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June 25, 2020

This week we want to shed some light on a project from Robel Dagnew and colleagues from UCLA called CerebraLux, a wireless system for optogenetic stimulation.

Optogenetic methods have been a crucial tool for understanding the role that certain neural cell populations have in modulating or maintaining a variety of behaviors. This tool requires a light source to be passed through a fiber optic probe, and in many experimental setups this is achieved through a long fiber optic cable to attach the light source to the probe. This long cable can impose limitations on experiments where animals are behaving freely around behavior chambers or mazes. One obvious solution is to deliver light via a wireless controller communicating with a headmounted light source, but existing systems can be cost-prohibitive or to build in a labĀ  requires access to specialized manufacturing equipment. To address the need for a a low-cost wireless optogenetic probe, Dagnew and colleagues developed CerebraLux which is built using off-the-shelf and accessible custom parts. This device consists of two major components: the optic component which features a milled baseplate capable of holding and connecting an optic fiber and LED (a part of the electronic portion); and the electronic component which features a custom-printed circuit board (PCB), lithium battery, IR receiver, LED, and magnets to align and connect the two components of the device. The device is controlled via a custom GUI (built with the TkInter Python 2.7 library) which sends pulses to the device via an Arduino Uno. More details about the build of these components and the process for communicating with the device via the GUI are available in Dagnew et. al. The CerebraLux design and operations manual, which includes access to the 3D design files for the milled parts, the print design for the PCB, and code for communicating with the device, is available in the appendix of the paper, while the code for the GUI is available from the Walwyn Lab website. Be sure to check out the paper for information about how they validated the device in vivo. The cost of all the component parts (as of 2017) comes in just under $200, providing to be a cost-effective solution for labs seeking a wireless optogenetic probe.

Read more about CerebraLux here!

Dagnew, R., Lin, Y., Agatep, J., Cheng, M., Jann, A., Quach, V., . . . Walwyn, W. (2017). CerebraLux: A low-cost, open-source, wireless probe for optogenetic stimulation. Neurophotonics, 4(04), 1. doi:10.1117/1.nph.4.4.045001


July 12, 2019

Sebastien Delcasso from the Graybiel lab at MIT published a method for developing a brain implant called “HOPE” for combining with optogenetics, pharmacology, and electrophysiology:

HOPE (hybrid-drive combining optogenetics, pharmacology, and electrophysiology) is a method that simplifies the construction of a drivable and multi-task recording implant. HOPE is a new type of implant that can support up to 16 tetrodes, and allows for recordings of two different brain areas in a mouse at the same time, along with simultaneous optogenetic or pharmacological manipulation. The HOPE implants are open-source and can be recreated in CAD software and subsequently 3D printed, drastically lowering the cost of an electrophysiological implant. Additionally, instead of waiting months for a custom-made implant, these can be printed within a few hours.

The manuscript provides detailed instructions on constructing the implant, and allows for users to individually modify it for their own needs (and can be modified to be used in rats or non-human primates). Additionally, HOPE is meant to be used in experiments with paired electrophysiological experiments with either optogenetic or pharmacological manipulations, which will inevitably open the door to many more experiments. The implant is intended for microdrive recordings, and the actual implant is only made up of six 3D printed parts, an electrode interface board (EIB), and five screws.

The authors validate the implant by first successfully recording striatal neurons, using transgenic PV-Cre mice to optogenetically inhibit parvalbumin interneurons, and then using muscimol infused into the striatum in a head-fixed mouse preparation. HOPE is a novel open-source neural implant that can be paired with multiple methods (recordings, optogenetics, and pharmacology) to help in manipulating and subsequently recording brain activity.



More details of their implant can be found on their project site and on the project GitHub.

Delcasso, S., Denagamage, S., Britton, Z., & Graybiel, A. M. (2018). HOPE: Hybrid-Drive Combining Optogenetics, Pharmacology and Electrophysiology. Frontiers in neural circuits, 12, 41.



June 27, 2019

Carlos Ribeiro’s lab at Champalimaud recently published their new project called optoPAD in eLife:

Both the analysis of behavior and of neural activity need to be time-precise in order to make any correlation or comparison to each other. The analysis of behavior can be done through many methods (as seen by many featured projects on this site!). The Ribeiro lab has previously published their work on flyPAD (Itskov et al., 2014), which is a system for automated analysis of feeding behavior in Drosophila with high temporal precision. However, in attempts to manipulate specific feeding behaviors, the group wanted to go one step further to manipulate neural activity during feeding, and needed a method to do so that would be precise enough to compare with behavior.

In their new manuscript, Moreira et al. describe the design and implementation of a high-throughput system of closed-loop optogenetic manipulation of neurons in Drosophila during feeding behavior. Named optoPAD, the system allows for specific perturbation of specific groups of neurons. They use optoPAD as a method to induce appetitive and aversive effects on feeding through activating or inhibiting gustatory neurons in a closed-loop manner. OptoPAD is a combination of the previous flyPAD system with an additional method for stimulating LEDs for optogenetic perturbation. They also used their system combined with Bonsai, a current open-source framework for behavioral analysis.

The system first uses flyPAD to measure the interaction of the fly with the food given in an experiment. Then, Bonsai detects when the fly interacts with a food electrode, then sending a signal to a microcontroller which will turn on an LED for optogenetic perturbation of neurons in the fly. The authors additionally highlight the flexibility and expandability of the optoPAD system. They detail how flyPAD, once published and then implemented in an optogenetics framework by their group, had been successfully adapted by another group, which is a great example of the benefit of open-source sharing of projects.


Details on the hardware and software can be found at the Ribeiro lab Github. More details on flyPAD, the original project, can be found on their github as well.

Information on FlyPAD can also be found on the FlyPAD website and in the FlyPAD paper .

Moreira, J. M., Itskov, P. M., Goldschmidt, D., Steck, K., Walker, S. J., & Ribeiro, C. (2019). optoPAD: a closed-loop optogenetics system to study the circuit basis of feeding behaviors. eLife, doi: 10.7554/eLife.43924