Dear Czech-BioImaging users,

we would like to invite you to a second free 2-hr advanced online training workshop on ”Remote access for electron microscopy” on June 20th, 10:00 a.m. - 12:00 p.m. CEST (09:00-11:00 a.m. BST). The workshop is co-organized by ZEISS, Euro-BioImaging and Instruct as part of the eRImote project.

The deadline to register for the workshop is 7th June.

The workshop will be delivered by training and application specialists from ZEISS and is targeted at facility staff and advanced users.

The workshop will cover:

• Setting up remote access via TeamViewer etc.
• Controlling the microscope remotely: appropriate UI and software tools
• Application use case (FIB-SEM)
• Predictive service for diagnosis and provision

followed by plenty of time for Q&A.

REGISTER

Dear Czech-BioImaging users,

we would like to invite you to the regular "Entry-Level Super-Resolution Microscopy course" organised by the CzBI facility Microscopy Service Centre, at the Institute of Experimental Medicine of the Czech Academy o Sciences located in the Krč Campus. The course takes place from 22 to 24 May 2024 and covers theoretical and practical aspects of an “entry-level” super-resolution imaging methods based on the principle of Optical-Photon-Reassignment available in the core facility at confocal microscopes Zeiss LSM880 with AiryScan and Olympus SpinSR10 with OSR.

The entry level course can be followed by the advanced course SUPER-RESOLUTION IN LIGHT MICROSCOPY organized Light Microscopy Core Facility, Institute of Molecular Genetics of the Czech Academy of Sciences, which takes place one month later.

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COURSE WEBSITE

Dear Czech-BioImaging users,

if you want to learn the principles of TEM and SEM and selected advanced techniques EM, you are invited to the practical course Advanced EM - 3D Imaging.

This 3-day course takes place on 11-13 June 2024, at the Laboratory of Electron Microscopy (LEM), Biology Centre of the Czech Academy of Sciences, České Budějovice, and focuses on electron tomography, cryo-single particle analysis (including the whole workflow of sample preparation, screening, data acquisition and processing), and negative staining method..

• Registration fee for 1 day: 500 CZK
• Registration fee for 3 days: 1 500 CZK

Contact person: Marie Vancová 

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COURSE WEBSITE

Dear Czech-BioImaging users,

we would like to invite you to join an upcoming 2-day course "Napari for Beginners", organized by the Imaging Methods Core Facility (IMCF) at BIOCEV intended as a gateway to Napari, a dynamic open-source software that leverages the Python programming language to offer interactive image visualization and advanced solutions in image processing and analysis.

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Here’s what you can expect:

• Introductory sessions focused on the installation and understanding of Conda, Python, and Napari.
• Learning to navigate through the Napari interface.
• Conducting basic image operations within Napari.
• Exploring various Napari plugins essential for common image analysis tasks like segmentation.
• Going through an example image analysis workflow to apply the learned concepts in practice.

COURSE WEBSITE

All communication concerning the event should be addressed to cockovaz@natur.cuni.cz

Dear Czech-BioImaging users,

if you are interested in advanced EM image processing techniques involving AI tools, you are invited to the practical course WORKSHOP OF ADVANCED ANALYSIS AND PROCESSING OF VOLUME EM DATA.

This 3-day course takes place on 15-17 May 2024, at the Laboratory of Electron Microscopy, Biology Centre of the Czech Academy of Sciences, České Budějovice, and focuses on stitching, alignment, advanced filtering and segmentation including AI powered approaches in electron microscopy.

Registration deadline: April 22, 2024. 

Contact persons: Jiří Týč, František Kitzberger

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Here’s what you can expect:

This hands-on workshop is focused on advances in the data processing, segmentation and
analysis obtained from the volume electron microscopy imaging techniques. Its main goal is to

make the participants familiar with the new tools available for the data analysis mainly the AI-
tools to make the image analysis and segmentation as effective and fast as possible.

The program is dedicated to people who already have some experience with basic data
processing. We will focus on work with “advanced” tools of Microscopy Image Browser and
AMIRA (Thermo Fisher Sci.), such as AI powered segmenting tool - Segment Anything Model
from META (MIB), AI Assisted Tool for CryoEM (AMIRA), deep learning (MIB and AMIRA),
volume/surface rendering (MIB and AMIRA), etc.
Participants are required to bring their own laptop and have a google account active. Both
MIB and AMIRA will be run on remote desktops.

COURSE WEBSITE

Dear Czech-BioImaging users,

if  you wish to analyze your microscopy image data efficiently using techniques of artificial intelligence, you are invited to the practical course AI-BASED SEGMENTATION AND TRACKING.

This intensive 1-day course takes place on May 14, 2024, at the Light Microscopy Core Facility, Institute of Molecular Genetics of the Czech Academy of Sciences, and focuses intensively on image data segmentation and cell tracking using state-of-the-art deep learning methods.

Registration deadline: April 30, 2024 (23:59 CET)

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Here’s what you can expect:

This one-day course focuses intensively on image data segmentation and cell tracking using state-of-the-art deep learning methods like StarDist, Cellpose, Omnipose, and MitoSegNet. It demonstrates how segmentation aids in analyzing image-based objects and how tracking applies segmentation to study cells dynamically over time. TrackMate, a plugin in Fiji, integrates StarDist and Cellpose for cell segmentation and tracking. The course also covers the Delta2 framework for tracking dense bacteria populations and explores ZeroCostDL4Mic, a cloud computing framework with advanced deep learning methods for microscopy tasks like segmentation, object detection, and denoising. The course aims to highlight the practicality and user-friendly nature of these deep learning techniques.

Also, a sponsor’s lecture on Apeer.com, Zeiss’s cloud platform, will focus on image processing, including machine and deep learning. At the course’s end, participants can actively practice segmentation and cell measurement using a virtual reality system from the same company.

COURSE WEBSITE

Dear Czech-BioImaging users,

if you are interested in microscopy and would like to acquire images in high resolution to describe and reveal structures behind the limit of the resolution, do not miss the practical course SUPER-RESOLUTION IN LIGHT MICROSCOPY.

This intensive 3-day program, taking place from June 12 to 14, 2024, at the Light Microscopy Core Facility, Institute of Molecular Genetics of the Czech Academy of Sciences, promises a deep dive into the world of high-resolution imaging.

Registration deadline: May 5, 2024 (23:59 CET)

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Here’s what you can expect:

• comprehensive program full of techniques ranging from advanced confocal methodologies to super-resolution structured illumination and nanoscopy strategies STED and SMLM
• balanced blend of theory and practice, with hands-on sessions to apply what you learn
• 15 lectures combined with 9 practical sessions,1:50 h each
• 2 online lectures given by leading experts in the field
• 9 implementations of SR techniques together with image post-processing approaches.
• 7 advanced microscopy systems

At the end of the course, you will obtain an official certificate. Limited number of spots is offered for this exclusive course – only 15 seats are available. 

LEARN MORE

Dear Czech-BioImaging users,

we are are excited to share the news about the next Euro-BioImaging User Forum on Image Data.

The event features many excellent presentations including one from Czech-BioImaging namely user, Shiladitya Mitra and Light Microscopy Core Facility at the IMG member Michaela Blazikova. It will take place on Tuesday, March 26th, 2024 from 14:00-17:00 CET and the topic is “Image Data.” This event will highlight innovative image analysis and image data management solutions at Euro-BioImaging Nodes. It will feature user presentations as well as presentations from image data and image analysis experts from the Nodes, focusing on the technical aspects of the work.

Everyone is welcome!

 

More on EuBI website      Program      Register

Dear Czech-BioImaging users,

we are happy to announce that registration and abstract submission to the annual Czech-BioImaging scientific conference Imaging Principles of Life 2024 are now open!

You are all welcome to join us and enjoy the excellent presentations of keynote expert speakers on topics from the fields of biological and medical imaging. The conference is open to the Czech-BioImaging users and everyone interested in microscopy.

• REGISTRATION DEADLINE: 16 August 2024
• ABSTRACT SUBMISSION DEADLINE: 16 August 2024
• CONFERENCE DATE: 30 September 2024 -  Wednesday 2 October, 2024
• CONFERENCE VENUE: Amande Hotel located in Hustopeče

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LEARN MORE

For more information, feel free to contact us at: conference@czech-bioimaging.cz

*Czech-BioImaging Annual Scientific Conference is funded by the Ministry of Education, Youth and Sports of the Czech Republic. (LM 2023050)

Dear Czech-BioImaging users,

we present you an opportunity to participate in a European network of 13 partners & universities that will host all PhD candidates during secondments - a PhD. student in correlative imaging is needed within the EU-funded Marie Sklodowska-Curie Doctoral Networks Action CLEXM.

Due to visa difficulties of their designated PhD candidate, they need to re-start the application process with a focus on EU-citizens that did not reside in Germany in the last two years and that do not require a working permit for Germany. The candidate is expected to start in summer!

The project will give candidates the opportunity to work closely with different imaging modalities while allowing them to network with other candidates and other project supervisors. The title of the project (find attached) is:
"Developing Super-resolution cryo-fluorescence microscopy and its correlative combination with Cryo-focused ion beam scanning electron microscopy and soft x-ray microscopy as an innovative tool in biomedical research and diagnostics"

More information here.

Please contact Prof. Dr. Andreas Walter if interested at: andreas.walter@hs-aalen.de