Doctorate in Applied and Engineering Physics  

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Thesis Proposal for the

Doctorate Program in Applied and Engineering Physics (DAEPHYS)

Starting in the Academic Year 2016/2017

Proposal 034

Title:Lensless endoscopes for fluorescence microscopy based diagnosis
Objectives (recommended length: 2000-3000 char):
Fluorescence microscopy targets molecules by taking advantage of the exogenous emission of these molecules or by using exogenous fluorescent probes. Whatever is the molecular target, it will emit fluorescence when excited, providing its spatial location with a resolution limited only by the wavelength of the probing light and by the instrument optics. Moreover, there is a spectral shift between the probing light and the molecular target response, yielding an excellent sensitivity.
In the recent years, fluorescence endoscopy has gained an increasing clinical relevance, particularly for early detection of pre-cancerous and cancerous tissues. Clinical applications can be found in several medical specialties, particularly in Gastroenterology but also in Obstetrics and Gynecology, Otolaryngology and Urology. The need for in vivo and in situ histologic tissue visualization sub-cellular resolution prompted the development of endomicroscopy based on the confocal principle for optical sectioning.
The main objective of this research project is the development of lensless endoscopes capable of providing depth-resolved images with sub-cellular resolution, using as contrast fluorescence intensity and lifetime. These endoscopes are intended for in vivo studies for clinical diagnosis, based mainly on endogenous fluorescence.
The proposed development will test innovative solutions with the objective of obtaining low cost, integrated devices, with a small footprint in the clinical setup. The term lensless denotes the absence of distal optics or mechanical components and implies research on novel methods for image scanning and formation. Lensless approaches have been suggested by exploring the simultaneous transmission of the whole image within a single-core multimode waveguide, using the higher order modes to convey the image information, followed by reconstruction behind the fiber. A different approach is based on optical fiber bundles with simultaneous illumination of all cores at the proximal end and phase control of the light emerging at the distal end for producing, by interference, a focused scanning beam in a similar way to phased-array radar. Solutions based on the control of randomized light fields or phase control of distal emerging beams for producing a focused scanning beam are among the possibilities that will be investigated.
Another objective of the project is the use of Fiber Bragg Gratings (FBGs) for spectroscopic resolution of excitation and emission light without external dedicated components (spectrometers or spectral filters). It also intended to investigate the use of optical delay lines for time-gating in fluorescence lifetime imaging microscopy (FLIM) studies. These developments contribute to the goal of simple devices with small footprint, an important requirement for low cost, easy manufacturing and use in clinical environment.
Framework (recommended length: 500-2000 char):
Fluorescence endoscopy has established itself as a sensitive technique for early diagnosis of pre-cancerous and cancerous lesions in several medical specialties. Fluorescence microscopy techniques provide molecular information, particularly lifetime-resolved techniques which are sensitive to the local environment of the fluorophore. However, the dissemination of fluorescence endoscopy is hampered by the cost and complexity of the required instrumentation.
Endoscopic FLIM is difficult as it requires collecting many photons, leading to long acquisition times. This may be overcome by wide-field time-gated schemes with structured illumination for optical sectioning or by confocal scanning with fast time-correlated single photon counting (TCSPC). Adjustable optical delay lines can simplify the instrumentation by providing synchronization between the excitation pulse and the camera gating on time-gated setups.
Spectral resolution can be implemented through FBG technology, which had been used as fiber sensors or, in optical communications, in spectral filters. They are inscribed inside the optical fiber core and can present a FWHM (Full Width at Half Maximum) lower than 0.01 nm, with easiness of choosing the central wavelength. This technology can also be used for filtering broadband light sources into a very narrow emission line.

IBILI has a large know-how on FLIM that includes one photon and multiphoton excitation techniques and both time-gated and TCSPC instrumentation. It has also expertise in structured illumination microscopy and confocal microscopy as well as large experience on optical coherence tomography that can be useful for phase control and interferometric techniques.

The Aveiro University/I3N has a long time experience working with FBG. Its facilities are very well equipped, including a femtosecond laser and a FBG inscription system using a UV laser, for the proper implementation of this proposal.
Tasks (recommended length: 1000-3000 char):
T1 – Literature review;

T2 – Study, simulation and implementation of lensless methods for image formation. The study will focus on image transmission through single multimode fiber via its multiple spatial modes and will require the development of methods to cancel the distortion induced by mode dispersion. This task comprises the development of algorithms for image reconstruction. Alternative methods for lensless endoscopy may be evaluated here. A simple broadband LED source for steady-state endomicroscopy will be developed here. This development provides a low-cost simple system with potential for technology transfer during the project execution (to be conducted at Coimbra University/IBILI and at Aveiro University/I3N);

T3 – Optical fiber Bragg grating manufacturing and process optimization, through femtosecond or UV laser technologies, specially designed for spectral analyses and high spectroscopic resolution of excitation and emission light (to be conducted at the Aveiro University/I3N);

T4 – Spectral analyses in fluorescence microscopy using FBGs. Wavelength resolution studies of the probing light and spectral shift between the probing light and the molecular target response, using FBGs (to be conducted at the Aveiro University/I3N);

T5 – Methods for radiometric calibration in endoscopic fluorescence systems. This task aims to evaluate the use of proprietary methods for radiometric calibration, licensed to Perceive3D, on the quantification and calibration of fluorescence intensity measurements obtained through endoscopic systems. (Perceive3D)

T6 –System integration and performance analysis. The developed instrumentation and algorithms will be integrated and evaluated. System testing will use existing facilities at IBILI (Fluorescence lifetime imaging systems – time-gated and TCSPC; animal experimentation facilities);

T7 – Papers and thesis writing and preparation for public defense.
Research centre/lab or R&D unit hosting the thesis project:
IBILI - Instituto de Imagem Biomédica e Ciências da Vida
University to which the thesis project will be presented:
UC - Universidade de Coimbra
DAEPHYS Scientific Domain in which the project fits:
Optical technology
Relation of the project to the Scientific Domains of DAEPHYS:
This proposal main objective is the development of lensless endoscopes capable of providing depth-resolved images with sub-cellular resolution. Most of the work is related with optical technologies (fluorescence, emission, transmission, optical fiber, Bragg gratings) and a great engineering component is foreseen. Therefore, the research topic is inherently related to, and perfectly suitable for the “Optical Technology” scientific domain of the Doctorate in Applied and Engineering Physics.
Candidate profile:
We are looking for a dedicated, hardworking candidate, with know-how in the areas of optics, optoelectronic instrumentation, programming and data analysis
Does this proposal involve more than one University?:
Synergies between the two Universities participating in the proposal:
DAEPHYS strongly encourages the presentation of thesis projects in co-supervision by researchers from two of the universities participating in the Program. In this field, explain the benefits resulting from the proposed co-supervision and the involvement of elements from the two universities, e.g. building critical mass teams, profiting from existing infrastructures or advanced equipments, profiting from expert technical know-how, etc. If the proposal involves only one University, write n/a.
(recommended length: 500-1000 char)
: The proposal relies on the synergy between the expertise and facilities of the Universities of Coimbra (UC) and Aveiro (UA), combining the know-how on fluorescence microscopy from UC with the expertise on fiber optics sensors and systems from UA. From the point of view of the involved research units, it is a collaborative effort with great potential to extend past the proposed project since the development of fiber-based spectroscopy diagnostics and therapeutics is undergoing a large growth in the biomedical sciences. Joining the current know-how of the two Universities allows them to play a significant role in the developing field of endomicroscopy, something that would be difficult to attain when considering each University in an isolated manner.
Does this proposal involve a company?:
Proposals involving a company:
DAEPHYS strongly encourages the presentation of thesis projects involving a company, preferably a high-tech company. These proposals have to: 1) be centered on a technological problem in which the partner company has been (or plan / would like to be) involved; 2) have a co-supervisor on the enterprise; 3) include part of the project to be carried out in the company.
(recommended length: 500-1000 char)
: Fluorescence based diagnosis require quantitative results for measuring analytes concentration, performing longitudinal assessments of disease evolution and therapy efficacy or in multicenter trials.
Perceive3D is a company specialized in computer vision technology applied to clinical endoscopy. It owns proprietary calibration technology that may be applied to fluorescence imaging. This calibration technology is currently applied for image enhancement and computer-aided surgery using conventional endoscopic cameras. The company has obvious, strong incentives to explore the application of its Intelectual Property in new, emerging domains such as fluorescence endoscopy. The involvement of Perceive3D allows the assessment of an innovative technology with the potential of providing quantitative fluorescence measurements in a clinical endoscopy environment. If successful, this will be a highly valuable scientific contribution and a very relevant feature for the economic value of the project



Name:António Miguel Lino Santos Morgado
Institution:IBILI - Instituto de Imagem Biomédica e Ciências da Vida / Dep. Física - Univ. de Coimbra
link to CV or indication of ORCID ID:



Name:Nélia Jordão Alberto
Institution:Instituto de Telecomunicações (IT- Aveiro) / Universidade de Aveiro
link to CV or indication of ORCID ID:;



Name:Rui Melo
Institution:Perceive 3D, SA
link to CV or indication of ORCID ID:


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