Image analysis has become a keystone of the life sciences research. The diversity of imaging modalities and the development of advanced microscopy techniques raised the necessity of image processing and analysis workflows to obtain quantitative results in a feasible way. The Computer Optimized Microscopy workshop provides a series of mixed theoretical and practical sessions aimed to show the image processing workflow needed to extract quantitative information over different basic and advanced microscopy techniques. From beginning to end, a first general view of image processing basics will be followed by a more detailed focusing on specific applications.
The course is aimed at researchers and facility staff members working with digital images obtained by a range of optical microscopy techniques. Although no initial experience in image processing is required it is recommended to have some knowledge of the field.
Language: English.
2 - 6 October 2023.
Facultat de Biologia, Edifici Prevosti, Room IP3
Av. Diagonal, 643. 08028, Barcelona.
Software used: Fiji
General modules:
• Parameters to optimize image acquisition
• Introduction to some Fiji tools
• Image restoration
• Segmentation and binary operations
• Automation of the process: introduction to the imageJ macro language
Specific applications:
• Colocalization of molecules
• Cell tracking
• 3D reconstruction
• FRAP analysis
• High content screening
• Machine/Deep learning
• Macro programming for specific applications
It is necessary for the student to have a personal laptop to carry out the workshop.
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Registration fee: 350€
Registration fee includes admission, workshop materials, social dinner, lunches and coffee breaks.Payment of the registration fee should be done only after acceptance to the course. This will be announced by email 10 days after the closing of pre-registrations.
Motivation letter submission:
Candidates are asked to send a motivation letter (250 words maximum) explaining their background in the field and their interest in this course.
Deadline for registration: July 31st
For more information, please, contact us: com_workshop@ccit.ub.edu
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| Time | Session | Speaker |
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| 09:00 - 9:30h | Welcome | Manel Bosch |
| 09:30 - 11:00h | Optimization of image acquisition | José Manuel Morante |
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| 11:00 - 11:30h | Coffee break | |
| 11:30 - 13:30h | Quantifiable parameters in Fiji | José Manuel Morante |
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| 13:30 - 15:00h | Lunch | |
| 15:00 - 17:00h | Image restoration: Filters | José Manuel Morante |
| 17:00 - 17:30h | Coffee Break | |
| 17:30 - 19:30h | Image segmentation I: Segmentation methods | Manel Bosch |
| Time | Session | Speaker |
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| 09:00 - 11:00h | Image segmentation II: Binary operations | Manel Bosch |
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| 11:00 - 11:30h | Coffee break | |
| 11:30 - 13:30h | 3D Reconstruction | Manel Bosch |
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| 13:30 - 15:00h | Lunch | |
| 15:00 - 17:00h | Introduction to macro language | Gemma Martín/María Calvo |
| 17:00 - 17:30h | Coffee Break | |
| 17:30 - 19:30h | Introduction to macro language | Gemma Martín/María Calvo |
| 21:30 | Social Dinner | |
| Time | Session | Speaker |
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| 09:00 - 11:00h | Colocalization | Manel Bosch |
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| 11:00 - 11:30h | Coffee break | |
| 11:30 - 13:30h | FRAP | Diego Megías |
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| 13:30 - 15:00h | Lunch | |
| 15:00 - 17:00h | Mitochondrial Morphology Analysis | María Calvo |
| 17:00 - 17:30h | Coffee Break | |
| 17:30 - 19:30h | Mitochondrial Morphology Analysis Macro programming | María Calvo |
| Time | Session | Speaker |
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| 09:00 - 11:00h | Cell tracking | Joan Repullés |
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| 11:00 - 11:30h | Coffee break | |
| 11:30 - 13:30h | Organelle Contacts Analysis: ContactJ | María Calvo |
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| 13:30 - 15:00h | Lunch | |
| 15:00 - 17:00h | ContactJ Macro Programming | Gemma Martín |
| 17:00 - 17:30h | Coffee break | |
| 17:30 - 19:30h | MosaicExplorerJ: 3D stitching of TB datasets | Julien Colombelli |
| Time | Session | Speaker |
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| 09:00 - 11:00h | High content screening | Anna Lladó |
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| 11:00 - 11:30h | Coffee break | |
| 11:30 - 13:30h | Machine/Deep learning for HCS | Chong Zhang |
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| 13:30 - 15:00h | Lunch | |
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Organization
Centres Científics i Tecnològics. Universitat de Barcelona.
Coordinator: Manel Bosch. Advanced Optical Microscopy
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Sponsors
 
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 Manel Bosch. Centres Científics i Tecnològics. Universitat de Barcelona. CCiTUB
Maria Calvo. Centres Científics i Tecnològics. Universitat de Barcelona. CCiTUB
Julien Colombelli. Institute for Research in Biomedicine (IRBB)
Anna Lladó. Institute for Research in Biomedicine (IRBB)
Gemma Martín. Centres Científics i Tecnològics. Universitat de Barcelona. CCiTUB
Diego Megías. Instituto de Salud Carlos III
José Manuel Morante. Biotechnology and Biomedicine (BIOTECMED) of the Universitat de València
Joan Repullés. Institute of Agrifood Research and Technology. (IRTA)
Chong Zhang. Institute for Research in Biomedicine (IRBB)
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Registration fee: 350€
Registration fee includes admission, workshop materials, social dinner, lunches and coffee breaks.Payment of the registration fee should be done only after acceptance to the course. This will be announced 10 days after the closing of pre-registrations.
Motivation letter submission:
Candidates are asked to send a motivation letter (250 words maximum) explaining their background in the field and their interest in this course.
Deadline for registration: July 31st
Please, fill out the form to register: Registration Form
For more information, please, contact us: com_workshop@ccit.ub.edu
NOTES: Remember that this is a pre-registration. You will receive a confirmation email 10 days after the closing of pre-registrations indicating if your application is finally accepted or not. Number of seats is limited. The course is subject to the enrollment of a sufficient number of students. The student is not inscribed into the course until the payment is done. In case of cancelling the enrollment by the student, the student has to inform 15 days before the course starts.
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