Research and Thesis Projects

This project involves the precise manufacturing of microelectrode arrays designed to interact with neural tissues at a microscale level. Different microfabrication techniques will be utilized to engineer highly sensitive electrodes with dimensions below 10 um.

We seek to explore novel methods and materials to enhance the functionality and biocompatibility of these neural interfaces. Students engaged in this project will delve into the process of designing, fabricating, and characterizing microelectrodes. Additionally, the development of specialized techniques for neural stimulation and imaging using these interfaces can be integrated into the scope of the project, aligning with the interests and skills of the student.

The research offers opportunities for Master's theses or semester projects tailored to the individual's background and expertise. We welcome enthusiastic students from various disciplines, including nanotechnology, mechanical engineering, biomedical engineering, materials science, electrical engineering and related fields. Prior experience or familiarity with cleanroom protocols and semiconductor processing techniques is considered advantageous for this project, but it is not a mandatory requirement.

The minimum duration of the project is 6 months. The cleanroom is located in Basel.

Dr. Fernando Cardes | fernando.cardes@bsse.ethz.ch

Neural interfaces aim to create connections between neurons and computers, facilitating advanced electrophysiology studies and paving the way for restoring lost functions in the nervous system. CMOS technology enables low-noise recording from thousands of electrodes in parallel, either in vitro or in vivo.

The central functionality of most neural interfaces is action potential detection, which necessitates low-noise amplifiers optimized for power and area efficiency. In this project, students will be involved in various stages of the design process, including system design, amplifier topology selection, noise/power/area optimization, layout, and post-layout simulations. Long projects may also encompass the tape-out and testing of chips, providing a comprehensive experience in neural interface development.

The position is located in Basel and is available for master's thesis and semester projects throughout the year. Part-time remote work arrangements can be discussed.

Dr. Fernando Cardes (Fernando.cardes@bsse.ethz.ch)

During the last decade, a compelling body of evidence on the capacity of pluripotent stem cells (PSCs) to self-organize into 3D tissue structures has been brought up. These so-called organoids have been derived from both embryonic and induced pluripotent stem cells (iPSC), and used to shed light into the complex mechanisms of multicellular self-organization across a wide range of tissue types. Protocols for brain organoids from mammals, including human PSCs, have been successfully established, and it has been demonstrated that brain organoids can recapitulate some molecular and cellular features of in vivo corticogenesis with remarkable similarity in vitro.

Although the brain organoid field has made impressive progress during the last couple of years, there are some important limitations that currently hamper their direct translational application and interpretability. In particular, key questions regarding the functionality of the evolving neuronal circuitry have remained open. In this project, we will record from Dup15q/control brain organoids using high-density microelectrode arrays (HD-MEAs) and examine the mechanisms underlying their ongoing electrical activity in more detail.

The candidate should have a background in neuroscience, biology, physics or a related scientific field. Moreover, she/he should be willing to learn new experimental techniques as well as run analysis and to work in a vibrant inter-disciplinary environment. Some knowledge and experience in MATLAB, Python or a comparable programming language is a plus. The minimum duration of the project is 6 months

Specifically, we aim to: compare organoids obtained from healthy control and patient lines, probe organoid electrophysiology at the single-cell and network level, track the development of neuronal connectivity and dynamics, as well as stimulate organoids electrically and/or pharmacologically.

What you will learn: how to induce, culture and maintain organoids, how to slice organoids on a vibratome, how to plate organoids and perform HD-MEA recordings, how to analyze the data using MATLAB, Python & R.

Applicants should submit a brief letter of motivation (1/2 page) and an up-to-date CV to Dr. Manuel Schröter (manuel.schroeter@bsse.ethz.ch) or Aayush Marishi (aayush.marishi@bsse.ethz.ch). Please do not hesitate to get in contact, if you have any queries.

CMOS microelectrode arrays allow studying the electrical activity of neurons. In-vitro neural networks can be cultured on top of thousands of very small electrodes (<10um), which can detect action potentials from hundreds of neurons simultaneously.

The student will develop an FPGA-based platform to expand the capabilities of our CMOS microelectrode arrays, allowing real-time spike detection and massive stimulation of neurons. Since most of the hardware required for the platform is already available, the student will focus on developing different algorithms in VHDL. Minor wet-lab tasks with neurons would be ideally included in the project, in order to test the developed algorithms. Depending on the experience and interests of the student, the development of other algorithms in C++/Python can be included as part of the project.

The position is located in Basel and is available for master's thesis and semester projects throughout the year. Part-time remote work arrangements can be discussed.

Dr. Fernando Cardes | fernando.cardes@bsse.ethz.ch

In vitro studies using high-density CMOS microelectrode arrays (MEAs) enable groundbreaking insights into the functioning of neural networks outside the living body. These advanced tools provide unparalleled spatial and temporal resolution, allowing researchers to:

• Study Neural Dynamics: Precisely observe neuronal behavior, connectivity, and activity in controlled environments.
• Advance Drug Discovery: Test drug efficacy and safety in vitro before progressing to in vivo studies.
• Understand Neurological Disorders: Explore the mechanisms underlying conditions such as epilepsy, neurodegeneration, and psychiatric disorders.

High-density CMOS MEAs play a vital role in capturing complex neural signals with high fidelity. Advanced software solutions are essential for enabling key functionalities, such as allowing experimenters to select specific areas of neural tissue for study, or visualizing neuronal signals in real time.

Key Responsibilities

• Develop, optimize, and maintain software for in vitro neural studies using CMOS MEAs.
• Implement algorithms for real-time neural data acquisition, processing, and visualization.
• Enhance usability and functionality of software for researchers conducting experiments.
• Collaborate with neuroscientists and engineers to align software with research needs.
• Create clear, user-friendly documentation for software tools and workflows.

Requirements

• Proficiency in Python; C++ and conda knowledge is a plus.
• Strong documentation skills for clear, user-friendly guides.
• Effective communication and teamwork for interdisciplinary collaboration.

Location & Application

This internship is for a 6-month duration, with flexible options for remote or on-site work (in Basel, Switzerland) based on project requirements and candidate preferences. Applicants should submit a CV highlighting relevant experience in software development, including any portfolio or repository links (e.g., GitHub) if available. Additionally, please include information about availability, specifying when you would be ready to start. While the position is open immediately, the actual start date will depend on administrative processes. Incomplete applications will not be considered.

This project is also available as Master thesis or semester project.

Dr. Fernando Cardes

fernando.cardes@bsse.ethz.ch

CMOS microelectrode arrays allow studying the electrical activity of neurons. In-vitro neural networks can be cultured on top of thousands of very small electrodes (<10um), which can detect action potentials from hundreds of neurons simultaneously.

We are interested in analyzing the evolution of neural activity over several weeks, combining electrical recordings with electrical stimulation to evoke certain firing patterns. In this context, we can offer different Master/Bachelor theses or semester project tailored to the experience and interests of the student.

Students interested in working with neurons in the lab are encouraged to contact me to discuss potential projects. Since the project can be approached from different angles, students from very diverse background are welcome, including: biology, neuroscience, biomedical engineering, electrical engineering (specially with experience in FPGA programming), computer science...

The position is located in Basel and is available for master's thesis and semester projects throughout the year.

Dr. Fernando Cardes | fernando.cardes@bsse.ethz.ch

Neural interfaces are aimed at creating links between neurons and computers, enabling advanced electrophysiology studies and opening paths to restoring lost functions in the nervous system. CMOS technology allows for low-noise recording from thousands of electrodes in parallel, either in-vitro or in-vivo.

We are developing CMOS neural interfaces integrating different functionalities, including the detection of action potentials, stimulation of neurons, or impedance imaging. In this context, we can offer Master theses and semester projects tailored to the experience and interests of the student. These project may be, for example:

• Design of the analog front-end for a CMOS neural interface in 180nm. This may include the design of low-noise amplifiers, filters, analog to digital converters, sigma-delta modulators, etc. Potential tasks would be: system design, circuit design and simulation, noise/power/area optimization, layout, parasitics extraction, post-layout simulations.

• Design of a LVDS buffer for high-speed (>1Gbps) communication between the neural interface and the PC. Potential tasks would be: circuit design and simulation, speed/power optimization, LVDS receiver selection, PCB design.

• Design of the on-chip digital signal processing and control logic. Potential tasks would be: VHDL/Verilog coding, synthesis, place and route, area/power optimization, simulation.

Students interested in PCB design, programming or signal processing are also encouraged to contact me for other possible projects. The position is located in Basel and is available for master's thesis and semester projects throughout the year. Part-time remote work arrangements can be discussed.

Dr. Fernando Cardes (Fernando.cardes@bsse.ethz.ch)

Neural interfaces are aimed at creating links between neurons and computers, enabling advanced electrophysiology studies and opening paths to restoring lost functions in the nervous system. CMOS technology allows for low-noise recording from thousands of electrodes in parallel, either in-vitro or in-vivo.

We are developing CMOS-based neural interfaces integrating different functionalities, including the detection of action potentials, stimulation of neurons, and impedance imaging. This instruments require real-time communication with a host computer, which is achieved combining FPGAs and System on a Chip.

The backbone of the system is already implemented and tested, but there are multiple functionalities that need to be implemented to fully exploit the capabilities of our CMOS neural interfaces. In this Master thesis or semester project, the student will learn about CMOS technology and embedded systems, understand the existing solution, and develop different software tools to enable new electrophysiological studies.

This project requires some previous experience with Python and C++. Basic knowledge of VHDL is advantageous, but not required. The position is located in Basel and is available for master's thesis and semester projects throughout the year. Part-time remote work arrangements can be discussed.

Dr. Fernando Cardes (Fernando.cardes@bsse.ethz.ch)