Job Posting

PhD: Multi-modal minimally invasive holographic endoscope for deep brain imaging

Expiration Date: 30/04/2021 18:00 - Europe/Brussels

The methods of holographic endoscopy have recently emerged as a powerful platform to introduce sub-cellular resolution microscopy deep inside tissues of living organisms, including brain. Our laboratory of Complex Photonics (lead by Prof. Čižmár, has been developing cutting edge multi-mode fibre based endoscopes and applying them in brain imaging in animal models in vivo. These minimally-invasive endoscopes can reach deep subcortical locations in the brain which are not accessible by other optical methods of similar resolution.

This PhD work will focus on expanding the capabilities of the system with two new modalities: optical manipulation of cells using optogenetics and extracellular electrophysiological recordings. Optogenetics is a unique tool that enables manipulation of cellular activity with light. Electrophysilogy has been a golden standard method of neuroscience for the past fifty years which allows recordings of local field potentials (LFP) and multi-unit activity (MUA) of neurons. Uniquely, these modalities will be implemented within the same thin endoscopic probe which serves for imaging. Implementation of electrophysiology will be carried out in collaboration with Prof. Massimo de Vittorio and Dr. Ferruccio Pisanello (Instituto Italiano de Technologia).

The candidate will develop/modify optical setups and the software for hardware control and data acquisition and processing (Lab View, Matlab, C++). Knowledge and experience in programing or optical set-up building is required. Experience with microscopy, fluorescence microscopy or electrophysiology is desirable.

The work will be carried out at the Institute of Scientific Instruments of the Academy of Sciences of the Czech Republic with the possibility of full-time employment. The PhD student will be a part of a European Commission project “DEEPER: Deep brain photonic tools for cell-type specific targeting of neural diseases" (, which is funded within the European Union’s Horizon 2020 research and innovation actions scheme as is just starting at this institute. This Consortium clusters world-leading experts in molecular photonic tools, optical technology, pre-clinical, clinical brain research and innovative start-ups in an endeavour of providing new tools to tackle the mechanisms underlying the pathogenesis of neurological disease.

In case of interest, please contact Hana Uhlirova at This email address is being protected from spambots. You need JavaScript enabled to view it..

Supervisor: Dr. Hana Uhlířová

Discipline keywords: Applied Physics, Fiber optics, Endoscopy, Optical set-ups, In vivo imaging, Fluorescence, Optogenetics, Electrophysiology, Local field potentials, LFP, Multi-unit activity, MUA, MATLAB, Lab View, C++

Postdoctoral positions Advanced photonic neural Interfaces for deep brain regions

Application Deadline: 23 March 2021

The Center for Biomolecular Nanotechnologies at Istituto Italiano di Tecnologia - IIT in Arnesano, Lecce, Italy, is seeking for 3 (three) Postdocs interested in applying and developing new optical and optoelectronic devices for interfacing with the brain.

The successful candidates will join a thriving neuroscience and technology mix at the Center for Biomolecular Nanotechnologies of IIT, in a young and interdisciplinary research team composed by physicists, material scientists, engineers and neuroscientists. Our overall aim is to develop a new generation of neural interfaces based on novel photonic methods and conceptually new optoelectronic interactions with neural cells. Activities include basic research, market-oriented technology development and translational research of medical devices. The selected personnel will be expected to focus on the following challenging activities.

  • Three positions will be in the framework of the European Project DEEPER, GA 101016787, aiming at developing a set of optical and optoelectronic methods to interface and study  brain circuitry in deep brain regions. The project involves a large European Consortium including 10 academic and scientific institutes from 8 European Countries (IT,CH, UK, GE, CZ, FR, IL, SP) and two Start-up companies located in Italy and Germany. The focus of the selected candidates will be on
  • Combine tapered optical fibers with micro-light emitting diodes for micro endoscopy with tapered optical fibers (Position related to the European Project DEEPER, GA 101016787,
  • Realize electrodes for extracellular recording of neural activity on multifunctional endoscopes (Position related to the European Project DEEPER, GA 101016787,
  • Realization of minimally invasive endoscopes by coupling tapered fibers to multiphoton microscopes and/or using of digital holography (Position is related to the European Project DEEPER, GA 101016787,

DEEPER is a research project funded from the European Union’s Horizon 2020 research and innovation actions (RIA) scheme under grant agreement no. 101016787.