FISHing for RNAs: classical to single molecule approaches

Time	Session	Location
13:30 – 16:00	Familiarise with EMBL eCampus platform, and prime on pre-course work, exercises and learning materials. Get access to pre-course material Gather outstanding questions related to the course from participants’ research and brief introductions in order to integrate them into the focus of the practical sessions.	Online

Time	Session	Location
13:00	Welcome Coffee	ISG Hotel
13:00 – 13:15	Welcome and course overview	ISG Hotel
13:15 – 16:00	Ice breaking activity and Flash talks (and Q&A) and activity in groups with concurrent coffee break	ISG Hotel
16:00 – 16:45	Discussion Session: Pre-recorded talk on Histology overview and applications Emerald Perlas – EMBL Rome, Italy	ISG Hotel
16:45 – 17:30	Discussion session: Pre-recorded talk on Subcellular localization of mRNAs in neuronal memory circuits  Florence Besse – Institut de Biologie Valrose, France	ISG Hotel
17:30 – 18:00	Coffee break	ISG Hotel
18:00 – 18:45	Discussion session: Pre-recorded talk on RNA detection methods Imre Gaspar – Turbine.ai, Hungary	ISG Hotel
18:45 – 19:30	Discussion session: Pre-recorded talk on RNA-protein condensates Mainak Bose	ISG Hotel
19:30 – 20:00	Check-in	ISG Hotel
20:00 – 21:00	Dinner in ISG Hotel Restaurant	ISG Hotel Restaurant

Time	Session	Location
08:40 – 08:50	Bus from hotel to EMBL ATC Entrance	ISG Hotel bus stop
08:50 – 09:00	Overview of the day Imre Gaspar – Turbine.ai, Hungary	Courtyard Room A & B
09:00 – 09:20	Lab safety instructions and house notes (orientation in EMBL ATC)	Courtyard Room A & B
09:20 – 09:50	Practical: Probe design, production theory and demo of probe design Imre Gaspar – Turbine.ai, Hungary	Training Lab A & B
09:50 – 10:35	Practical: Theory and demo of smFISH and HCR-ISH Imre Gaspar – Turbine.ai, Hungary Mainak Bose – Indian Institute of Technology Kharagpur	Training Lab A & B
10:35 – 10:50	Coffee break	In front of Training Lab A & B
10:50 – 11:35	Practical: Probe design and production (continued) Probe preparation (ddUTP + dye conjugation) Imre Gaspar – Turbine.ai, Hungary	Training Lab A & B
11:35 – 12:20	Lecture: Spatial RNA biology from molecules to tissues – Sinem Sakka – EMBL, Germany	Courtyard Room A & B
12:20 – 13:20	Lunch break	EMBL canteen
13:20 – 14:05	Practical: Conventional ISH Introduction and theory of conventional ISH Emerald Perlas – EMBL Rome, Italy Sara Di Persio, University of Rome, La Sapienza Erika De Sensi, EMBL Rome Jeet Banerjee – Indian Institute of Technology Kharagpur, India	Training Lab A & B
14:05 – 16:05	Practical: Conventional ISH (continued) (section pre-treatment, Proteinase K digest, acetylation, hybridization set-up) Emerald Perlas – EMBL Rome, Italy Sara Di Persio, University of Rome, La Sapienza Erika De Sensi, EMBL Rome Jeet Banerjee – Indian Institute of Technology Kharagpur, India With flexible coffee break	Training Lab A & B
16:05 – 16:35	Practical: smFISH + HCR-ISH 3a: sm FISH: Probe labeling set-up Florence Besse – Institut de Biologie Valrose Imre Gaspar – Turbine.ai, Hungary Mainak Bose – Indian Institute of Technology Kharagpur Jeet Banerjee – Indian Institute of Technology Kharagpur	Training Lab A & B
16:35 – 16:50	Coffee break	In front of Training Lab A & B
16:50 – 17:35	Lecture: Super-resolution RNA imaging with aptamers Murat Sunbul – Institute of Pharmacy and Molecular Biotechnology, Germany	Courtyard Room A & B
17:35 – 19:15	Student presentations (everyone will present their scientific project)	Courtyard Room A & B
19:15 – 20:45	Dinner with discussion on career topics	EMBL Canteen
20:45	Bus back to hotel	EMBL bus stop

Time	Session	Location
08:40 – 08:50	Bus from hotel to EMBL ATC Entrance	ISG Hotel bus stop
08:50 – 09:00	Overview of the day Emerald Perlas – EMBL Rome, Italy	Courtyard Room A & B
09:00 – 10:00	Practical: Conventional ISH (continued) Post-hybridisation washes Emerald Perlas – EMBL Rome, Italy Sara Di Persio, University of Rome, La Sapienza Erika De Sensi, EMBL Rome Jeet Banerjee – Indian Institute of Technology Kharagpur, India	Training Lab A & B
10:00 – 10:45	Lecture: RNA condensate plasticity during development and in response to the environment Arnaud Hubstenberger – Institut de Biologie Valrose, France	Courtyard Room A & B
10:45 – 11:00	Coffee break	In front of Training Lab A & B
11:00 – 12:00	Practical: Conventional ISH (continued) Staining set-up Emerald Perlas – EMBL Rome, Italy Sara Di Persio, University of Rome, La Sapienza Erika De Sensi, EMBL Rome Jeet Banerjee – Indian Institute of Technology Kharagpur, India	Training Lab A & B
12:00 – 13:00	Lunch with discussion on next career steps	EMBL canteen
13:00 – 15:15	Practical: smFISH + HCR-ISH (continued) 3a and b: sm FISH: probe purification and QC and HCR_ISH specimen pre-work and hybridization setup Florence Besse – Institut de Biologie Valrose Imre Gaspar – Turbine.ai, Hungary Mainak Bose – Indian Institute of Technology Kharagpur Jeet Banerjee – Indian Institute of Technology Kharagpur with concurrent coffee break (during centrifugation time)	Training Lab A & B
15:15 – 16:15	Practical: Conventional ISH (continued) Washing and mounting of specimen Emerald Perlas – EMBL Rome, Italy Sara Di Persio, University of Rome, La Sapienza Erika De Sensi, EMBL Rome Jeet Banerjee – Indian Institute of Technology Kharagpur, India	Training Lab A & B
16:15 – 17:00	Lecture: Single-molecule RNA FISH detection protocols for plants Stefanie Rosa – Swedish University of Agricultural Sciences	Courtyard Room A & B
17:00 – 17:30	Coffee break	Courtyard Room A & B
17:30 – 19:00	Student presentations	Courtyard Room A & B
19:00 – 20:30	Dinner and Pub Quiz	EMBL canteen
20:30 – 20:40	Departure to Hotel	EMBL Bus stop

Time	Session	Location
08:40 – 08:50	Bus from hotel to EMBL ATC Entrance	ISG Bus Stop
08:50 – 09:00	Overview of the day Florence Besse – Institut de Biologie Valrose, France	Courtyard Room A & B
09:00 – 11:15	Practical: smFISH + HCR-ISH (continued) 3a and 3b: HCR-ISH: washes smFISH pre-hybridisation set-up for incubation HCR-ISH: Amplification set-up for reaction smFISH hybridisation Florence Besse – Institut de Biologie Valrose, France Imre Gaspar – Turbine.ai, Hungary Mainak Bose – Indian Institute of Technology Kharagpur Jeet Banerjee – Indian Institute of Technology Kharagpur With concurrent coffee break	Training Lab A & B
11:15 – 12:00	Lecture: Data visualization in Biology Helena Jambor – University of Applied Sciences of the Grisons, Switzerland	Courtyard Room A & B
12:00 – 13:00	Group photo followed by lunch break	EMBL canteen
13:00 – 15:30	Practical: Conventional ISH (continued) Conventional ISH imaging Emerald Perlas – EMBL Rome, Italy Sara Di Persio, University of Rome, La Sapienza Erika De Sensi, EMBL Rome With concurrent coffee break	Training Lab A & B
15:30 – 16:15	Lecture: RNA self-assembly and cellular organization Ankur Jain – Whitehead Institute for Biomedical Research, USA	Courtyard Room A & B
16:15 – 18:15	Practical: smFISH + HCR-ISH (continued) 3a and 3b: smFISH & HCR-ISH: washes and specimen mounting Florence Besse – Institut de Biologie Valrose, France Imre Gaspar – Turbine.ai, Hungary Mainak Bose – Indian Institute of Technology Kharagpur Jeet Banerjee – Indian Institute of Technology Kharagpur Discussion: In parallel with the discussion on imaging, covering image collection and microscope settings, led by Mainak Bose, Indian Institute of Technology Kharagpur With concurrent coffee break	Training Lab A & B and Courtyard Room A & B
18:15 – 19:15	Dinner	EMBL canteen
19:15 – 20:15	Discussion on responsible conduct of research: Experimental design and Standards and controls in the ISH field Moderator: Helena Jambor – University of Applied Sciences of the Grisons, Switzerland	Courtyard Room A & B
20:15 – 20:25	Bus back to hotel	EMBL bus stop

Time	Session	Location
08:40 – 08:50	Bus from hotel to EMBL ATC Entrance
08:50 – 09:00	Overview of the day Mainak Bose	Courtyard Room A & B
09:00 – 10:30	Practical: Imaging in groups (smFISH and HCR-ISH) Mainak Bose – Indian Institute of Technology Kharagpur Jeet Banerjee – Indian Institute of Technology Kharagpur Sara Di Persio, University of Rome, La Sapienza Florence Besse Practical lecture and trouble shooting: Basics of imaging processing Imre Gaspar – Turbine.ai, Hungary	ALMF and Courtyard Room A & B
10:30 – 10:45	Coffee break	In front of Courtyard Room A & B
10:45 – 12:15	Practical: Imaging in groups (smFISH and HCR-ISH) Mainak Bose – Indian Institute of Technology Kharagpur Jeet Banerjee – Indian Institute of Technology Kharagpur Sara Di Persio, University of Rome, La Sapienza Florence Besse Practical lecture and trouble shooting: Basics of imaging processing Imre Gaspar – Turbine.ai, Hungary	ALMF and Courtyard Room A & B
12:15 – 13:15	Lunch	EMBL canteen
13:15 – 14:00	Lecture: RNA localization and local translation at cell protrusions Stravoula Mili – NIH, USA	Courtyard Room A & B
14:00 – 17:00	Practical: ISH image analysis Basics ISH image processing and analysis Imre Gaspar – Turbine.ai, Hungary Mainak Bose – Indian Institute of Technology Kharagpur Jeet Banerjee – Indian Institute of Technology Kharagpur Discussion: Meet the speakers and discussion of outstanding questions	Computer Training Lab and Courtyard Room A & B
17:00 – 17:25	Coffee break	In front of Courtyard Room A & B
17:25 – 18:10	Lecture: Super-resolution high-trhoughput imaging methods Edouard Unterauer – Max Planck Institute of Biochemistry, Germany	Courtyard Room A & B
18:10 – 19:00	Bus to restaurant over ISG Hotel	EMBL bus stop
19:00 – 22:00	Dinner and Bowling night	Firebowl Heidelberg

Time	Session	Location
08:40 – 08:50	Bus from hotel to EMBL ATC Entrance
08:50 – 09:00	Overview of the day Elisabeth Zielonka – EMBL Heidelberg, Germany	Courtyard Room A & B
09:00 – 10:15	Practical: ISH image analysis Basics ISH image processing and analysis (continued) Imre Gaspar – Turbine.ai, Hungary Mainak Bose – Indian Institute of Technology Kharagpur Jeet Banerjee – Indian Institute of Technology Kharagpur Discussion: Meet the speakers and discussion of outstanding questions	Computer Training Lab and Courtyard Room A & B
10:15 – 10:30	Coffee break	In front of Courtyard Room A & B
10:30 – 12:00	Practical: ISH image analysis Basics ISH image processing and analysis (continued) Imre Gaspar – Turbine.ai, Hungary Mainak Bose – Indian Institute of Technology Kharagpur Jeet Banerjee – Indian Institute of Technology Kharagpur Discussion: Meet the speakers and discussion of outstanding questions	Computer Training Lab and Courtyard Room A & B
12:00 – 13:00	Lunch	EMBL canteen
13:00 – 15:30	Group work: Participants preparing group presentations supported by trainers with concurrent coffee break	Courtyard Room A & B
15:30 – 16:30	Discussion: Group Data Presentations incl. discussions with concurrent coffee break	Courtyard Room A & B
16:30 – 17:00	Wrap up and feedback	Courtyard Room A & B
17:00 – 17:45	Bus to ISG Hotel, Heidelberg Train station and city centre	EMBL bus stop

Time	Session	Location
14:00 – 16:00	Discussion on the course knowledge implementation in the home laboratories and potential questions and challenges.	Online

The course is limited to 16 participants. For selection purposes, please note that your application will not be considered without a letter of motivation.

Registration fees

Your registration for the event includes:

• Admission to the event
• Possibility to submit an abstract (if applicable)
• Meals and coffee breaks
• Course materials
• Access to the e-learning platform
• A letter to support your visa application (for more information, check the ‘Travel and accommodation’ tab)

For this EMBO course, the fees include accommodation and transportation to and from the ISG Hotel to the venue

Academia	€550
PhD Student	€550
Industry	€1000

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.

Cancellation policy

If you are no longer able to take part in the course, please inform your course contact responsible for this event. Your registration and the submitted motivation letter will be deleted.

Please also check our Terms and Conditions for the cancellation policy.

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

1. Include your relevant skills, experience and qualifications showing why you would be suitable for the course.
2. 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 2,000 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.

Please note it is not possible to apply after the motivation letter deadline!

Selection

The selection results will be announced by email to all applicants. We aim to announce 3 weeks (21 days) after the motivation letter submission deadline but delays may occur.

Further details

For further information about registration and motivation letter submission please refer to the FAQ page.

Financial assistance

Limited financial assistance is provided by the EMBL Advanced Training Centre Corporate Partnership Programme and EMBO in the form of travel grants, childcare grants, and accessibility grants.

Your place in the meeting is only confirmed by paying the registration fee, which is mandatory even when receiving a fee waiver.

Travel grant

The travel grant will cover the cost of travel (airfare, train, bus, taxi, and 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.

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. Receipts must be provided via email with your signature for all costs incurred within two months of completion of travel.

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, child-care facility, or 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

EMBO accessibility grant

For EMBO Practical Course participants with accessibility needs, there is the possibility to apply for an accessibility grant to offset costs incurred by participants or speakers when participating at a course. Eligible costs include costs incurred for equipment or adaptations to the course environment, or travel costs for an event companion to assist the participant or speaker during the course where necessary. While we do our best to accommodate needs, please note that extensive changes to the course environment might not be possible. Priority will be given to early-stage researchers.

A maximum amount of €500 can be awarded per participant applying for an EMBO accessibility grant. In order to apply for this grant for EMBO Practical Courses, you must be registered by the application deadline. 

Application

You may apply for financial assistance when submitting your motivation letter. In the application system, you will be asked which type of grant you want to apply for.

Applications for financial support will not influence the outcome of the selection results.

Results

Grant allocations are announced by email to all applicants after the selection results.

Selection for financial assistance 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.

Please note that for childcare grants, 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.

Visa

We can send you a registration confirmation to support your visa procedure (not an official invitation letter). Please contact the Conference Officer responsible for your event. Read our FAQ for more information.

Travel

If you are travelling to Heidelberg via aeroplane, train, car, or long-distance bus, you can find useful information on our travel information page.

Accommodation

Accommodation in twin rooms, including breakfast is also part of the registration fee. Accommodation will be booked for the selected participants at the ISGHotel for the default dates of Saturday, 25 September to Friday, 1 October 2027.

In case you would like to have a single room, please let the hotel know and please note that you will be required to pay a surcharge per night (availability of single rooms may be limited). This should be paid by you directly to the ISGHotel during your stay.

We recommend that all course participants stay at the ISG Hotel for the course.

Please note that as of 1 October 2025, Heidelberg City Council is introducing an overnight stay tax for tourists visiting Heidelberg (including work related trips). The cost will be 3.50 EUR per night for the first five nights of a consecutive stay and will be added to the hotel’s nightly rate. Please contact the individual hotel directly if you have any questions.

Local transportation

Course shuttle buses

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.

Other local transportation

In addition to the shuttle busses, there is also the public bus 28 that serves the EMBL campus and taxis can be easily booked at any time. For more information, please refer to the local transportation (RNV) website.

You may also walk from the ISG Hotel to EMBL (takes up to 30 minutes)

Map to walk from ISG Hotel to EMBL

Further details

Address: EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany

For more information about accommodation and travel, please refer to the FAQ page.

Here you will find useful information for when you are onsite at the event.

Catering

All meals and coffee breaks are included in the registration fee. Our catering staff will prepare a 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 computer training lab or wet labs.

Internet

Wi-Fi is available on campus 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.

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.

Charging stations

There are lockers available next to the stairs leading down into the Auditorium. You will find some of those equipped with sockets to charge your smartphone/tablet etc.

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.

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.

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 course.

Lost and found

‘’Lost and Found’’ items are kept at the registration desk until the end of the course.

Nursing room

There is a nursing room available in the ATC Rooftop Lounge on level A29.

Room for prayers, meditation, and yoga

There is a room for prayer, yoga, and meditation, located on level E0 behind the Auditorium. Please be respectful of others using the room.

EMBL campus map

Health and safety notes

Please take a moment to read our health and safety policy.

• Do not smoke in any EMBL building.
• Eating and drinking is prohibited in the Auditorium and 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.
• Be prepared to answer the following questions: 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

The Heidelberg University Hospital or ‘Universitätsklinikum‘ has a 24 hour accident and emergency facility and is at ‘Im Neuenheimer Feld 672’. It is a 8km or a 20 minute taxi ride away from EMBL. In a medical emergency, the ambulance service generally transports patients to this hospital.

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.

The EMBL course and conference office team are able to advise you on where to turn for emergency or non-emergency medical treatment in Heidelberg and can assist you in making appointments and / or arranging transport to get to the pharmacy or a doctor of your choice if necessary. Please note, we are not however permitted to personally accompany you off-campus.

Sightseeing

A variety of activities in Heidelberg can be found on the website of Heidelberg Marketing.

Technical requirements

Below you will find the software and technical requirements for this course. You will need admin rights to be able to install the software on your computer and we recommend you try this before the course. If you do not have admin rights, please contact your technical support team in advance to make sure the software can be installed.

Software requirements will be shared in due course.

Additional software

The EMBL eCampus learning platform will be used to collaborate, communicate and network with all of the course participants. All participants will receive information on how to join shortly before the course. We recommend using Chrome, Safari or Mozilla Firefox browsers for eCampus. 

Zoom will be used for the live talks and Q&A sessions. More information will be provided closer to the start of the course.

Other information

While using the software during the course, please make sure you have nothing else using your bandwidth. We recommend using a wired connection.

Please find additional information including FAQs and terms and conditions on our Information for Participants page.