Conference Guide

General Information

Organizers

Program

Venues

Internet at the Conference

Presenter Information

Abstracts

Teamwork for Outreach Activity

Prepared by: I. Grulkowski

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General Information

The 2nd BE-OPTICAL School consists of a series of

interdisciplinary courses at the intermediate level presented by the

members of BE-OPTICAL network, which are experts in their fields,

as well as by the external invited lecturers. The School is open to

PhD students, postdocs and senior researchers interested in recent

developments in the following fields:

optical technologies for high-resolution imaging, metrology and

sensing;

tissue optics and biophotonics;

data analysis techniques.

The School will also include sessions on Scientific Writing and

Clinical Trials. There is no registration fee.

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Honorary Patronage

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Organizers & Partners

Organizing Committee

Chair: Ireneusz Grulkowski

Co-chair: Maciej Wojtkowski

Coordination & Operational Support:

Ewa A. Kaszewska,

Ewa Maczynska,

Anna Pawlus,

Krzysztof “Chris” Szulzycki

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Financial Support

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Program

Tuesday, May 2

08:30-09:00 Registration

09:00-09:15 Welcome & Opening

Session 1. Optical technologies for high-resolution imaging, metrology and sensing 09:15-10:45 R. J. Zawadzki, The How and the Why of in vivo cellular

resolution imaging in the retina: history and future directions (Keynote Lecture)

10:45-11:00 Coffee break

11:00-12:00 A. Giacomotti, Nano-textured materials for bio-sensing and microscopy

12:00-14:00 Lunch

Session 2. Tissue optics and biophotonics

14:00-15:30 J. Pujol, Spectroscopy and hyperspectral imaging for biomedical applications

15:30-15:45 Coffee break

15:45-17:15 M. Vilaseca, Laser therapy

17:30-19:30 Visit to the Torun Center for Astronomy in Piwnice (Night Sky Viewing; bus transfer provided)

19:30-22:30 Welcome reception

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Wednesday, May 3

09:00-09:15 Registration

Session 3. Statistics, data analysis and classification tools

09:15-10:45 U. Parlitz, Introduction to Machine Learning

10:45-11:00 Coffee break

11:00-12:00 C. Masoller, Introduction to nonlinear time series analysis tools

12:00-14:00 Lunch

Session 4. ESR presentations

14:00-15:30 S. Mojiri, Multi-plane 3D Super Resolution Optical Fluctuation Imaging (SOFI)

M. Gonzalez Pisfil, Super-resolution and time-resolved microscopy: a novel tool for dynamics measurements in live cells

V. Kappadan, Multi-modal fluorescence imaging of contracting intact hearts

R. A. Quiñonez Uribe, Imaging and Analysis Tools for Optogenetic Cardiac Electrophysiology

S. Alayew Bogale, Multiphoton laser scanning microscopy as applied to imaging cardiac myocardium

M. Hamkalo, Development of spatio-temporal coherence manipulation in removal of image distortions

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Wednesday, May 3 (cont’d)

Session 4. ESR presentations (cont’d)

15:30-15:45 Coffee break

15:45-17:15 T. Alterini, Hyperspectral imaging system for the dynamic recording of the ocular fundus

A. Rodriguez Aramendia, Ophthalmic long-range Swept-Source OCT imaging

A. Jiménez Villar, Comparison of SS-OCT systems for anterior segment imaging

D. Halpaap, Speckle Reduction in Double Pass Ocular Imaging

A. Nehuen Gortari, Improved microscopy performance through substrate nanostructuration

S. Qin, Introduction of Imaging Scanning Microscope

P. Amil, Feature detection in ocular image databases

17:15-19:00 Student Teamwork for Outreach Activity (making the promotional videos)

19:00-21:00 Conference Dinner (Sala Mieszczanska u Golebiewskich / Burghers’ Chamber, ul. Wysoka 10, Torun)

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Thursday, May 4

09:00-09:15 Registration

09:15-12:30 BE-OPTICAL Supervisory Board Meeting

Session 5. Transferable skills

09:15-10:45 Ch. Mack, Getting Published: How to write a good science paper – Part I (Invited)

10:45-11:00 Coffee break

11:00-12:30 Ch. Mack, Getting Published: How to write a good science paper – Part II (Invited)

12:30-14:30 Lunch

Session 6. Statistics, data analysis and classification tools (cont’d)

14:30-16:00 C. Otero, Introduction to biostatistics and its applications in clinical studies (Invited)

16:00-16:15 Coffee break

16:15-17:45 U. Parlitz, Nonlinear modelling and data assimilation

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Friday, May 5

09:00-09:15 Registration

Session 7. Transferable skills (cont’d)

09:15-10:25 L. Gonzalez, How to Prepare a Clinical Trial

10:25-11:00 Coffee break

11:00-12:10 C. Mas, Ethics in Clinical Studies

12:10-13:00 Closing Remarks

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Venues

Lectures

The 2nd BE-OPTICAL School will take place at the Institute of

Physics of the Nicolaus Copernicus University in Torun, Poland, on

May 2-5, 2017.

Institute of Physics

Nicolaus Copernicus University

ul. Grudziadzka 5

87-100 Torun, Poland

http://www.fizyka.umk.pl/wfaiis/

The lectures will be given in the lecture hall (auditorium) 2.10 of the

Center for Quantum Optics at the Institute of Physics (2nd floor).

Lunches

Each participant organizes the lunches on his/her own. There is

a lot of restaurants in the Old Town where you can compose your

lunch for a flat rate. Cash and credit cards accepted. We do

recommend the following restaurants in the vicinity of conference

place:

1 – Stary Toruń (Polish dumplings), ul. Most Pauliński 2-10

2 – Koi Sushi (sushi), ul. Małe Garbary 19

3 – Metropolis (pizza & pasta), ul. Podmurna 28

4 – Jan Olbracht (traditional food & microbrewery), ul. Szczytna 15

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5 – Manekin (pancakes), ul. Rynek Staromiejski 16

6 – Pasta & Basta (pizza & pasta), ul. Rynek Staromiejski 10

7 – Kartoflarnia (potato dishes), ul. Rynek Staromiejski 2

8 – Stary Młyn (Polish dumplings), ul. Łazienna 28/1

9 – Szeroka No. 9 (fine dining), ul. Szeroka 9

10 – Leniwa (Polish dumplings), ul. Ślusarska 5

11 – Czarna Oberża (home food), ul. Rabiańska 9

12 – Loft79 (pizza & burgers), ul. Dąbrowskiego 6

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Torun Center for Astronomy in Piwnice (Night Sky Viewing &

Welcome BBQ Reception) – Tue, May 2, 7:30-10:30 p.m.

The Astronomical Observatory of the Torun Center for

Astronomy of the Nicolaus Copernicus University is located in

Piwnice – the village situated ca. 14 km from Torun.

Torun Center for Astronomy

87-148 Piwnice, Poland

http://www.ca.umk.pl/en

The bus will departure at 7:30 p.m. from the Institute of Physics, and

will come back from the Observatory at 10:30 p.m.

Conference Dinner – Wed, May 3, 7:00-9:00 p.m.

The conference dinner will take place in the restaurant

Sala Mieszczanska u Golebiewskich / Burghers’ Chamber

ul. Wysoka 10

87-100 Torun, Poland

http://www.golebiewscy.catering/index.html

Warm meals and non-alcoholic beverages will be served. You need

to pay by yourself for alcoholic beverages.

BE-OPTICAL Supervisory Board Meeting – Thr, May 4, 9:15 am –

12:30 pm

Board Meeting will take place in the seminar room 2.15 of the

Center for Quantum Optics at the Institute of Physics (2nd floor).

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Maps

Astronomical Observatory

Welcome Reception

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Old Market

N. Copernicus Monument

Faculty of Physics

Conference / Lectures

Conference Dinner

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Complimentary Internet at the Conference

wireless internet

network: konferencja

login & password: provided with the badge

Other Practical Information

May 1 is the Labor Day in Poland (holiday).

May 2 is the Day of the Polish Flag.

May 3 is the Constitution Day in Poland (holiday).

Polish zloty (PLN) is the currency in Poland.

Presenter Information

Conference room has a computer workstation / laptop, projector,

screen, laser pointer, and a white board with markers.

All presenters are requested to come to lecture room with their

laptops or memory devices to confirm their presentation display

settings.

The presenters are asked to adjust timing of their presentations to

allow the audience to ask questions during / after their talks.

Presentations of ESRs will take 10 minutes + 3 minutes for

discussion.

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Abstracts

Session 1. Optical technologies for high-resolution imaging,

metrology and sensing

R. J. Zawadzki, The How and the Why of in vivo cellular resolution

imaging in the retina: history and future directions (Keynote Lecture)

Routine imaging of live cells in the human eye is one of the

great achievements of modern Optical Engineering that has been

just recently accomplished in both clinical and basic science. There

are physical limitations, beside pupil size, such as aberrations of the

human eye, limiting the resolution (image quality) of retinal images.

Novel retinal imaging instruments overcome some of these

limitations by allowing visualization of single cells within the retina of

living eye offering resolution, sensitivity and specificity not possible

just a decade ago. This is why the future applications of cellular

resolution retinal imaging have the potential to truly revolutionize

how we diagnose and monitor progression and treatment of many

eye diseases.

In this lecture, I will review the progress that is being made in

developing adaptive optics based high resolution retinal imaging

systems for human (clinical) and animal (mice) applications. I will

also present the basic operating principles of cellular resolution in-

vivo retinal imaging modalities including adaptive optics (AO) and its

combination with optical coherence tomography (OCT) and scanning

light ophthalmoscopy (SLO). The costs and benefits of live cell

imaging including examples of current and possible future

applications of these technologies will be discussed as well.

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A. Giacomotti, Nano-textured Materials for Bio-sensing and

Microscopy

Nanophotonics combines the unique assets of nanotechnology

and optics to observe, transform and manipulate nature at the

nanoscale. It offers extreme sensitivity and high spatial selectivity,

which prove to be exceptional assets for bi-sensing applications and

fluorescence microscopy. Still we are on the verge of a technological

revolution that will bring to us a multitude of biophotonic devices that

will interact with biological (nano) systems to largely improve our

knowledge and control capabilities in a near future.

In this lecture I will discuss two emblematic nano-textured

photonic materials that have been used for more than one decade

for biophotonic applications: plasmonic metallic structures and

dielectric waveguides, such as photonic crystals. I will introduce the

basic principles of these nanophotonic platforms, focusing on the

spatial and/or spectral electromagnetic confinement properties,

which are at the heart of sensing and microscopy applications.

On the plasmonic side I will review surface plasmon resonance

(SPR) as well as localized SPR bio-sensors, whereas in the photonic

approach I will focus on photonic crystal cavity sensors. We are also

going to see how such tight light confinement can be used to achieve

high spatial localization of fluorescent molecules for cell imaging.

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Session 2. Tissue optics and biophotonics

J. Pujol, Spectroscopy and Hyperspectral Imaging for Biomedical

Applications

In this course, an overview of conventional spectroscopy and

its use in the biomedical field will be given. Firstly, the fundamentals

of absorbance and fluorescence spectroscopy will be described as

well as the main tissue chromophores and fluorophores. Then, the

main parts of spectrometers will be analyzed as well as typical point-

based probe configuration (with fiber optics) used for medical

applications. The strategies to minimize the specularly reflected light

coming from the first surface of the skin will be described. Finally,

novel spectroscopic systems based on imaging sensors (multi and

hyperspectral imaging systems) will be presented. It will be shown

that they allow for a better diagnosis in some diseases as they have

improved spatial resolution. The main biomedical applications of

such systems such as in skin cancer diagnosis and ocular fundus

photography will be commented.

M. Vilaseca, Laser therapy

The course will give an overview of the physical mechanisms

involved in the light‐tissue interaction. The main effects of light on

tissue will be described: photoablation, thermal interactions,

photomechanical and photochemical effects. This knowledge will

then be used to understand how these interactions have resulted in

new photonic therapies, i.e., how lasers are used in medicine and

biology to treat several diseases. Some of the applications will be

analyzed such as refractive-LASIK and cataract surgery,

dermatology, cancer treatment etc. In every case, details of the

state of the art technology will be discussed.

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Session 3. Statistics, data analysis and classification tools

U. Parlitz, Introduction to Machine Learning

TBA

C. Masoller, Introduction to nonlinear time series analysis tools

In this talk I will review several approaches for the analysis of

observed data. First, linear methods of time-series analysis (Fourier

analysis and linear correlations) will be reviewed. Then, methods

based on the concept of state-space reconstruction, which allow

computing characteristic measures of unpredictability and

dimensionality of the underlying dynamics (the Lyapunov exponents

and fractal dimensions), will be introduced. Next, methods based on

symbolic analysis and complex network representation of time-

series will be presented. These methods can be used to classify

biomedical signals and can even give some predictability regarding

future values of the time series. I will conclude by discussing the

possibility of anticipating abrupt transitions and distinguishing

stochastic from deterministic dynamics from observed data.

References

[1] H. Kantz and T. Schreiber, Nonlinear Time Series Analysis

(Cambridge University Press, 2004).

[2] M. Zanin et al, “Permutation entropy and its main biomedical and

econophysics applications: a review”. Entropy 14 (2012), pp. 1553–

1577.

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Session 4. ESR presentations

S. Mojiri, Multi-plane 3D Super Resolution Optical Fluctuation

Imaging (SOFI)

M. Gonzalez Pisfil, Super-resolution and time-resolved

microscopy: a novel tool for dynamics measurements in live cells

V. Kappadan, Multi-modal fluorescence imaging of contracting

intact hearts

R. A. Quiñonez Uribe, Imaging and Analysis Tools for Optogenetic

Cardiac Electrophysiology

S. Alayew Bogale, Multiphoton laser scanning microscopy as

applied to imaging cardiac myocardium

M. Hamkalo, Development of spatio-temporal coherence

manipulation in removal of image distortions

T. Alterini, Hyperspectral imaging system for the dynamic

recording of the ocular fundus

A. Rodriguez Aramendia, Ophthalmic long-range Swept-Source

OCT imaging

A. Jiménez Villar, Comparison of SS-OCT systems for anterior

segment imaging

D. Halpaap, Speckle Reduction in Double Pass Ocular Imaging

A. Nehuen Gortari, Improved microscopy performance through

substrate nanostructuration

S. Qin, Introduction of Imaging Scanning Microscope

P. Amil, Feature detection in ocular image databases

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Session 5. Transferable Skills

Ch. Mack, Getting Published: How to write a good science paper

Publishing is an extremely important part of the process of

science, and often an important part of the career of scientists and

engineers. But to the early-career author (or student preparing their

first publication), the peer-reviewed journal writing and publishing

process can be intimidating, and possibly a bit mysterious. What are

journal editors and reviewers looking for? What does it take to get

your work published?

Of course, the first place to start is by doing good research on

an important topic. But you still have to write a good paper. This talk

will focus on what it takes to get published, and in particular how to

write a good science paper. I’ll share some of my secrets on writing

a good paper (OK, they’re not really secrets, but these skills are not

often taught in school). The good news is you don’t have to be a good

writer to write a good paper. But you do have to be a careful and

knowledgeable writer. With practice, you can become a good writer

as well.

Session 6. Statistics, data analysis and classification tools

C. Otero, Introduction to biostatistics and its applications in clinical

studies

This lecture will look at: 1) the basic statistical concepts, e.g.,

types of variables, central tendency, dispersion, normality,

confidence intervals and standard errors, among others; 2) the most

used statistical hypothesis tests in clinical research, both parametric

and non-parametric, e.g., Cochran’s Q, t-test, Mann-Whitney U,

Wilcoxon signed-rank, ANOVA’s, among others; 3) how to perform

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power analysis and 4) how to appropriately report statistical results.

Finally, it will be commented on some of the most useful and

currently available statistical software tools.

U. Parlitz, Nonlinear modelling and data assimilation

TBA

Session 7. Transferable Skills

L. Gonzalez, How to Prepare a Clinical Trial

1.-What is “clinical trial”?

The goal of this lecture is to bring an overview of the clinical trials

with medication/medical devices, also provide the guidelines on how

to start up the research, requirements, expectations and monitoring.

Phases

Protocol

Interventors

Monitoring

2.-What is “good clinical practice”?

ICH-International conference on harmonization

Declaration of Helsinki

Inspection/Auditing

3.-Observational studies

C. Mas, Ethics in Clinical Studies

Starting a clinical study, according to current legislation,

means to get the approval of Health Authorities and this process

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includes the study evaluation by an Ethical Committee. We will give

an overview on:

Legislation: Current regulations and directives

Ethical committee: Members and functions

Evaluation process: requirements and documents

Follow up of clinical trial: Results and finalization

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Teamwork for Outreach Activity

Teamwork for outreach is an essential part of the meeting. The

BE-OPTICAL ESRs have been divided into four groups according to

their topic:

Super-resolution imaging (S. Mojiri, A. Escobet Montalbán, M.

Gonzalez Pisfil)

Cardiac imaging (V. Kappadan, R. A. Quiñonez Uribe, S. Alayew

Bogale, M. Hamkalo)

Ophthalmic imaging (T. Alterini, A. Rodriguez Aramendia, A.

Jiménez Villar)

Image analysis (D. Halpaap, A. Nehuen Gortari, S. Qin, P. Amil)

The students contact each other by social media to coordinate

the preparations and acquire the multimedia before the conference.

Each group works together to merge the movies and finish their draft

versions at the conference. The movies will be presented at the

closing ceremony and will be available at the BE-OPTICAL web-

page.

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Contact

Dr hab. Ireneusz Grulkowski

Institute of Physics

Nicolaus Copernicus University

ul. Grudziadzka 5

87-100 Torun, Poland

Tel.: +48/56/6112467

Fax: +48/56/6112411

e-mail: igrulkowski (at) fizyka.umk.pl