23 November - 28 November 2025
Volume electron microscopy by automated serial SEM
Christel Genoud, Amanda Lewis, Paolo Ronchi, Yannick Schwab
Description OverviewSpeakersProgrammePractical informationSponsorsMedia kit Overview Course overview Recent developments in scanning electron microscopes SEM have led to ground breaking opportunities in volume imaging of cells and tissues This course aims to provide extensive theoretical and practical knowledge on the three main techniques for volume EM based on SEM microtome based serial block face SEM focused ion beam SEM and array tomography The participants will be able to assess the potential of each technique to understand which fits best with their own projects and acquire the theoretical background to understand the different techniques as well as how to optimize the imaging conditions the data processing analysis and management This course will further contribute to disseminating knowledge on fast evolving techniques to a growing community of vEM users and service providers This event has been granted the following EMBO sustainability badge Grade 2 of 3 Speakers Speakers trainers and staff Ilya Belevich University of Helsinki Finland Benedikt Best EMBL Heidelberg Germany Chandni Bhickta EMBL Heidelberg Germany Davi Bock University of Vermont USA Chris Bleck Howard Hughes Medical Institute Janelia Research Campus USA Mandy Boermel EMBL Heidelberg Germany Jemima Burden University College London United Kingdom Lucy Collinson Francis Crick Institute United Kingdom Nedal Darif EMBL Heidelberg Germany Marta Di Fabrizio University College London United Kingdom Christel Genoud University of Lausanne Switzerland Manuel Gunkel EMBL Heidelberg Germany Moritz Helmstaedter Max Planck Institute for Brain Research Germany Julian Hennies EMBL Heidelberg Germany Jacob Hoogenboom Delft University of Technology The Netherlands Annele Kremer VIB Ghent Belgium Anna Kreshuk EMBL Heidelberg Germany Amanda Lewis EPFL Lausanne Switzerland Rachel Mellwig EMBL Heidelberg Germany Andreas M ller Dresden University of Technology Germany Viola Oorschot EMBL Heidelberg Germany Andreia Pinto Leica Heidelberg Germany Ines Romero Brey EMBL Heidelberg Germany Paolo Ronchi EMBL Heidelberg Germany Nadav Scher EMBL Heidelberg Germany Yannick Schwab EMBL Heidelberg Germany R za Shahidi Heidelberg University Germany Adrian Wanner Paul Scherrer Institut PSI Switzerland Ian White Laboratory for Molecular Cell Biology United Kingdom Evgenia Zagoriy EMBL Heidelberg Germany Alexandra Zakieva EMBL Heidelberg Germany Scientific organisers Christel Genoud University of Lausanne Switzerland Amanda Lewis EPFL Lausanne Switzerland Paolo Ronchi EMBL Heidelberg Germany Yannick Schwab EMBL Heidelberg Germany Course organisers Catherine Casas Saavedra EMBL Heidelberg Germany Irena Provaznikova EMBL Heidelberg Germany Programme Are you on social media Post using EMBOvEM and don t forget to tag EMBLEvents Some pre course work such as watching pre recordings and protocol reading with estimated time 0 10 hours will be required and will be shared in advance of the course Some speakers may need to join virtually to give their lecture or Q A and the programme is subject to change Day 1 Sunday 23 November 2025 Timings Europe CETProgrammeLocation13 45 14 15Welcome registration and light refreshmentsRoom 20214 15 14 45House notes and course overviewRoom 20214 45 15 30The challenges of volume EM in Biology Yannick Schwab EMBL Heidelberg GermanyRoom 20215 30 18 30Networking Flash talk presentations from students with concurrent coffee break Ice breaking activity Challenges Expectations from participants Treasure huntRoom 20218 30 19 30DinnerEMBL Canteen19 30Bus to Premier Inn Hotel Day 2 Monday 24 November 2025 Timings Europe CETProgrammeLocation08 30Bus from Premier Inn Hotel08 50 09 00Overview of the day and organisational matters Led by the course Scientific OrganisersRoom 20209 00 10 00Basics Signal detection in SEM Jacob Hoogenboom Delft University of Technology The NetherlandsRoom 20210 00 11 00Basics of SEM sample preparationAmanda Lewis EPFL Lausanne SwitzerlandRoom 20211 00 11 45Coffee break and meet the speakersRoom 20211 45 12 45Basics Introduction to SBF SEM and FIB SEM Christel Genoud University of Lausanne SwitzerlandRoom 20212 45 13 30Lunch EMBL Canteen13 30 17 30Practicals 5 groups practicals A E in parallelAll staffPractical A FIB SEMAnneke Kremer VIB Ghent BelgiumPaolo Ronchi EMBL Heidelberg GermanyNadav Scher EMBL Heidelberg GermanyPractical B SBF SEM CXEMMandy Boermel EMBL Heidelberg GermanyNedal Darif EMBL Heidelberg GermanyChristel Genoud University of Lausanne SwitzerlandRachel Mellwig EMBL Heidelberg GermanyInes Romero Brey EMBL Heidelberg GermanyAdrian Wanner Paul Scherrer Institut PSI SwitzerlandPractical C Array Tomography AT Jemima Burden University College London UKViola Oorschot EMBL Heidelberg GermanyReza Shahidi Heidelberg University GermanyIan White University College London UKPractical D CLEMChandni Bhickta EMBL Heidelberg GermanyMarta Di Fabrizio University College London United KingdomManuel Gunkel EMBL Heidelberg GermanyAmanda Lewis EPFL Lausanne SwitzerlandPractical E Image processingIlya Belevich University of Helsinki FinlandBenedikt Best EMBL Heidelberg GermanyJulian Hennies EMBL Heidelberg GermanyYannick Schwab and Andreas M ller will move in between practical groupsIncluding flexible coffee break at participants convenienceEMCF ALMF CTL17 30 17 45Coffee break with meet the speakerRoom 20217 45 19 00Parallel demo sessions Katana TFS cryo vEM Leica EMCF room 202 IC19 00 20 00Pizza dinner in ATC Rooftop Lounge with adjoining roundtable discussionATC Rooftop Lounge20 00 21 00FAIR EM data role play gameAlexandra Zakieva EMBL Heidelberg GermanyATC Rooftop Lounge21 00Bus to Premier Inn Hotel Day 3 Tuesday 25 November 2025 Timings Europe CETProgrammeLocation08 30Bus from Premier Inn Hotel08 50 09 00Overview of the day and organisational matters Led by course organisersRoom 20209 00 10 00Basics Introduction to array tomography Ian White University College LondonUnited KingdomRoom 20210 00 11 00Data processing raw stack alignment and registration Julian Hennies EMBL HeidelbergGermanyRoom 20211 00 11 30Coffee break with meet the speakersRoom 20211 30 12 30Data segmentation and morphometricsAndreas M ller Dresden University of Technology GermanyRoom 20212 30 13 15LunchCourtyard Room foyer13 15 14 00Talk from course sponsor Itziar Serna Martin ThermofisherCourtyard Room14 00 18 30Practicals 5 groups practicals A E in parallelAll staffPractical A FIB SEMAnneke Kremer VIB Ghent BelgiumPaolo Ronchi EMBL Heidelberg GermanyNadav Scher EMBL Heidelberg GermanyPractical B SBF SEM CXEMMandy Boermel EMBL Heidelberg GermanyNedal Darif EMBL Heidelberg GermanyChristel Genoud University of Lausanne SwitzerlandRachel Mellwig EMBL Heidelberg GermanyInes Romero Brey EMBL Heidelberg GermanyAdrian Wanner Paul Scherrer Institut PSI SwitzerlandPractical C Array Tomography AT Jemima Burden University College London UKViola Oorschot EMBL Heidelberg GermanyReza Shahidi Heidelberg University GermanyIan White University College London UKPractical D CLEMChandni Bhickta EMBL Heidelberg GermanyMarta Di Fabrizio University College London United KingdomManuel Gunkel EMBL Heidelberg GermanyAmanda Lewis EPFL Lausanne SwitzerlandPractical E Image processingIlya Belevich University of Helsinki FinlandBenedikt Best EMBL Heidelberg GermanyJulian Hennies EMBL Heidelberg GermanyYannick Schwab and Andreas M ller will move in between practical groupsIncluding flexible coffee break at participants convenienceEMCF ALMF CTL18 30 19 00Bus to downtown Heidelberg via Premier Inn Hotel19 30 21 30Downtown course dinner and networkingUrban Kitchen Day 4 Wednesday 26 November 2025 Timings Europe CETProgrammeLocation08 30Bus from Premier Inn Hotel08 50 09 00Overview of the day and organisational matters Led by course organisersRoom 20209 00 10 00Advanced Correlative imaging Paolo Ronchi EMBL Heidelberg GermanyRoom 20210 00 11 00Advanced Enhanced FIB SEM plasma FIB SEM Christopher Bleck Howard Hughes Medical Institute Janelia Research Campus USARoom 20211 00 11 30Coffee break and meet the speakersRoom 20211 30 12 30Advanced multi SEMJacob Hoogenboom Delft University of Technology The NetherlandsRoom 20212 30 13 15LunchEMBL Canteen13 15 13 30Talk from course sponsor Frederic Leroux DiatomeRoom 20213 30 17 30Practicals 5 groups practicals A E in parallelAll staffPractical A FIB SEMAnneke Kremer VIB Ghent BelgiumPaolo Ronchi EMBL Heidelberg GermanyNadav Scher EMBL Heidelberg GermanyPractical B SBF SEM CXEMMandy Boermel EMBL Heidelberg GermanyNedal Darif EMBL Heidelberg GermanyChristel Genoud University of Lausanne SwitzerlandRachel Mellwig EMBL Heidelberg GermanyInes Romero Brey EMBL Heidelberg GermanyAdrian Wanner Paul Scherrer Institut PSI SwitzerlandPractical C Array Tomography AT Jemima Burden University College London UKViola Oorschot EMBL Heidelberg GermanyReza Shahidi Heidelberg University GermanyIan White University College London UKPractical D CLEMChandni Bhickta EMBL Heidelberg GermanyMarta Di Fabrizio University College London United KingdomManuel Gunkel EMBL Heidelberg GermanyAmanda Lewis EPFL Lausanne SwitzerlandPractical E Image processingIlya Belevich University of Helsinki FinlandBenedikt Best EMBL Heidelberg GermanyJulian Hennies EMBL Heidelberg GermanyYannick Schwab and Andreas M ller will move in between practical groupsIncluding flexible coffee break at participants convenienceEMCF ALMF CTL17 30 18 45Parallel demo sessions Webknossos Katana TFS cryo vEM Leica Flex Lab A B EMCF room 202 IC18 45 19 45Dinner EMBL Canteen19 45Bus to Premier Inn Hotel Day 5 Thursday 27 November 2025 Timings Europe CETProgrammeLocation08 30Bus from Premier Inn Hotel08 50 09 00Overview of the day and organisational matters Led by course organisersRoom 20209 00 09 45Applications of vEM 4Moritz Helmstaedter Max Planck Institute for Brain Research GermanyRoom 20209 45 10 30Applications of vEM 1Lucy Collinson Francis Crick Institute United KingdomRoom 20210 30 11 00Coffee break and meet the speakersRoom 20211 00 12 00Data morphofeatures in vEM datasetsAnna Kreshuk EMBL Heidelberg GermanyRoom 20212 00 12 15Group photoATC entrance12 15 13 00Lunch EMBL Canteen13 00 13 30Guest talk Davi Bock University of Vermont USARoom 20213 30 18 30Practicals 5 groups practicals A E in parallelAll staffPractical A FIB SEMAnneke Kremer VIB Ghent BelgiumPaolo Ronchi EMBL Heidelberg GermanyNadav Scher EMBL Heidelberg GermanyPractical B SBF SEM CXEMMandy Boermel EMBL Heidelberg GermanyNedal Darif EMBL Heidelberg GermanyChristel Genoud University of Lausanne SwitzerlandRachel Mellwig EMBL Heidelberg GermanyInes Romero Brey EMBL Heidelberg GermanyAdrian Wanner Paul Scherrer Institut PSI SwitzerlandPractical C Array Tomography AT Jemima Burden University College London UKViola Oorschot EMBL Heidelberg GermanyReza Shahidi Heidelberg University GermanyIan White University College London UKPractical D CLEMChandni Bhickta EMBL Heidelberg GermanyMarta Di Fabrizio University College London United KingdomManuel Gunkel EMBL Heidelberg GermanyAmanda Lewis EPFL Lausanne SwitzerlandPractical E Image processingIlya Belevich University of Helsinki FinlandBenedikt Best EMBL Heidelberg GermanyJulian Hennies EMBL Heidelberg GermanyYannick Schwab and Andreas M ller will move in between practical groupsIncluding flexible coffee break at participants convenienceEMCF ALMF CTL18 30 19 30DinnerEMBL Canteen19 30 20 30Q A SessionRoom 20220 30Bus to Premier Inn Hotel Day 6 Friday 28 November 2025 Timings Europe CETProgrammeLocation08 30Bus from Premier Inn Hotel08 50 09 00Overview of the day and organisational mattersLed by course organisersRoom 20209 00 09 45Applications of vEM 1Adrian Wanner Paul Scherrer Institut PSI SwitzerlandRoom 20209 45 10 30Advanced Cryo FIB SEMEvgenia Zagoriy EMBL Heidelberg GermanyRoom 20210 30 11 00Coffee break and meet the speakersRoom 20211 00 12 15Pararell demo sessions Webknossos Katana TFS cryo vEM Leica Flex Lab A B EMCF room 202 IC12 15 13 15Lunch EMBL Canteen13 15 17 45Practicals 5 groups practicals A E in parallelAll staffPractical A FIB SEMAnneke Kremer VIB Ghent BelgiumPaolo Ronchi EMBL Heidelberg GermanyNadav Scher EMBL Heidelberg GermanyPractical B SBF SEM CXEMMandy Boermel EMBL Heidelberg GermanyNedal Darif EMBL Heidelberg GermanyChristel Genoud University of Lausanne SwitzerlandRachel Mellwig EMBL Heidelberg GermanyInes Romero Brey EMBL Heidelberg GermanyAdrian Wanner Paul Scherrer Institut PSI SwitzerlandPractical C Array Tomography AT Jemima Burden University College London UKViola Oorschot EMBL Heidelberg GermanyReza Shahidi Heidelberg University GermanyIan White University College London UKPractical D CLEMChandni Bhickta EMBL Heidelberg GermanyMarta Di Fabrizio University College London United KingdomManuel Gunkel EMBL Heidelberg GermanyAmanda Lewis EPFL Lausanne SwitzerlandPractical E Image processingIlya Belevich University of Helsinki FinlandBenedikt Best EMBL Heidelberg GermanyJulian Hennies EMBL Heidelberg GermanyYannick Schwab and Andreas M ller will move in between practical groupsIncluding flexible coffee break at participants convenienceEMCF ALMF CTL17 45 18 00Feedback and wrap up Room 20218 00Bus from EMBL to Heidelberg train station and Hotel Premiere Inn Practical information Registration fees and motivation letter The course is limited to 20 participants For selection purposes please note that your application will not be considered without a letter of motivation Registration Registration fees include admission course materials meals and coffee breaks This EMBO course includes accommodation and transportation to and from the ISG Hotel to the venue Academia 550PhD Student 550Industry 1100 A letter to support your visa application will be issued on request once payment of the registration fee is confirmed We recommend that you book your visa appointment as soon as possible to avoid any delay with your visa application Confirmation and payment The registration fee should be paid only after acceptance to the course The results will be announced approximately 2 3 weeks after the application deadline Motivation letter submission After you have logged in and successfully registered you will receive an email asking you to submit your motivation letter Click on the link provided and enter your motivation letter in the text box provided Alternatively you can submit your motivation letter by clicking on the link on the confirmation page directly after registering Instructions Include your relevant skills experience and qualifications showing why you would be suitable for the course Explain why you would like to attend including what you can contribute and how you think you will benefit from the course Please note The limit of 2000 characters refers to manually typed text and excludes spaces If an error occurs try using a different web browser preferably Google Chrome or Mozilla Firefox If you copy paste the text into the form hidden formatting might still be included which may cause the text to exceed the 2 000 character limit resulting in an error message We recommend you clear all formatting before pasting in the text If you have special symbols in your text make sure you are using Unicode characters otherwise these will not be recognised For detailed instructions please watch our video on how to submit a course motivation letter Further details For further information about registration and motivation letter submission please refer to the FAQ page Financial assistance Financial assistance Limited financial assistance is provided by the EMBL Advanced Training Centre Corporate Partnership Programme and EMBO in the form of registration fee waivers travel grants and childcare grants Your place in the meeting is only confirmed by paying the registration fee which is mandatory even when receiving a fee waiver Registration fee waiver The fee waiver will cover the registration sum that you have paid to attend the course Travel grant The travel grant will cover the cost of travel airfare train bus taxi accommodation visa and or registration fees and is provided up to specified caps which are normally as follows up to 500 for any participant travelling to an EMBO Practical Course up to 1000 for any participant working in Chile India Singapore or Taiwan travelling to an EMBO Practical Course Registration fees are only covered for EMBO Practical Courses The organisers may reduce the grant cap to accommodate more participants Recipients will be notified of their travel cap amount when they are informed of the outcome of their application Original receipts must be provided with your signature for all costs incurred within two months of completion of travel Scanned copies cannot be accepted Childcare grants There is the possibility to apply for a childcare grant to offset child care costs incurred by participants speakers trainers and organisers when attending a course Eligible costs include but are not limited to fees for a babysitter or child care facility and travel costs for a caregiver Please note that priority will be given to early stage researchers There is a limited amount of funding available for the childcare grants and funds will be distributed amongst eligible applicants Boehringer Ingelheim Fonds travel grant Applies to selected courses only Availability will be indicated during the abstract or motivation letter submission process This grant covers costs related to your attendance to the course registration travel and accommodation costs The grant is restricted to PhD students and postdocs who conduct basic biomedical research Whether you are eligible to apply for a travel grant depends on when you received your university entrance qualification e g Abitur A Levels High School Diploma Final State Examination for PhD and MD students as well as graduates the university entrance qualification must not have been obtained more than 11 years ago at the time of the envisaged course for postdocs the university entrance qualification must not have been obtained more than 13 years ago at the time of the envisaged course Selection The scientific organisers will select the recipients of registration fee waivers during the participant selection process for courses Results will be announced approximately 6 8 weeks before the event start date however for some events this may be delayed Selection results do not impact your admission to the meeting Selection for registration fee waivers and travel grants is based on scientific merit your current work or study location the reasons for needing financial support and the impact this event will have on your career Childcare grants will be allocated in the same timeframe 6 8 weeks before the event start date Please note that priority will be given to early stage researchers Further details Check out this list of external funding opportunities For further information about financial assistance please refer to the FAQ page Accommodation and travel Hotel Accommodation in twin rooms including breakfast is included in the registration fee Accommodation will be booked for the selected participants at the Premier Inn Hotel Heidelberg City Center Hotel branch Kurf rsten Anlage 23 69115 Heidelberg for the default dates of Sunday 23 November to Saturday 29 November 2025 6 nights The hotel can be contacted via this e mail adress to book the room In case you would like to have a single room please contact the hotel directly please note that you will be required to pay an additional cost availability of single rooms may be limited This should be paid by you directly to the hotel during your stay We recommend that all course participants stay at the Premier Inn Hotel Heidelberg City Center Hotel branch Kurf rsten Anlage 23 69115 Heidelberg for the course Travel information For travel information please see here If you are travelling to the conference within Germany then you are eligible for the Deutsche Bahn Event Ticket called the Veranstaltungsticket in German This will result in a lower ticket price if your travel distance to Heidelberg is more than 100 km You need to provide proof of your event attendance when purchasing the ticket For more information in English see here or in German see here You can book your ticket here Local transport Shuttle buses will go from the ISG Hotel to EMBL and back mornings and evenings A bus schedule and location of the bus stops will be made available prior to the meeting Further details Address EMBL Heidelberg Meyerhofstra e 1 69117 Heidelberg Germany For more information about accommodation and travel please refer to the FAQ page On site information Catering All meals and coffee breaks are included in the registration fee Our catering staff will prepare a wide variety of vegetarian meals meat and fish dishes soups pasta fresh fruit and vegetables as well as a variety of desserts Please wear your badge at all times when serving yourself No food or drinks are allowed in the laboratories Electricity and charging station In most places the electricity is 220 volts AC 50 cycles An adaptor and a plug that fits the German socket may be needed for your appliances laptop i e American Japanese etc A USB charging station for electronic devices is available at the registration desk EMBL Merchandise If you are interested in purchasing EMBL merchandise products presented in the glass display in the registration area please email the EMBL shop to place an order or get in contact with your Course Organiser Kindly note the EMBL shop is only open upon request and all purchases must be made in cash Euros only Health and safety notes Please read EMBL s COVID 19 safety policy for on site events Do not smoke in any EMBL building Eating and drinking is prohibited in all laboratories Do not enter any restricted areas or the laboratories unless instructed to do so If first aid is required The first aid room is located next to the ATC Registration Desk room 10 205 Dial the Emergency number 222 from any EMBL internal phone only Where is the accident What happened How many injured Emergency number 06221 387 7821 from mobile phones Please report all accidents to the conference officer at the registration desk In case of fire Press the nearest fire alarm button or the Emergency number 222 from any internal phone A loud fire alarm will go off if an evacuation is required On hearing the alarm leave the building immediately following the escape route and fire wardens and head to one of the meeting points Do not use the lifts Beyond first aid Please remember to bring your own medication if needed to the conference Note that the next pharmacy is a 4 minute drive from the EMBL but for many medications you will be required to see a doctor to get a prescription Ensure in advance that your medical insurance will cover you during your visit in the event that you do need to see a doctor while in Heidelberg In any case the EMBL Course and Conference Office will assist you to get to the pharmacy and a doctor of your choice if necessary Internet Wi Fi is available on campus Log in using the EMBL Events network and the event specific password which will be provided on site The eduroam network secure worldwide roaming access service developed for the international research and education community is also available Lost and found Lost and Found items are kept at the registration desk until the end of the conference Luggage There are lockers available on site to store your luggage which require a 2 EURO coin to operate There is another luggage room on level E0 which is free to use but remains unlocked during the conference Nursing room There is a nursing room available in the ATC Rooftop Lounge on level A29 Photography During the conference an EMBL Photographer may be taking photos If you would not like to appear in these please inform the photographer or a member of the Course and Conference Office Printing We can help to print your boarding pass train ticket Please send it to events embl de and collect your print outs at the registration desk Room for prayer yoga and meditation There is a room for prayer meditation and yoga located on level E0 behind the Auditorium Please be respectful of others using the room Sightseeing A variety of activities in Heidelberg can be found on the website of Heidelberg Marketing Travel to and from the venue During the event we provide conference shuttle buses to and from EMBL In addition there is the public bus 39A that serves the EMBL campus and taxis can be easily booked at any time Information on the shuttle buses can be found on the individual event website and more detailed information on travelling to EMBL can be found on our Travel Information page Map to walk from ISG Hotel to EMBL Additional information Please find additional information including FAQs and terms and conditions on our Information for Participants page Sponsors Event sponsor Sponsorship opportunities We offer a variety of event 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OverviewSpeakersProgrammePractical informationSponsorsMedia kit Overview Course overview Recent developments in scanning electron microscopes (SEM) have led to ground-breaking opportunities in volume imaging of cells and tissues. This course aims to provide extensive theoretical and practical knowledge on the three main techniques for volume EM based on SEM: microtome-based serial block-face SEM, focused ion beam SEM, and array tomography. The participants will be able to assess the potential of each technique to understand which fits best with their own projects, and acquire the theoretical background to understand the different techniques as well as how to optimize the imaging conditions, the data processing, analysis and management. This course will further contribute to disseminating knowledge on fast-evolving techniques to a growing community of vEM users and service...
EMBO Practical Course
EMBL Heidelberg
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