Open Hardware seminars

Edmund will present why to use FPGAs when building scientific instruments, when and why to use open source FPGA tools, the history of their development, their development status, currently supported FPGA families and functions, current developments in design languages and tools, the community, freely available design blocks, and possible future developments.

Due to the unsuitability of benchtop imaging for tasks that require unrestrained movement, investigators have tried, for almost two decades, to develop miniature 2P microscopes-2P miniscopes–that can be carried on the head of freely moving animals. In this talk, I would first briefly review the development history of this technique, and then report our latest progress on developing the new generation of 2P miniscopes, MINI2P, that overcomes the limits of previous versions by both meeting requirements for fatigue-free exploratory behavior during extended recording periods and satisfying demands for further increasing the cell yield by an order of magnitude, to thousands of neurons. The performance and reliability of MINI2P are validated by recordings of spatially tuned neurons in three brain regions and in three behavioral assays. All information about MINI2P is open access, with instruction videos, code, and manuals on public repositories, and workshops will be organized to help new users getting started. MINI2P permits large-scale and high-resolution calcium imaging in freely-moving mice, and opens the door to investigating brain functions during unconstrained natural behaviors.

Controlling biological processes using light has increased the accuracy and speed with which researchers can manipulate many biological processes. Optical control allows for an unprecedented ability to dissect function and holds the potential for enabling novel genetic therapies. However, optogenetic experiments require adequate light sources with spatial, temporal, or intensity control, often a bottleneck for researchers. Here we detail how to build a low-cost and versatile LED illumination system that is easily customizable for different available optogenetic tools. This system is configurable for manual or computer control with adjustable LED intensity. We provide an illustrated step-by-step guide for building the circuit, making it computer-controlled, and constructing the LEDs. To facilitate the assembly of this device, we also discuss some basic soldering techniques and explain the circuitry used to control the LEDs. Using our open-source user interface, users can automate precise timing and pulsing of light on a personal computer (PC) or an inexpensive tablet. This automation makes the system useful for experiments that use LEDs to control genes, signaling pathways, and other cellular activities that span large time scales. For this protocol, no prior expertise in electronics is required to build all the parts needed or to use the illumination system to perform optogenetic experiments.

The Open Science movement advocates for more transparent, equitable and reliable science. It focusses on improving existing infrastructures and spans all aspects of the scientific process, from implementing systems that reward pre-registering studies and guarantee their publication, all the way to making research data citable and freely available. In this context, open source tools (and the development ethos supporting them) are becoming more and more present in academic labs, as researchers are realizing that they can improve the quality of their work, while cutting costs. In this talk an overview of OS tools for neuroscience will be given, with a focus on software and hardware, and how their use can bring scientific independence and make research evolve faster.