14 September - 19 September 2025
Advanced methods in bioimage analysis
Ignacio Arganda-Carreras, Anna Klemm, Perrine Paul-Gilloteaux, Christian Tischer
Description OverviewTrainers speakers staffProgrammePractical informationSponsorsMedia kit Overview This course will take place at EMBL Heidelberg with the option to attend virtually Course overview Bioimage analysis has become a keystone of biological research the deluge of data produced by increasingly advanced microscopes calls for experts able to guide life scientists in the methods and software to be used to produce quantitative knowledge from this data Due to the complexity of the data without such expert guidance it is very likely that image analysis algorithms may be applied incorrectly possibly even producing erroneous results Moreover the diversity of imaging modalities analysis algorithms and software solutions is growing so rapidly that even experts are overwhelmed This advanced course concentrates on teaching cutting edge concepts and tools for quantitative image analysis and will seek to upgrade the competencies of future bioimage analysis experts on both theoretical algorithm advancements as well as on practical implementation skills Audience This course is aimed at early career scientists and staff scientists working in microscopy or image analysis facilities who already have experience in bioimage analysis Moreover participants should already provide or show a clear intent of providing bioimage analysis support to other researchers with less or no experience in bioimage analysis In selecting participants we look for scientific excellence immediate application of the methods learned motivation to disseminate and networking skills We expect a solid background in bioimage analysis and at least basic programming skills Modules resources Image analysis workflow and data management Using AI and natural language processing for image analysis Cells and particles tracking Spatial statistics and omics integration Deep learning for bioimage analysis Image based behaviour modeling Spatial modeling and shape analysis Open science reproducible research and women in science Learning outcomes For each module participants will learn both theoretical and practical aspects of the latest developments in the fields of bioimage analysis concepts and tools After this course participants are expected to be able to confidently operate and interface with a representative selection of open and closed source image analysis software Participants should be able to apply what they have learnt to their own image data as well as to image data of their colleagues What past participants say about the course The EMBL practical course on Advanced Methods in Bioimage Analysis represents a turning point in my career As a Ph D student having the opportunity to meet network and learn with the most experienced researchers in this topic changed how I analyze my images and speed up my image analysis workflows Fernanda Garcia Fossa Institute of Biology University of Campinas This event has been granted the following EMBO sustainability badge Grade 3 of 3 Trainers speakers staff Speakers trainer and staff Philippe Andrey INRAE Versailles France Ignacio Arganda Carreras University of the Basque Country UPV EHU Spain Fynn Beuttenm ller EMBL Heidelberg Germany Beth Cimini Broad Institute USA Robert Haase University of Leipzig Germany Wangjun Hu Heidelberg University Germany Anna Klemm Scilifelab Uppsala University Sweden Nikolai K hler Heidelberg University Germany Anna Kreshuk EMBL Heidelberg Germany Matthew McCormick fideus labs USA Perrine Paul Gilloteaux CNRS UAR BioCore Nantes University France Norman Rzepka scalable minds Germany Suganya Sivagurunathan Scilifelab Uppsala University Sweden Jean Yves Tinevez Institut Pasteur France Pavel Tomancak Max Planck Institute of Molecular Cell Biology and Genetics Germany Christian Tischer EMBL Heidelberg Germany Britta Velten Heidelberg University Germany Carolina W hlby Scilifelab Uppsala University Sweden Virginie Uhlmann University of Z rich Switzerland Kevin Yamauchi ETH Z rich Switzerland Scientific organisers Ignacio Arganda Carreras University of the Basque Country UPV EHU Spain Anna Klemm Scilifelab Uppsala University Sweden Perrine Paul Gilloteaux University of Nantes France Christian Tischer EMBL Heidelberg Germany Course organisers Julia Patricia Nohle Course and Conference Officer EMBL Heidelberg Germany Irena Provaznikova Senior Scientific Training and Digital Learning Manager EMBL Heidelberg Germany Programme Are you on social media Post using EMBOBioImage and don t forget to tag EMBLEvents Please note 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 For registered participants recorded talks will be accessible on demand for 4 weeks after the end of the event unless indicated otherwise Day 0 Onboarding Monday 08 September 2025 Time Europe Berlin SessionLocation14 00 15 00Virtual Onboarding Testrun Zoom testingPre course material material on eCampusOnline Day 1 Sunday 14 September 2025 Time Europe Berlin SessionLocation12 45 13 00Bus from ISG to EMBLISG Hotel13 00 13 30WelcomeWelcome to EMBL House notes safety and course overviewCourtyard Room A B13 30 15 00Networking part 1 Virtual poster sessionGroup sessionsCourtyard Room A B15 00 15 30Coffee breakCourtyard Room A B15 30 17 00Networking part 2 Virtual poster sessionFlash talksCourtyard Room A B17 00 18 00Treasure hunt onsite participants only Courtyard Room A B18 00 19 00DinnerEMBL Canteen19 00 20 00Networking part 3 Virtual poster sessionATC Rooftop Lounge20 00Bus from EMBL to ISG Hotel Day 2 Monday 15 September 2025 Time Europe Berlin SessionLocation08 40 09 00Transport from ISG to EMBL09 00 10 45Overview of the day 5 min Practical session 1 Image Analysis workflow and data managementIncluding Q A on pre recorded lectureVirginie Uhlman University of Z rich Switzerland Assisted by Perrine Paul Gilloteaux CNRS UAR BioCore Nantes University France Christian Tischer EMBL Heidelberg GermanyComputer Training Lab10 45 11 15Coffee break and meet the trainersOutside CTL11 15 13 00Practical session 1 Image Analysis workflow and data management continued Including Q A on pre recorded lecture Virginie Uhlman University of Z rich Switzerland Assisted by Perrine Paul Gilloteaux CNRS UAR BioCore Nantes University France Christian Tischer EMBL Heidelberg GermanyComputer Training Lab13 00 14 00Lunch short walk in the forest optional EMBL Canteen14 00 14 30Lecture 1 Women in sciencePerrine Paul Gilloteaux CNRS UAR BioCore Nantes University France14 30 16 15Practical session 2 Using AI and natural language processing to help image analysisIncluding Q A on pre recorded lecture breaks as needed Led by Robert Haase University of Leipzig Germany Assisted by Ignacio Arganda Carreras University of the Basque Country UPV EHU Spain Christian Tischer EMBL Heidelberg GermanyComputer Training Lab16 15 16 45Coffee break and meet the trainersOutside CTL16 45 18 30Practical session 2 Using AI and natural language processing to help image analysis continued with debrief Led by Robert Haase University of Leipzig Germany Assisted by Ignacio Arganda Carreras University of the Basque Country UPV EHU Spain Christian Tischer EMBL Heidelberg GermanyComputer Training Lab18 30 20 15Pizza Dinner Onsite NetworkingATC Rooftop Lounge20 15Bus from EMBL to ISG Day 3 Tuesday 16 September 2025 Time Europe Berlin SessionLocation08 40 08 55Bus from ISG to EMBL Heidelberg08 55 09 00Overview of the dayCourtyard Room A B09 00 10 45Practical session 3 TrackingIncluding Q A on pre recorded lecture Led by Jean Yves Tinevez Institut Pasteur France Assisted by Ignacio Arganda Carreras University of the Basque Country UPV EHU Spain Perrine Paul Gilloteaux CNRS UAR BioCore Nantes University FranceComputer Training Lab10 45 11 15Coffee breakOutside CTL11 15 13 00Practical session 3 Tracking continued Including Q A on pre recorded lecture Led by Jean Yves Tinevez Institut Pasteur France Assisted by Ignacio Arganda Carreras University of the Basque Country UPV EHU Spain Perrine Paul Gilloteaux CNRS UAR BioCore Nantes University FranceComputer Training Lab13 00 14 00Lunch short walk in the forest optional EMBL Canteen14 00 15 30Practical session 4 Behavior Modeling Led by Kevin Yamauchi Assisted by Ignacio Arganda Carreras University of the Basque Country UPV EHU Spain Perrine Paul Gilloteaux CNRS UAR BioCore Nantes University FranceComputer Training Lab15 30 16 00Coffee break and meet the speakerOutside CTL16 00 16 15Course group photoOutside ATC16 00 18 00Practical session 4 Behavior Modeling continued with debrief Led by Kevin Yamauchi Assisted by Ignacio Arganda Carreras University of the Basque Country UPV EHU Spain Perrine Paul Gilloteaux CNRS UAR BioCore Nantes University FranceComputer Training Lab18 00 18 30Lecture 2 Research Integrity virtual talk Beth Cimini Broad Institute USACourtyard Room A B18 30 20 15Tapas Dinner Onsite NetworkingRooftop Lounge20 15Bus from EMBL to ISG Day 4 Wednesday 17 September 2025 Time Europe Berlin SessionLocation08 40 08 55Bus from ISG to EMBL Heidelberg08 55 09 00Overview of the dayCourtyard Room A B09 00 10 45Practical session 5 Spatial statistics and omics integrationIncluding Q A on pre recorded lecture Led by Britta Velten Heidelberg University Germany Assisted by Anna Klemm Scilifelab Uppsala University Sweden Nikolai K hler and Wangjun Hu Heidelberg University GermanyComputer Training Lab10 45 11 15Coffee break and meet the speakerOutside CTL11 15 13 00Practical session 5 Spatial statistics and omics integration continued Including Q A on pre recorded lecture Led by Britta Velten Heidelberg University Germany Assisted by Anna Klemm Scilifelab Uppsala University Sweden Nikolai K hler and Wangjun Hu Heidelberg University GermanyComputer Training Lab13 00 14 00LunchEMBL Canteen14 00 15 00Keynote lecture Image based exploration of molecular and morphological components of tissueCarolina W hlby Uppsala University SwedenCourtyard Room A B15 00 16 45Round Table discussion Led by Anna Klemm and Suganya Sivagurunathan Scilifelab Uppsala University SwedenCourtyard Room A B16 45 17 00Transport from EMBL to ISGEMBL19 00 19 15Bus from ISG downtownISG19 15 21 30Downtown Heidelberg course dinnerat Oskar Vinothek RestaurantDowntown Day 5 Thursday 18 September 2025 Time Europe Berlin SessionLocation08 40 09 00Bus from ISG to EMBL Heidelberg09 00 10 00Lecture 4 Introduction to working with OME ZarrChristian Tischer EMBL Heidelberg GermanyJosh Moore German BioImaging GermanyCourtyard Room A B10 00 11 00Lecture 5 Software presentation and key challenge subsequent Q ANorman Rzepka scalable minds GermanyCourtyard Room A B11 00 12 00Lecture 6 Open science and bioimage analysis virtual Pavel Tomancak Max Planck Institute of Molecular Cell Biology and Genetics GermanyCourtyard Room A B12 00 13 00LunchEMBL Canteen13 00 14 00Lecture 7 Software presentation and key challenge subsequent Q A virtual Matthew McCormick fideus labs USACourtyard Room A B14 00 15 45Software Practical Work on your own data with Software representativesComputer Training Lab15 45 16 15Coffee break and meet the speakersOutside CTL16 15 18 00Software Practical Work on your own data with Software representativesComputer Training Lab18 00Bus from EMBL to ISGATC Entrance18 30 21 00BBQ and networking at ISG HotelISG Hotel Day 6 Friday 19 September 2025 Time Europe Berlin SessionLocation08 45 09 00Bus from ISG to EMBL Heidelberg09 00 10 45Practical session 6 AI for Life SciencesIncluding Q A on pre recorded lectureLed by Fynn Beuttenm ller EMBL Heidelberg Germany Assisted by Ignacio Arganda Carreras University of the Basque Country UPV EHU Spain Anna Klemm Scilifelab Uppsala University SwedenComputer Training Lab10 45 11 15Coffee break and meet the trainersOutside CTL11 15 13 00Practical session 6 AI for Life Sciences continued Including Q A on pre recorded lecture Led by Fynn Beuttenm ller EMBL Heidelberg Germany Assisted by Ignacio Arganda Carreras University of the Basque Country UPV EHU Spain Anna Klemm Scilifelab Uppsala University Sweden Computer Training Lab13 00 14 00Lunch short walk in the forest optional EMBL Canteen14 00 15 45Practical session 7 Statistical spatial analysis and modeling with BIP Including Q A on pre recorded lecture Led by Philippe Andrey INRAE Versailles France Assisted by Perrine Paul Gilloteaux CNRS UAR BioCore Nantes University France Christian Tischer EMBL Heidelberg GermanyComputer Training Lab15 45 16 00Coffee break and meet the trainersOutside CTL16 00 17 45Practical session 7 continued Statistical spatial analysis and modeling with BIP Including Q A on pre recorded lecture Led by Philippe Andrey INRAE Versailles France Assisted by Perrine Paul Gilloteaux CNRS UAR BioCore Nantes University France Christian Tischer EMBL Heidelberg GermanyComputer Training Lab17 45 18 00Wrap up Course debrief by organizers with discussionCourtyard Room A B18 00Bus downtown and to train station Practical information Registration fees and motivation letter The course is limited to 20 onsite and 6 virtual 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 500PhD Student 500Industry 1100Virtual Academia PhD 190Virtual Industry 250 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 400 for participants travelling to an EMBL Course within Europe up to 1000 for participants travelling to an EMBL Course from outside Europe 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 Application If you are attending virtually you can apply for financial assistance in the submission portal by the abstract deadline Read the instructions on how to apply for financial assistance Only submissions for financial assistance will be accepted Presentation abstracts cannot be submitted here and will be declined In your application you will be asked to summarise your current work answer questions regarding why your lab cannot fund your attendance and how your attendance will make a difference to your career Application for financial support will not affect the outcome of your registration application For some events applications for Childcare Grants will still be done by email Information about the grant will be sent out shortly after the abstract motivation letter deadline Please contact the event Conference Officer if you have any questions 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 ISG Hotel for the default dates of 13 to 19 6 nights 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 an additional cost of 22 50 per night availability of single rooms may be limited This should be paid by you directly to the ISG Hotel during your stay We recommend that all course participants stay at the ISG Hotel 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 Technical requirements and event software 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 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 Virtual participation guidelines Guidelines Do not broadcast the course to unregistered participants Do not share your login details with others You are encouraged to tweet and post about the event Tweet unless the speaker specifically says otherwise but be mindful of unpublished data Please do not capture transmit or redistribute data presented at the meeting Video library of the recorded talks during the event and for 4 weeks afterwards Please note at the request of individual speakers some talks are not recorded Additional information can be found in our Code of Conduct Health and well being It is important to stay healthy and move around especially when you are attending an event virtually We have put together a few coffee break stretches and yoga videos in eCampus for you to enjoy during the event How to ask questions Questions during and after the talks can be asked in the live streaming platform If time runs out or you think of a question later you can use the EMBL eCampus forum or send a direct message to the speaker trainer Time zone The programme is planned based on the Europe Berlin time zone unless otherwise stated As many virtual participants are attending from around the world we do our best to accommodate as many time zones as possible when creating the programme Please take your time zone into consideration when planning your attendance Additional information Please find additional information including FAQs and terms and conditions on our Information for Participants page Sponsors Event sponsors Media partners Microcscopy and Analysis a Wiley journal Sponsorship opportunities We offer a variety of event sponsoring possibilities with the flexibility to select a set sponsorship package or combine individual sponsorship options to suit your event budget Discounts are available for companies sponsoring multiple events at EMBL Heidelberg View other events or contact sponsorship embl de for further information If you are interested in becoming a media partner of this event please visit our media partnerships webpage Request a sponsorship brochure Warning EMBL wishes to warn sponsors of EMBL conferences and courses of fraudulent schemes purporting to offer sponsorship opportunities on behalf of EMBL or affiliated with EMBL officials One current scam campaign of which we are aware is conducted using the name Judy Eastman judy gopcontact a2hosted com and entails approaches to sponsors offering sponsorship opportunities on EMBL s behalf Please be kindly advised that all 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OverviewTrainers, speakers, staffProgrammePractical informationSponsorsMedia kit Overview This course will take place at EMBL Heidelberg, with the option to attend virtually. Course overview Bioimage analysis has become a keystone of biological research: the deluge of data produced by increasingly advanced microscopes calls for experts able to guide life scientists in the methods and software to be used to produce quantitative knowledge from this data. Due to the complexity of the data, without such expert guidance, it is very likely that image analysis algorithms may be applied incorrectly, possibly even producing erroneous results. Moreover, the diversity of imaging modalities, analysis algorithms and software solutions is growing so rapidly that even experts are overwhelmed. This advanced course concentrates on teaching cutting-edge concepts and tools for quantitative image analysis...
EMBO Practical Course
EMBL Heidelberg, Virtual
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