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Brinks Lab

Department                           Imaging Physics

Principal investigator           Daan Brinks

E-mail address                       d.brinks@tudelft.nl

Website                                   https://www.brinkslab.org/

 

Optical engineering for voltage imaging

Suitable as a BEP? Yes

Suitable as a MEP? Yes

Suitable as an Academic Research Project? Yes

Techniques:

  • Optics
  • Imaging
  • Engineering

We have several project available in the lab focused on optical engineering of (additions to) microscopy setups for particular imaging challenges, particularly focused on imaging electrical activity in networks of neurons in tissue.

Further reading (click to link to article)

A compact microscope for voltage imaging

 

Engineering voltage indicator proteins

Suitable as a BEP? Yes

Suitable as a MEP? Yes

Suitable as an Academic Research Project? Yes

Techniques:

  • AI
  • Cloning
  • Imaging

We have several projects available on the engineering of voltage indicator proteins. this can take a fully computational approach (we have in the past used LLMs for protein evolution, or structural info from alphafold) or a practical approach (ab initio engineering, evolution), or something in between. the end goal is to create protein sensors with improved properties for imaging membrane potential.

Further reading (click to link to article)

Exploring Bioelectricity with Ace2N-mNeon during Zebrafish Embryogenesis

In Vivo Plasmonic Enhancement of the Photocycle Dynamics and Fluorescence of Genetically Encoded Voltage Indicators

Expanding the family of genetically encoded voltage indicators with a candidate Heliorhodopsin exhibiting near-infrared fluorescence

 

Data analysis of voltage imaging data

Suitable as a BEP? Yes

Suitable as a MEP? Yes

Suitable as an Academic Research Project? Yes

Techniques:

  • Image analysis
  • Signal analysis
  • Python

The data we obtain come with unique analysis challenges depending on the experiment. in the project falling under this umbrella you will focus on image processing and analysis and signal processsing and analysis, typically creating analysis pipelines for generalized use. examples of this have included work on analyzing fluorescence lifetime data to assess changes in membrane potential in cell development; analysis of spike signals during learning processes of mice; analysis of in vitro spike data to assess chemical assays or disease models.

Further reading (click to link to article)

Linking the genotypes and phenotypes of cancer cells in heterogenous populations via real-time optical tagging and image analysis

Modeling and AI for neuroscience

Suitable as a BEP? Yes

Suitable as a MEP? Yes

Suitable as an Academic Research Project? Yes

Techniques:

  • Machine learning
  • Python
  • Computational biophysics

We use machine learning and modeling to gain a deeper understanding of the activity data we measure in neural networks. examples of work here include designing networks for reinforcement learning based on measured dynamics, using machine learning to extract underlying physical parameters from measured data and capturing dynamics in networks of cells in circuit or state models extract biophysical principles aligning with observed changes in behavior.

Further reading (click to link to article)

Modular Recurrence in Contextual MDPs for Universal Morphology Control

Learning Physics From Video: Unsupervised Physical Parameter Estimation for Continuous Dynamical Systems

 

(Example) projects submitted by lab in past years

(2024-2025) Voltage imaging

Supervisor: Marco Post, m.g.post@tudelft.nl

We address neuroscience questions through functional imaging. We develop tools with roots in physics, biochemistry, optics, mathematics and nanofabrication and we’re interested in how brain cells work on every level, from biophysical principles to consequences in behavior and from subcellular compartments to complete organisms.

Techniques

  • Cloning
  • Protein engineering
  • Fluorescence imaging
  • Cell culture
  • Smart microscopy
  • Machine learning

Further reading

https://www.brinkslab.org/publications.html