neuro-anatomical data. It can be used to render data from publicly available data set (e.g. Allen Brain atlas) as well as user generated experimental data.

JASP

JASP is a cross-platform statistical software program with a state-of-the-art graphical user interface. The JASP interface allows you to conduct statistical analyses in seconds, and without having to learn programming or risking a programming mistake.

PiDose

PiDose is an open-source tool for scientists performing drug administration experiments with mice. It allows for automated daily oral dosing of mice over long time periods (weeks to months) without the need for experimenter interaction and handling.

pyControl

pyControl is a system of open source hardware and software for controlling behavioural experiments, built around the Micropython microcontroller. pyControl makes it easy to program complex behavioural tasks using a clean, intuitive, and flexible syntax for specifying tasks as state machines.

pyPhotometry

pyPhotometry is system of open source, Python based, hardware and software for neuroscience fiber photometry data acquisition, consisting of an acquisition board and graphical user interface. pyPhotometry supports data aquisition from two analog and two digital inputs, and control of two LEDs via built in LED drivers with an adjustable 0-100mA output.

SLEAP

SLEAP (Social LEAP Estimates Animal Poses) is a multi-animal pose tracker based on deep learning. It is the successor of LEAP (Pereira et al., Nature Methods, 2019) and was designed to deal with the problem of tracking body landmarks of multiple freely interacting animals.

Neuroimaging Informatics Tools and Resources Collaboratory (NITRC)

NeuroImaging Tools & Resources Collaboratory is an award-winning free web-based resource that offers comprehensive information on an ever expanding scope of neuroinformatics software and data. Since debuting in 2007, NITRC has helped the neuroscience community make further discoveries using software and data produced from research that used to end up lost or disregarded.

PiVR

PiVR is a system that allows experimenters to immerse small animals into virtual realities. The system tracks the position of the animal and presents light stimulation according to predefined rules, thus creating a virtual landscape in which the animal can behave.

ReproNim: A Center for Reproducible Neuroimaging Computation

ReproNim’s goal is to improve the reproducibility of neuroimaging science and extend the value of our national investment in neuroimaging research, while making the process easier and more efficient for investigators.

Simple Behavioral Analysis (SimBA)

Several excellent computational frameworks exist that enable high-throughput and consistent tracking of freely moving unmarked animals. SimBA introduce and distribute a plug-and play pipeline that enables users to use these pose-estimation approaches in combination with behavioral annotation for the generation of supervised machine-learning behavioral predictive classifiers.

DataJoint

DataJoint is an open-source library for managing and sharing scientific data pipelines in Python and Matlab. DataJoint allows creating and sharing computational data pipelines, which are defined as databases and analysis code for executing steps of activities for data collection and analysis.

Neurodata Without Borders

Neurodata Without Borders is a data standard for neurophysiology, providing neuroscientists with a common standard to share, archive, use, and build analysis tools for neurophysiology data. NWB is designed to store a variety of neurophysiology data, including data from intracellular and extracellular electrophysiology experiments, data from optical physiology experiments, and tracking and stimulus data.

OpenDrop Digital Microfluidics Platform

OpenDrop a modular, open source digital microfludics platform for research purposes. The device uses recent electro-wetting technology to control small droplets of liquids. Potential applications are lab on a chip devices for automating processes of digital biology.

Stytra

Stytra, a flexible, open-source software package, written in Python and designed to cover all the general requirements involved in larval zebrafish behavioral experiments. It provides timed stimulus presentation, interfacing with external devices and simultaneous real-time tracking of behavioral parameters such as position, orientation, tail and eye motion in both freely-swimming and head-restrained preparations.

An Open-source Anthropomorphic Robot Hand System: HRI Hand

We present an open-source anthropomorphic robot hand system called HRI hand. Our robot hand system was developed with a focus on the end-effector role of the collaborative robot manipulator. HRI hand is a research platform that can be built at a lower price (approximately $500, using only 3D printing) than commercial end-effectors.

Open Source Automated Western Blot Processor

Researchers in the biomedical area are always involved in methodologies comprising several processes that are repetitive and time-consuming; these researchers can take advantage of this time for other more important things.

OpenNeuro

A free and open platform for sharing MRI, MEG, EEG, iEEG, and ECoG data. With OpenNeuro, you can: Browse and explore public datasets and analyses from a wide range of global contributors.

Small cost efficient 3D printed peristaltic pumps

The project overall aim is to provide cost efficient solution to drive microfluidics systems for e.g. cell culture and organ on a chip applications. Pumps, valves and other accessories are ofter expensive to buy or very expensive to custom made.

Stackable titre plates for organ on a chip applications

Organ on a chip is typically difficult to achieve due to large technical challenges such as fabrication of chips and systems and biological challenges such as co-culture of cells. In this project we have developed a system to stack 12 well plates inserts on top of each other where each plate holds a tissue.

cellfinder

cellfinder is software from the Margrie Lab at the Sainsbury Wellcome Centre for automated 3D cell detection and registration of whole-brain images (e.g. serial two-photon or lightsheet imaging). It’s a work in progress, but cellfinder can:

DeepLabCut

DeepLabCut™ is an efficient method for 3D markerless pose estimation based on transfer learning with deep neural networks that achieves excellent results (i.e. you can match human labeling accuracy) with minimal training data (typically 50-200 frames).

MNE-Python

MNE is a software package for processing electrophysiological signals primarily from magnetoencephalographic (MEG) and electroencephalographic (EEG) recordings, and more recently sEEG, ECoG and fNIRS. It provides a comprehensive solution for data preprocessing, forward modeling (with boundary element models), distributed source imaging, time–frequency analysis, non-parametric multivariate statistics, multivariate pattern analysis, and connectivity estimation.

Nilearn

Nilearn is a Python module for fast and easy statistical learning on NeuroImaging data. It leverages the scikit-learn Python toolbox for multivariate statistics with applications such as predictive modelling, classification, decoding, or connectivity analysis.

A Cartesian Coordinate Robot for Dispensing Fruit Fly Food

The fruit fly, Drosophila melanogaster, continues to be one of the most widely used model organisms in biomedical research. Though chosen for its ease of husbandry, maintaining large numbers of stocks of fruit flies, as done by many laboratories, is labour-intensive.

Bonsai

Bonsai is a high-performance, easy to use, and flexible visual programming language for designing closed-loop neuroscience experiments combining physiology and behaviour data. Bonsai has allowed scientists with no previous programming experience to quickly develop their own experimental rigs and is also being increasingly used as a platform to integrate new open-source hardware and software from the experimental neuroscience community.

Ethoscopes

Ethoscopes are machines for high-throughput analysis of behavior in Drosophila and other animals. Ethoscopes provide a software and hardware solution that is reproducible and easily scalable. They perform, in real-time, tracking and profiling of behavior by using a supervised machine learning algorithm, are able to deliver behaviorally triggered stimuli to flies in a feedback-loop mode, and are highly customizable and open source.

Bonvision

BonVision is an open-source closed-loop visual environment generator developed by the Saleem Lab and Solomon Lab at the UCL Institute of Behavioural Neuroscience in collaboration with NeuroGEARS. BonVision’s key features include:

Poseidon

The Poseidon is an open-source syringe pump and microscope system. It uses 3D printed parts and common components that can be easily purchased. It can be used in microfluidics experiments or other applications.

DeepLabStream

DeepLabStream is a python based multi-purpose tool that enables the realtime tracking of animals and manipulation of experiments. Our toolbox is adapted from the previously published DeepLabCut (Mathis et al., 2018) and expands on its core capabilities.

LED Zappelin’

Two-photon (2P) microscopy is a cornerstone technique in neuroscience research. However, combining 2P imaging with spectrally arbitrary light stimulation can be challenging due to crosstalk between stimulation light and fluorescence detection.

SpikeInterface

SpikeInterface is a unified Python framework for spike sorting. With its high-level API, it is designed to be accessible and easy to use, allowing users to build full analysis pipelines for spike sorting (reading-writing (IO) / preprocessing / spike sorting / postprocessing / validation / curation / comparison / visualization) with a few lines of code.

Addgene’s AAV Data Hub

AAV are versatile tools used by neuroscientists for expression and manipulation of neurons. Many scientists have benefited from the high-quality, ready-to-use AAV prep service from Addgene, a nonprofit plasmid repository. However, it can be challenging to determine which AAV tool and techniques are best to use for an experiment.

FishCam

We describe the “FishCam”, a low-cost (500 USD) autonomous camera package to record videos and images underwater. The system is composed of easily accessible components and can be programmed to turn ON and OFF on customizable schedules.

neuTube

neuTube is an open source software for reconstructing neurons from fluorescence microscope images. It is easy to use and improves the efficiency of reconstructing neuron structures accurately. The framework combines 2D/3D visualization, semi-automated tracing algorithms, and flexible editing options that simplify the task of neuron reconstruction.

OpenTrons

Today, biologists spend too much time pipetting by hand. We think biologists should have robots to do pipetting for them. People doing science should be free of tedious benchwork and repetitive stress injuries.

Deep Cinac

Two-photon calcium imaging is now widely used to infer neuronal dynamics from changes in fluorescence of an indicator. However, state of the art computational tools are not optimized for the reliable detection of fluorescence transients from highly synchronous neurons located in densely packed regions such as the CA1 pyramidal layer of the hippocampus during early postnatal stages of development.

Fingertip laser sensor

The fingertip laser project makes use of the sensor used in an Avago ADNS-9500 laser mouse, to improve the capabilities of robotic hands, giving them the capability to detect distance, surface type and slippage of grasped objects.

SciDraw

SciDraw is a free repository of high quality drawings of animals, scientific setups, and anything that might be useful for scientific presentations and posters. We want this repository to be as open as possible, so do not require signing up to post a drawing.

UC2

The open-source optical toolbox UC2 [YouSeeToo] simplifies the process of building optical setups, by combining 3D-printed cubes, each holding a specific component (e.g. lens, mirror) on a magnetic square-grid baseplate. The use of widely available consumables and 3D printing, together with documentation and software, offers an extremely low-cost and accessible alternative for both education and research areas.

Head-Mounted Mesoscope

The advent of genetically encoded calcium indicators, along with surgical preparations such as thinned skulls or refractive index matched skulls, have enabled mesoscale cortical activity imaging in head-fixed mice. Such imaging studies have revealed complex patterns of coordinated activity across the cortex during spontaneous behaviors, goal-directed behavior, locomotion, motor learning,and perceptual decision making.

Open Source Eye Tracking

The purpose of this project is to convey a location in 3 dimensional space to a machine, hands free and in real time. Currently it is very difficult to control machines without making the user provide input with their hands.

Open Source Syringe Pump Controller

Syringe pumps are a necessary piece of laboratory equipment that are used for fluid delivery in behavioral neuroscience laboratories. Many experiments provide rodents and primates with fluid rewards such as juice, water, or liquid sucrose.

Sample Rotator Mixer and Shaker

An open-source 3-D printable laboratory sample rotator mixer is developed here in two variants that allow users to opt for the level of functionality, cost saving and associated complexity needed in their laboratories.

Automated Operant Conditioning

Operant conditioning (OC) is a classical paradigm and a standard technique used in experimental psychology in which animals learn to perform an action to achieve a reward. By using this paradigm, it is possible to extract learning curves and measure accurately reaction times (RTs).

Heuristic Spike Sorting Tuner (HSST), a framework to determine optimal parameter selection for a generic spike sorting algorithm

Extracellular microelectrodes frequently record neural activity from more than one neuron in the vicinity of the electrode. The process of labeling each recorded spike waveform with the identity of its source neuron is called spike sorting and is often approached from an abstracted statistical perspective.

VocalMat

Mice emit ultrasonic vocalizations (USV) to transmit socially-relevant information. To detect and classify these USVs, here we describe the development of VocalMat. VocalMat is a software that uses image-processing and differential geometry approaches to detect USVs in audio files, eliminating the need for user-defined parameter tuning.

BossDB

BossDB is a volumetric database that lives in the AWS cloud. Hundreds of terabytes of electron microscopy, light microscopy, and x-ray tomography data are available for free download and study.

Neuroanatomy and Behaviour

Neuroanatomy and Behaviour (ISSN: 2652-1768) is a free open access journal for behavioural neuroscience and related fields. Powered by free open source software to eliminate costs and keep grant funds doing science.

3D Slicer

3D Slicer is a software for medical image informatics, image processing, and three-dimensional visualization. It’s extremely powerful and versatile with plenty of different options. It is a great tool for volume rendering, registration, interactive segmentation of images and even offers the possibility of running Python scripts thought an embedded Python interpreter.

Craniobot

The Craniobot is a cranial microsurgery platform that combines automated skull surface profiling with a computer numerical controlled (CNC) milling machine to perform a variety of cranial microsurgical procedures in mice.

Labmaker

LabMaker is a maker and assembly service for OPEN SCIENCE instruments. OPEN SCIENCE initiatives provide part lists or “Bill Of Materials” (BOM) for openly available scientific instruments. LabMaker bridges the gap between the BOM and the ready-to-use instrument for those not wanting to build by themselves.

MicroscoPy

An open-source, motorized, and modular microscope built using LEGO bricks, Arduino, Raspberry Pi and 3D printing. The microscope uses a Raspberry Pi mini-computer with an 8MP camera to capture images and videos.

Colaboratory

Colaboratory is a free Jupyter notebook environment that runs in the cloud. Your notebooks get stored on Google Drive. The great advantage is that you don’t have to install anything (however, for some features you need a Google account) on your system to use it.

Suite2P

Suite2P is a very modular imaging processing pipeline written in Python which allows you to perform registration of raw data movies, automatic cell detection, extraction of calcium traces and infers spike times.

Autoreward 2

The motivation to start this project arises when we started to include a new behavioral paradigm in the lab, an alternation T-mace with return arms (like the one in Wood e_t al.

Backlog

Bellow is a list of interesting projects related to science and research, that we didn’t have time to curate yet. Feel free to browse through them and make comments and suggestions!

Computer clusters

Here are two projects that use card sized computers as the basic units for computing clusters: A 64 node cluster, build using pi’s and lego, built at the University of Southampton.

OpenFlexure

OpenFlexure is a 3D printed flexure translation stage, developed by a group at the Bath University. The stage is capable of sub-micron-scale motion, with very small drift over time. Which makes it quite good, among other things, for time-lapse protocols that need to be done over days/weeks time, and under space restricted areas, such as fume hoods.

OpenFuge

OpenFuge describes all the materials and gives step by step instructions to the assembly of a centrifuge that is able to deliver 6000 G’s of force and to rotate at 9000 RPM, while being able to hold 4 eppendorf tubes.

Psychophysics toolboxes

Roughly put, psychophysics studies the relationships of physical stimuli and their respective elicited sensations and perception. Psyhophysics also relates to the techniques used to probe these relationships and the toolboxes here presented are mainly dealing with these techniques.

Pulse Pal

Pulse Pal is an open and inexpensive (~$210) alternative to pulse generators used in neurophysiology research, and is most often used to create precisely timed light trains in optogenetics assays.

Python, NumPy, SciPy & Matplotlib

Python is a free programming language that is widely used, most of the software developed for Linux is written in Python. It contains several libraries that cover a lot of problem domains, from asynchronous processing to zip files.

Red Pitaya

Red Pitaya is an computer+FPGA that has digital input and outputs and really fast analog inputs and outputs. It allows connection over ethernet and programming of custom routines. The system is powerful enough to have application in mostly all branches of neuroscience labs: oscilloscopes, signal generators and even a candidate for recording systems.

School of Data

School of Data is a global network that aims to train civil society in the practical use of the large amount of data available nowadays. The network is composed of individuals and organizations that carry out training programs, hands-on courses and other activities in different regions and countries of the world.

Spike Gadgets

A brief description of their current software (09.Sep.2016) is provided by one of their founders, Mattias Karlsson: State Script: Do you need to control lasers for optogenetics, stimulators, or other TTL-based devices with precise, temporally defined patterns?

Brainflow

BrainFlow BrainFlow is a library intended to obtain, parse and analyze EEG, EMG, ECG and other kinds of data from biosensors, it provides two APIs: Data Acquisition API to obtain data from BCI boards Signal Processing API which is completely independent and can be used without Data Acquisition API Both of these APIs are uniform for all supported boards, so it allows to write completely board agnostic code.

Genome RNAi

GenomeRNAi  is a database containing phenotypes from RNA interference (RNAi) screens in Drosophila and Homo sapiens. In addition, the database provides an updated resource of RNAi reagents and their predicted quality.

GogoFuge

GogoFuge is a good example of the power of opensource designs. IT was based on the idea of the DremelFuge and altered to be a tabletop centrifuge with vortex capability.

Green Brain

The Green Brain project wants to create an artificial Apis mellifera brain and implement said brain into a robot, that will be able to fly and and behave just like a honey bee!

Image, Office suites, and other general purpose software

If you are using Linux, changes are that this page is not that useful for you, since most of these programs come installed by default. For you who are not yet into linux, most of these programs have Windows/Mac versions:

Intelligent hearing aid

Ojoshi at instructables.com has posted a manual on how to build this arduino based hearing aid system. From his instructables page: it has tuning functionality that allows the wearer to tune the amplification to his or her needs.

IPipet

IPipet is a neat system to help you not to lose track of which wells you have already pipetted in or from. The idea is simple, you place a tablet running a link with your specific pipetting protocol under your source and destination plates.

Lab management software

Since organisation of ideas, stocks, and projects is a major concern (or at least should be) of labs and researchers, here is a small compilation of cost free sofware to help out:

Micro-Manager

Micro-Manager is an ImageJ plugin dedicated to the control of microscopes. Their intent is to have a “one fits all” software for the control of microscopes, stages, filters and cameras. A comprehensive list of supported devives can be found on devices section of the project webpage.

Neuromorpho

NeuroMorpho.Org is a centrally curated inventory of digitally reconstructed neurons associated with peer-reviewed publications. It contains contributions from over 100 laboratories worldwide and is continuously updated as new morphological reconstructions are collected, published, and shared.

NeuroTinker

NeuroTinker project is all about hardware emulated neurons. The creators made them in a way that each hardware neuron has excitatory and inhibitory inputs and one output that can be split up to affect dowsntream neurons.

NiBabel

NiBabel is a python package, under the NiPy project, that aims at unifying the process of opening different medical and neuroimaging file formats, including: ANALYZE, GIFTI, NIfTI1, MINC, MGH and ECAT as well as PAR/REC.

Nipy

NiPy is an effort to make brain imaging research easier and more clear. This is implemented by providing a series of software that deal with file IO, analysis, and interfaces & pipelines.

Nose poke device for rats using arduino and 3d printed parts

This is a small set of instructions on how to build a nose poke device for rats, using an arduino, some 3D printed parts and some off-the-shelf electronic components.

Open Microscopy Environment

The Open Microscopy Environment is a collaborative project between several labs. They are developing file formats and software standards for light microscopy. Within the project they have BIO-formats, a Java library for reading and writing data.

Operating systems

Linux is an open source operating system and it is the major OS used in servers and supercomputers. Ubuntu, one of the best known distributions has been gaining space in the personal computing scene, now days already being factory shipped by major manufacturers.

Super-Releaser

Ever thought about making soft robots? The folks at Super-Releaser have, and they are doing very cool projects! Some for medical applications and some for research purposes. Check one of their cool robots below:

5 Dollar PCR machine

The 5 dollar PCR machine is a project from David Ng. he created a very interesting design for the PCR machine. Instead of using eppendorfs, he is using teflon tubes and three different heating elements, which allows for cheaper (he has a working PCR machine for 5 dollars!

Open bionics

The Open bionics project was inspired by the Yale open hand project, aiming to develop light, affordable, and modular robot hands and myoelectric prosthesis. Also they want to make them easy to replicate using off the shelf materials.

Open prosthetics and robotics

With the rise of low cost 3D printers, and other cheap manufacturing tools, the field of robotics and prosthetics has been gaining quite a few open source projects. Two very nice compilations can be found at openrobot hardware and at Soft robotics toolkit.

Backyard Brains

Backyard brains started out producing low cost, portable, electrophysiology systems to bring neuroscience to classrooms and help promote it. “Backyard brains wants to be for neuroscience, what the telescope is for astronomers” – meaning that the idea is that with a couple of hundred dollars anyone can get one of these recording systems and start doing experiments, like amateur astronomers can buy telescopes and start observing the cosmos.

10$ smartphone microscope

This neat little project uses some plexi-glass, lens extracted from a laser pointer to harvest the power of smartphone cameras for some very big amplifications! Yoshinok manged to see cell plasmolysis and some other cool features with it.

Addgene

Addgene is a non-profit company that makes the share of plasmids easier by making a plasmid database and linking them to the papers where they were described. In this way they take on the job of maintaining plasmids and shipping them to requesting scientists.

Allen Brain Map

The Brain Map is one of the initiatives of the Allen Institute. It is a data portal that encompasses different projects: the Allen Institute has created a set of large-scale programs to understand the fundamentals of the cortex.

Attys

Attys is an wearable data acquisition device with a special focus on biomedical signals such as heart activity (ECG), muscle activity (EMG) and brain activity (EEG). It’s open firmware, open API and has open source applications on github in C++ and JAVA to encourage people to create their own custom versions for mobile devices, tablets and PC.

BB LED Matrix

This project uses a 32X32 LED array (1024 LEDs in total) and a beagle bone black board. The page describing the project has very nice explanations on how the whole system works (and LED displays in general).

Big Neuron

Big Neuron wants to create a standard for the field of single neuron reconstruction. Because the data available comes from different structures, different organisms, using different collection and analyses algorithms and is in the range of petabytes (according to the project site), there is a strong need for standards that will allow this huge amount of data to be compared.

Blinkenschild

Blinkenschild is a portable sign consisting of 960 RGB LEDs. The images/movies to be displayed are stored in a SD card in a Teensy3 board and controlled via bluetooth. Resolution is not as high as LCD monitors but the refresh rate is much higher:

Boinc

Boinc is a platform for volunteer computing. Briefly, volunteer computer is a system where computer processor’s idle time (those periods where your computer is on, but not being used for anything) is turned into calculation time via a custom written software.

BPM Biosignal

BPM Biosignal is a two stage amplifier created mainly for educational purposes. Check their YouTube Channel.

Brain Map

BrainMap expands the accessible DIY projects for brain activity measurements. This is the conclusion project of Patrick Dear and Mark Bunney Jr. at Cornell university where they used infrared leds to measure differences in blood flow at the scalp and map the motor cortex.

BrainBrowser

BrainBrowser is a collection of open source, web-based 3D data visualization tools, mainly for neuroimaging studies. It is built using open technologies such as WebGL and HTML5. It allows exploration of cortical surface models (MNI and Wavefront OBJ, as well as FreeSurfer ASCII surface format) and volumetric MINC data.

Computer Vision and motion tracking software

Motion tracking can be really useful in neurosciences, for automatic measurements of behaviour, among other things. Here you’ll find a small list of tracking softwares or libraries used to build such softwares:

Crowd funding

As many other things that are being decentralized with the advent of the internet, so is research. One of the very things being decentralized is the funding source for research projects.

Data repositories

In here are some examples of tools that can be used to share/store data collected. Published a paper and think that people would benefit from looking at the raw data? Want to make that data that has been stored for years useful?

DIY PCR

Katharina and Alex are developing a classic PCR machine: 16 samples and a heated lid. You can find more details of their project here Here is a demo video:

DremelFuge

DremelFuge is a very simple and clever centrifuge, buit perhaps not the safest one (be careful if you end up using it!). It takes advantage of 3d printing technology to print an adaptor that goes on to a Dremel (a precision tool that has really high rotation rates).

Fiji

Fiji is a distribution of ImageJ. The idea of the developers is to make the life of scientists easier by bundling ImageJ with nicely organised plugins and auto update function.

Interesting projects

It is great that there are other interesting projects out there that are also concerned with making science available to more people! Here is a short list of projects I came across.

NeuroElectro

NeuroElectro wants to extract information about neuron types, morphology, electrophysiology properties from papers, using text mining algorithms and gathers them in a database. Our goal is to facilitate the discovery of neuron-to-neuron relationships and better understand the role of functional diversity across neuron types.

Open BCI

BioAmp is a biopotential acquisition device (EEG, ECG, EMG, EOG, etc.) developed in the Prototyping Laboratory at the School of Engineering of the National University of Entre Rios (Argentina). Main features:

Open BCI

OpenBCI is a complete open source EEG system that can be built either on top of an Arduino (8-bit system), or on top of chipKIT (32-bit system), which gives the system more local memory and allows for faster speeds.

Open EEG

The openEEG project aims at describing and putting manuals for building a two channel EEG system for about U$200. More on instructions on how to build one, can be found here.

Open Ephys

Open Ephys is a great initiative to create a suite that encompasses hardware for LFP and spiking recording, optogenetics combined with custom written software for microstimulation, environmental stimuli, extracellular recording and optogen.

Open ExG

OpenHardwareExG: is a project that provides both open source hardware and software for the measurement and analysis of different types of biosignals From the project page: About the OpenHardwareExG project Project goals The main goal of the project is to build a device that allows the creation of electrophysiologic signal processing applications.

Open lab notebooks

Open notebooks are opening up science in the very first steps, making records of ideas, plans that didn’t work and protocols that failed available publicly. This allows others to avoid trailing the same dead end roads, saving time, money and human power.

Open PCR

Open PCR is an open source PCR machine with heated lid and space for 12 samples

Open science framework

From the Open science framework webpage: The Open Science Framework (OSF) is part network of research materials, part version control system, and part collaboration software. The purpose of the software is to support the scientist’s workflow and help increase the alignment between scientific values and scientific practices.

Open source brain

The open source brain project is a database of computational models of neural systems. From the website: Open Source Brain is a resource for sharing and collaboratively developing computational models of neural systems.

OpenSpritzer

A very neat picospritzer initially created by Joe (PI at Raimondo Lab) using basically a solenoid valve, microcontroller and a power source. Was later further developed by Chris at the Baden Lab, and collaboratively published as a peer reviewed article.

OpenStage

Open stage is a low-cost motorised microscope stage capable of movement in the micrometer range. It features manual control via a control-pad, different movement velocities and pc communication through the serial port.

Parallela

Parallela, an open source, open access card sized supercomputer, has the mission of bringing parallel computing to the masses by combining multiple RISC processors and very low power consumption. Produced by the Adapteva company.

PySpace

PySpace is a signal processing and classificiation environment for Python. Modular software for processing of large data streams that has been specifically designed to enable distributed execution and empirical evaluation of signal processing chains.

Python for Neurosciences (Frontiers collection)

Frontiers has created not one but two nice collections about open source software for neurosciences written in Python. Here is collection 1 Here is collection 2 In these collections the readers will find a lot of nice resources, ranging from stimulus generation, to data formatting and analysis.

Signal Generators

Every lab needs a signal generator once in a while. They are useful to see if your acquisition program is working properly, to test why a certain piece of equipment is not working properly or to generate cues and targets at behavioural paradigms.

Simulations

Ever thought about playing with a virtual worm? or interacting with a simulated bee brain? Sounds interesting no? These are just two projects that offer anyone the opportunity to play around with brain/neuronal simulations and models.

Skinner Box with RPi+Python

This project was developed by Katherine Scott to be presented at the PyCon 2014. She developed a skinner box for her pet rats using a raspberry pi and some 3D printed parts.

Stereo microscope

Although stereo microscopes are an essential piece of hardware in biology labs, sometimes we wish they had more features, like the possibility to record the magnified images with a camera, or have a better lighting system to enhance contrast on those small samples.

Syringe Pump

From the Pearce lab, this syringe pump was published in Plos One and is built using 3d printed parts, stepper motors and a raspberry pi, costing 5% or less than commercial available systems.

Takktile

Takktile, is a tactile sensor to be used on robotic applications. The developers want to make it move away from the closed walls of research institutions by making it open source and cheap.

tDCS

Although of simple complexity and using low currents, this tDCS machine is still to be considered a piece of equipment that could be dangerous both in the assembly and in the operation phases, so please inform yourself as best as you can before either of these steps!

Tensor Flow

Google has packaged their deeplearning machine learning tools and made it open source. The project is called tensorflow, and is available here. Some nice tutorials on the website, so that with a bit of patience, people can start to deep their toes into machine learning!

The Visible Human project

The Visible Human Project is a database of anatomical images (MR, CT and radiography) from male and female bodies. Information about the database is translated into a couple of different languages.

The Yale open hand project

The Yale open hand project, has a similar purpose of the open hand project, that is, to make prosthetic hands more widely available through the lowering of costs. They have a different design from the open hand project.

Vision Egg

Vision Egg is a Python library for generating visual stimuli. In more detail, it is a high level interface in between Python and OpenGL, and can use inexpensive consumer grade graphics cards to generate precise visual stimuli.

Web portals

Here are some open learning sources, they go from sites that interactively teach one how to code, to efforts in publishing free college textbooks. Khan Academy: Is composed of a series of lectures and exercises on a wide range of topics from basic multiplication to linear algebra and information theory.

YouTube as a resource for Open Science Hardware

When working with Open Hardware, Google search will become your friend, whether you want it or not. Other search engines, such as DuckDuckGo won’t cut it (it is much harder to find what you are looking for, especially in cases where you don’t know all specific terms).

About

We are network of collaborators trying to keep track and curate interesting open source projects related to neurosciences. If you have a project that you’d like to see listed here or if you know of a project that should be listed, drop us a line, via E-mail, or Twitter.

Team

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André Maia Chagas

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Agustín Solano

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Benjamin Paffhausen

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Gaspar Herrera

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Jesus J Ballesteros

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Matias Andina

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Miguel Fernandes

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