Category: Most Recent


April 17, 2019

In a recent Nature Protocol’s article, Edoardo Balzani and colleagues from Valter Tucci’s lab have developed and shared Phenopy, a Python-based open-source analytical platform for behavioral phenotyping.

Behavioral phenotyping of mice using classic methods can be a long process and is susceptible to high variability, leading to inconsistent results. To reduce variance and speed up to process of behavioral analysis, Balzani et al. developed Phenopy, an open-source software for recording and analyzing behavioral data for phenotyping. The software allows for recording components of a behavioral task in combination with electrophysiology data. It is capable of performing online analysis as well as analysis of recorded data on a large scale, all within a user-friendly interface. Information about the software is available in their publication, available from Nature Protocols.*

Check out the full article from Nature Protocols!

(*alternatively available on ResearchGate)

Cerebro Wireless Optogenetic System

April 5, 2019

Andy Lustig from the Karpova Lab at Janelia has developed, documented, and shared a system for wireless optogenetic stimulation.

Several commercial systems for wireless controlled optogenetic stimulation are available, however, as you might expect, these systems can be cost-prohibitive and often lack the ability to be customized. To address these limitations, Lustig developed his own wireless, open-source optogenetic stimulation system. It features Cerebro, a rechargeable, battery-powered wireless receiver; a head implant containing optical fibers and two independent laser diodes; a base station for transmitting radio signals to the Cerebro, controlled by a Windows computer via USB or by TTL; a charging dock; and Xavier, a user-friendly GUI for sending and logging base station commands. The full documentation for building this system is available on the Karpova Lab github.



Telemetry System for Recording EEG

March 29, 2019

In a 2011 Journal of Neuroscience Methods article, Pishan Chang and colleagues shared their design for an open-source, novel telemetry system for recording EEG in small animals.

EEG monitoring in freely-behaving small animals is a useful technique for observing natural fluctuations in neural activity over time. Monitoring frequencies above 80 Hz continuously over a period of weeks can be a challenge. Chang et al. have shared their design for a system that combines an implantable telemetric sensor, radio-frequency transmission, and an open-source data acquisition software to collect EEG data over a span of up to 8 weeks. Various modifications to the system  have increased the longevity of the device and reduced transmission noise to provide continuous and reliable data. Schematics of the device, transmission system, and validation results in a population of epileptic rodents are available in their publication.


Learn more from the Journal of Neuroscience Methods!


March 21, 2019

Victor Wumbor-Apin Kumbol and colleagues have developed and shared Actifield, an automated open-source actimeter for rodents, in a recent HardwareX publication.

Measuring locomotor activity can be a useful readout for understanding effects of a number of experimental manipulations related to neuroscience research. Commercially available locomotor activity recording devices can be cost-prohibitive and often lack the ability to be customized to fit a specific lab’s needs. Kumbol et al. offer an open-source alternative that utilizes infrared motion detection and an arduino to record activity in a variety of chamber set ups. A full list of build materials, links to 3D-print and laser-cut files, and assembly instructions are available in their publication.

Read more from HardwareX!


March 13, 2019

Suhasa Kodandaramaiah from the University of Minnesota, Twin Cities, has shared the following about Craniobot, a computer numerical controlled robot for cranial microsurgeries.

The palette of tools available for neuroscientists to measure and manipulate the brain during behavioral experiments has greatly expanded in the previous decade. In many cases, using these tools requires removing sections of the skull to access the brain. The procedure to remove the sub-millimeter thick mouse skull precisely without damaging the underlying brain can be technically challenging and often takes significant skill and practice. This presents a potential obstacle for neuroscience labs wishing to adopt these technologies in their research. To overcome this challenge, a team at the University of Minnesota led by Mathew Rynes and Leila Ghanbari (equal contribution) created the ‘Craniobot,’ 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 on mice. The Craniobot can be built from off-the-shelf components for a little over $1000 and the team has demonstrated its capability to perform small to large craniotomies, skull thinning procedures and for drilling pilot holes for installing bone anchor screws.

Read more about the Craniobot here. Software package for controlling the craniobot can be found on Github.


In a recent article, Jennifer Tegtmeier and colleagues have shared CAVE: an open-source tool in MATLAB for combined analysis of head-mounted calcium imaging and behavior.

Calcium imaging is spreading through the neuroscience field like melted butter on hot toast. Like other imaging techniques, the data collected with calcium imaging is large and complex. CAVE (Calcium ActiVity Explorer) aims to analyze imaging data from head-mounted microscopes simultaneously with behavioral data. Tegtmeier et al. developed this software in MATLAB with a bundle of unique algorithms to specifically analyze single-photon imaging data, which can then be correlated to behavioral data. A streamlined workflow is available for novice users, with more advanced options available for advanced users. The code is available for download from GitHub.

Read more from Frontiers in Neuroscience, or check it out directly from GitHub.

February 20, 2019

Francisco Romero Ferrero and colleagues have developed, an algorithm and software for tracking individuals in large collectives of unmarked animals, recently described in Nature Methods.

Tracking individual animals in large collective groups can give interesting insights to behavior, but has proven to be a challenge for analysis. With advances in artificial intelligence and tracking software, it has become increasingly easier to collect such information from video data. Ferrero et al. have developed an algorithm and tracking software that features two deep networks. The first tracks animal identification and the second tracks when animals touch or cross paths in front of one another. The software has been validated to track individuals with high accuracy in cohorts of up to 100 animals with diverse species from rodents to zebrafish to ants. This software is free, fully-documented and available online with additional jupyter notebooks for data analysis.

Check out their website with full documentation, the recent Nature Methods article, BioRXiv preprint, and a great video of tracking 100 zebrafish!

Open-source platform for worm behavior

February 13, 2019

In Nature Methods, Avelino Javer and colleagues developed and shared an open-source platform for analyzing and sharing worm behavioral data.

Collecting behavioral data is important and analyzing this data is just as crucial. Sharing this data is also important because it can further our understanding of behavior and increase replicability of worm behavioral studies. This is achieved by allowing many scientists to re-analyze available data, as well as develop new methods for analysis. Javer and colleagues developed an open resource in an effort to streamline the steps involved in this process — from storing and accessing video files to creating software to read and analyze the data. This platform features: an open-access repository for storing, accessing, and filtering data; an interchange format for notating single or multi-worm behavior; and file formats written in Python for feature extraction, review, and analysis. Together, these tools serve as an accessible suite for quantitative behavior analysis that can be used by experimentalists and computational scientists alike.


Read more about this platform from Nature Methods! (the preprint is also available from bioRxiv!)

Head-Mounted Camera System

February 6, 2019

Arne Meyer and colleagues recently shared their design and implementation of a head-mounted camera system for capturing detailed behavior in freely moving mice.

Video monitoring of animals can give great insight to behaviors. Most video monitoring systems to collect precise behavioral data require fixed position cameras and stationary animals, which can limit observation of natural behaviors. To address this, Meyer et al. developed a system which combines a lightweight head-mounted camera and head-movement sensors to detect behaviors in mice. The system, built using commercially available and 3D printed parts, can be used to monitor a variety of subtle behaviors including eye position, whisking, and ear movements in unrestrained animals. Furthermore, this device can be mounted in combination with neural implants for recording brain activity.

Read more here!


January 23, 2019

Hot off the press in eLife, Andrea Giovannucci and colleagues have shared their open-source software library, CaImAn, for one and two-photon Calcium Imaging data Analysis.

In vivo calcium imaging has gained popularity in recent years for its ability to record large quantities of neural activity from multiple brain areas over extended time periods. With advanced tools for recording and collecting data comes large quantities of data. With large datasets comes a need for streamlined ways to analyze it. Giovannucci and colleagues have developed and shared a toolbox for analyzing complex calcium imaging datasets. CaImAn, developed in the open-source Python language (with optional implementation in MATLAB), is designed to correct for motion, estimate spikes, detect new neurons, and assess neuronal activity and locations in a given timeframe. The software can be used on pre-recorded data or can also enabled for real-time analysis. CaImAn is available to download with examples from GitHub, and more information can be obtained through reading the aforementioned manuscript.

Check out GitHub, or the article from eLife!