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EMBO Practical Course

Advanced analysis and processing of volume electron microscopy data

20 – 26 September 2026 | České Budějovice, Czech Republic

  • Registration Deadline
  • 10 May 2026
  • Abstract Submission Deadline
  • 12 July 2026
  • Chosen Participants Will Be Notified By
  • 12 June 2026
  • Payment Deadline
  • 12 July 2026

Apply now!

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About the Practical Course

Electron microscopy, particularly Volume Electron Microscopy (vEM), is undergoing rapid technological transformation. Modern approaches such as Serial Block-Face SEM (SBF-SEM), Focused Ion Beam SEM (FIB-SEM), and multi-beam SEM now enable large-scale, high-resolution imaging of biological structures with unprecedented detail. Yet, data analysis remains a major bottleneck, limiting the full potential of these techniques.

Recent advances in artificial intelligence and deep learning are revolutionizing vEM workflows by streamlining segmentation, reducing manual effort, and increasing analysis throughput. Combined with high-performance computing, these tools make data processing more efficient, reproducible, and accessible.

This hands-on EMBO Practical Course provides practical training in advanced data processing, AI-assisted segmentation, and deep learning-based analysis. Participants will work with platforms such as MIB, Napari, EMPANADA, and Amira to confidently handle, analyze, and interpret complex vEM datasets. This EMBO Practical Course is open to researchers at various career stages with experience in imaging or data analysis.


About EMBO Courses and Workshops

EMBO Courses and Workshops are selected for their excellent scientific quality and timelines, provision of good networking activities for all participants and speaker gender diversity (at least 40% of speakers must be from the underrepresented gender).

Organisers are encouraged to implement measures to make the meeting environmentally more sustainable.

 
 

Programme

 

Registration

  • Registration Deadline
  • 10 May 2026
  • Abstract Submission Deadline
  • 12 July 2026
  • Chosen Participants Will Be Notified By
  • 12 June 2026
  • Payment Deadline
  • 12 July 2026

 

  • STUDENT/POSTDOCS EUR 450
  • ACADEMIC EUR 450
  • INDUSTRY EUR 900
  • STUDENT/POSTDOCS (virtual) EUR 150
  • ACADEMIC (virtual) EUR 150
  • INDUSTRY (virtual) EUR 300

In-person registration includes:

  • Admission to the course
  • Accommodation
  • Meals, coffee breaks
  • Public transport within České Budějovice for the duration of the course

Virtual registration includes:

  • Up to 10 virtual participants can attend the course.

The virtual registration fee covers admission only

Payment

Payment details will be sent to the selected participants together with the acceptance letter.

Cancellation policy

Registration fees are generally non-refundable. However, cancellations will be reviewed individually, and if the vacated spot would be successfully reallocated to a participant from the waiting list, a full refund will be issued.

Selection criteria

Experience in Imaging and Data Processing:

  • Preference will be given to applicants with prior experience in data processing and/or imaging, particularly in Volume Electron Microscopy (vEM). However, researchers from related fields looking to expand their expertise in vEM applications will also be considered.

Scientific Impact and Career Development:

  • Applicants will be evaluated on how the workshop aligns with their research needs and future career goals. Emphasis will be placed on selecting individuals who will actively apply and disseminate the acquired knowledge within their institutions and scientific communities.

Applicants need to provide:

  1. CV
  2. Letter of Motivation (1500 characters)
  3. Letter of Reference from the supervisor/head of the laboratory (500 characters)

Once selected, the applicant will be required to provide an abstract for a poster and flash talk.

Abstract guidelines

All abstracts should be submitted in English, with a maximal length of 400 words (excluding authors, affiliations and references).

Poster specifications

The maximum size of the poster shall be A1, in landscape format. The poster can have a smaller font, as the main idea behind it is to use it as a base for discussions during coffee breaks.

Travel grants and registration fee waivers

Travel grants and registration fee waivers are available for participants.

Selection of awardees is handled directly by the organizers. EMBO travel grants and registration fee waivers are allocated on the basis of the quality of the submitted abstract.

Applicants do not need to apply separately for these but should indicate on the registration form if they wish to be considered.

Additional travel grants are available for EMBC Associate Member States Chile, India, Singapore and Taiwan.

Child care grants

EMBO Courses and Workshops offers grants to offset additional childcare costs incurred by participants or speakers when participating at any EMBO Courses and Workshop funded meeting. Eligible costs include fees for a caregiver or child-care facility, travel costs for a caregiver, or travel costs for taking the child to the meeting etc. Please indicate on the registration form whether you would like to be considered for the grant. Please also describe how you intend to use the childcare grant and specify the sum that you will need.

Accessibility grants

EMBO offers accessibility grants to support participants at EMBO Courses & Workshops with any access needs. These grants cover up to 500 Euros for any additional costs e.g. to adapt the conference environment, or to be accompanied by someone to assist them where necessary.

Participants with access needs may apply for a grant via the registration system of the related EMBO event, or by emailing the organizers of the related EMBO event directly.


Code of conduct

Anti-harassment and non-discrimination policy

At EMBO, we believe that harassment and discriminatory behaviour are unacceptable in any setting.

Media and communications policy

Recording or communication of the presented data needs to be agreed upon by all concerned.

EMBO's code of conduct is applicable for all participants of this EMBO meeting and can be found here.

 

Contact

Jiří Týč

Email: jiri.tyc@paru.cas.cz

 

 

Venue

Accommodation

Accommodation is arranged at Hotel Budweis,

A single room will be issued to the accepted participants after registration

Transport

Participants travelling by plane may arrive either at Prague or Vienna airports, from which train connections to České Budějovice are available:

  • From Prague Airport, take a direct bus to the main train station (approx. €4) and then a direct train to České Budějovice (approx. €18 if purchased in advance). The total travel time is approximately 150 minutes.
  • From Vienna Airport, participants should take a train to Linz HBF and then transfer to another train to České Budějovice (tickets start at approximately €20). The total travel time is approximately 240 minutes.

Participants arriving by bus will disembark on top of the Mercury shopping centre, conveniently located opposite the main train station.

České Budějovice has a reliable public transport network. Bus line 3 connects Mercury shopping centre with both the hotel and the course venue. Single-ride tickets cost around €1 and can be paid for by card on board the buses. Upon registration, participants will receive a weekly public transport pass.

About the Area

České Budějovice (Budweis) is the capital of the South Bohemia region, located about 150 km south of Prague. Founded in 1265 by King Přemysl Otakar II, it offers a rich history, a beautiful main square, and a lively cultural scene.

The city is world-famous for its beer tradition. Brewing here dates back to the 13th century, and today two big breweries keep the tradition alive: Budvar, where the original Budweiser beer has been brewed since the 19th century, and Samson, the town brewery established in 1795. In addition, there are several minibreweries around the town.

The South Bohemian region is full of opportunities for sightseeing and leisure. Just a short trip away are two UNESCO World Heritage Sites:

  • Český Krumlov, a stunning medieval town with a castle overlooking the Vltava river.
  • Holašovice, a unique village with Baroque-style rural architecture.

In addition, the surrounding countryside offers picturesque landscapes, castles, lakes, and forests – ideal for day trips, hiking, or just relaxing before or after the course.

Sustainability at the meeting

The EMBO Courses & Workshops Programme assesses meetings based on the proposal and implementation of sustainability measures. Meetings can earn points across a range of measures, with each measure assigned a point value from one to five. These points classify the meeting into one of three sustainability levels, reflecting the organizers' commitment to enhancing the sustainability of their event. More information on the EMBO Courses & Workshops Sustainability Badge can be found here.

To support sustainability catering arrangements will feature vegetarian days, locally sourced ingredients, and bottled water + single-use items will be avoided. Travelling by train within Europe is recommended, and most, if not all, central European speakers/instructors/tutors will arrive by Land-based public transport. All course materials, including abstract books and programs, will be distributed electronically, and no plastic badges will be used.

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