Aggregator & curation of open source neurosicience projects
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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.
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.
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 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.
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.
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.
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 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.
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.
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.
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.
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.
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.
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).
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.
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 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 (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 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.
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 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.
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 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 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.
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.
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!
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 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 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.
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 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 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 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 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.
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 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.
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 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.
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!
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:
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 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.
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 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.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 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 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 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.
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.
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.
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.
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:
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!
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.
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 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.
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 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.
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 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.
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 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 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 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 is a two stage amplifier created mainly for educational purposes. Check their YouTube Channel.
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 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.
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:
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.
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?
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 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 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.
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 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.
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:
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.
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 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.
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 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.
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.
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.
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.
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, 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 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.
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.
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.
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.
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.
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.
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, 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.
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!
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 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, 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.
Here are some small tutorials I was able to create, to give neuroscience specific examples on how to use microcontrollers, or how to write a code for data analysis using python and so on.
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.
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.
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).
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.