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Workshop Image Analysis and Data Processing (not only) in Super- Resolution Microscopy

For the fourth year, the Viničná Microscopy Core Facility, a cutting-edge facility of the UK Physics Department, is hosting a unique workshop on Image Analysis and Data Processing (not only) in Super-Resolution Microscopy, bringing together top scientists and speakers to impart their knowledge to the participants. This year, the workshop will take place from 21 to 25 August. Lectures will be in a hybrid format. All information, registration and an interesting talk can be found below.
When Aug 21, 2023 10:00 AM to
Aug 25, 2023 05:00 PM
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Image analysis and data processing in superresolution microscopy 2023

WHEN: Aug 21 - Aug 25, 2023
WHERE: KONFMI Microscopy Center, Viničná 7, Praha 2, study room P09, B311

Lectures will be in a hybrid format (in-person and online), with hands-on sessions in person only (max. 15 participants).


Workshop participants can look forward to the following guests, software programs and activities:

  • Dr. Anna Klemm (University of Uppsala)

  • Prof. Rainer Heintzmann (IPHT, Jena) 

  • Dr Zdeněk Švindrych (Dartmouth College)

  • Dr. Marcelo Leomil Zoccoler (TU Dresden)

  • r.Nikita Vladimirov (UZH Zürich)

  • ThunderSTORM

  • Ilastik

  • StarDistNoise2Void

  • Napari

  • Arivis Vision4Introduction to 3D printing (Maker Institute) and the use of 3D printing to build the UC2 microscope (Prof. Rainer Heintzmann)Demonstration of the Airyscan microscope (Zeiss)

​Complete Program here

The Viničná Microscopy Core Facility is a state-of-the-art facility of the Faculty of Science of Charles University. For the fourth year it has been organizing a unique workshop Image Analysis and Data Processing (not only) in Super-Resolution Microscopy, where the best scientists and lecturers come together to share their knowledge with the participants. The word workshop is quite appropriate for this event, as there is a really large space dedicated to the practice and the number of participants selected for the face-to-face form of the workshop will be approximately the same as the number of speakers.

The organisers' intention is to introduce advanced image analysis to complete beginners and to enthuse them and teach them as many practical skills as possible during the five days of the workshop. So definitely don't expect a classical lecture format, but rather practical exercises and intensive discussions and interactions between participants and invited speakers.

Thanks to the contacts of the organizers, Zuzana Burdíková and Martin Schätz, the event will be attended by top scientists in the field. In addition to the basics of advanced image analysis and working with individual programs, this year's workshop will also focus on the use of artificial intelligence and neural networks. The course content thus reflects the rapid development of the field of image analysis and also introduces the latest approaches and methods.

Wondering what you can expect from the workshop and how it will run? Read the interview with Mgr. Zuzana Burdikova, Ph.D., from the Laboratory of Confocal and Fluorescence Microscopy and Zdeněk Švindrych, Ph.D., from the Geisel School of Medicine at Dartmouth:

The workshop is five days long and the programme is quite intensive. What speakers can we find in the programme and what has changed compared to previous years?

ZB: There are quite a lot of speakers. We have invited top scientists from different parts of Europe, who are also lecturers at EMBO courses (an organisation of excellent scientists focusing on natural sciences - ed.). We also give the chance to different companies to present their new products.

ZŠ: Zuzka is good at getting grants and other funds to pay for the speakers' travel and stay. This year it is mostly Mobility, Strategic Partnerships and Internationalization.

ZB: Every year we try to change the workshop program to reflect new developments in the field of image analysis, which is evolving very quickly. We select speakers at international conferences and an absolutely crucial criterion for us is how well they present. Our main concern is the satisfaction of the workshop participants and creating a comfortable home environment where no one is stressed even if they are not good at something. In addition to the speakers, we also have assistants who attend to the participants.

What news from the industry await participants this year?

ZŠ: Some things are repeated every year, but a lot of things are new this year. The most exciting developments right now are in artificial intelligence and neural networks. Software packages are being developed that make it relatively easy to apply these new techniques to image analysis.

ZB: Anna Klemm will give an interesting talk on TissUUmap, this is a web-based software for high-performance computing and image-based profiling in the cloud. It enables interactive visualization and real-time statistical analysis of large microscopic image datasets. They will present an AI-based approach that their team is currently developing at Uppsala University. Our team is also at a high level. Martin Schätz will give a talk on the open source software Ilastik, Jakub Soukup will give a talk on the open source software StarDist and Noise2Void, which are neural network based programs, e.g. they remove noise from images very efficiently, detect cell nuclei.

How significant is the penetration of artificial intelligence and neural networks in your field?

ZŠ: People were very resistant to it in the beginning because it's such a double-edged weapon. If you train a neural network to recognize a chicken and a rabbit, it will see chickens and rabbits everywhere, but it won't see a cell there anymore. So it always depends on how you train the neural network. That's why people still don't want to believe it completely. But for some things, like noise removal, it's great.

There is a maximum of twenty places reserved for attendance and the aim of the workshop is to be as interactive as possible and to work with the participants. What will the workshop programme look like?

ZB: We don't want to do a workshop where one speaker stands and says something, our goal is to interact with the participants as much as possible. The whole workshop is structured in such a way that anyone who is interested and wants to learn something is very welcome. The workshop program is really packed. On the opening day we will focus on giving all participants a chance to understand the basics of image analysis. We will start with an introductory lecture into superresolution microscopy, go through the available methodologies and then follow with an introductory lecture into image analysis. We want to get everyone in the same boat in the introduction so that everyone understands each other.

ZS: Then we will help the participants install the software to make sure that everything is running as it should and we are not stuck due to some technical difficulties. The words Fiji and ImageJ appear a lot in the workshop program, it is free software for working with scientific images. All microscopists work with this software, so we also want to give it a thorough treatment.

ZB: Then we will introduce our microscopy lab to the participants. We want them to see our instruments and possibly collaborate with us in the future.

ZB: During the following days we have specialised lectures and workshops. For example, we will introduce the ThunderSTORM plugin for Fiji. This part will be led by Zdenek Svindrych as one of the authors of this software.

ZŠ: This is a quite popular software package for superresolution microscopy, which is used by many people. We developed it in the Czech Republic with Guy Hagen at medical school about 12 years ago. 

ZB: It's a great pity that this rather well-known group under Professor Raschka at the first medical school broke up. We want to reintroduce this software at Charles University and build on the fact that the software was created here. Nowadays, many people are into Lightsheet microscopy because in it you generate a huge amount of data that needs to be processed somehow. So we invited Dr Nikita Vladimirov from Zurich and representatives from Arivis Vision4D software. This software is very intuitive and is therefore excellent for students who are not very familiar with image analysis.

ZB: We are preparing another workshop directly at Arivis and ImageJ, which will run twice a year starting next year. This workshop will be funded by the National Recovery Plan (NRP) and will be open to non-university participants.

You also allow online participation in the workshop. How will the online workshop format work?

ZŠ: Online participants will have access to some software so they can try a lot of things out for themselves. Unfortunately, we can't give them individual attention, because for the workshop to be of the quality we want, we only have the capacity to go through one computer lab, and 20 people is about what we can handle.  For some of the software, unfortunately we are only able to provide 20 licenses for those who will be attending on site. So those more expensive software will not be available for online participants to try out themselves.

ZB: We do have one person who will be online throughout the workshop to answer questions, but we can't walk all of these participants through the exercise and engage them to the same extent as the on-site participants.

Who are you primarily organizing the workshop for? Are you expecting participants primarily from Charles University, from across the country, or even from further afield?

ZB: The workshop is open to all, and participants from all over the world are applying. We are less than a month away from the event at the moment and so far we have approximately 95 participants. Some are from Czech universities, others from prestigious foreign universities, but we also have participants from private companies, such as Zeiss.

Published: Aug 11, 2023 02:30 PM

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