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About event
This comprehensive course is designed specifically for biologists to master cutting-edge image analysis software. It covers both the theory of image processing and its practical applications, focusing on precise and efficient image quantification, segmentation, and visualization techniques. Participants will gain hands-on experience with industry-leading commercial and open-source tools and elevate their data analysis skills to the next level.
The course also introduces the FAIR principles for scientific data and demonstrates effective strategies for data management using the OMERO database.
The course is organized by the Cellular Imaging Core Facility and the Data Management Core Facility of CEITEC MU, in collaboration with the Faculty of Informatics, Masaryk University.
Programme
Tuesday, December 2
- 08:30–09:00 Registration
- 09:00–09:10 Milan Esner: Welcome, course information
- 09:10–10:00 Michal Kozubek: Introduction to image processing and analysis
- 10:00–11:00 Tomáš Svoboda: FAIR, EOSC, Onedata platform for image sharing and its implementation in microscopy core facility
- 11:00–11:15 Coffee Break
- 11:15–11:30 Jaroslav Icha, Bruker: Data managment solution platform HIVE
- 11:30–12:30 Sebastian Beer, Hamamatsu: Detectors in microscopy
- 13:00–14:00 Lunch Break
- 14:15–15:15 Vladimir Ulman: Working with FIJI/ImageJ, Napari
- 15:15–16:00 Vladimir Ulman: Big data plugin in FIJI
- 16:00–16:30 Coffee Break
- 16:30–17:30 Vlada Ulman: AI tools in image processing and analysis
Wednesday, December 3
Imaris/Wojciech Jesionek
- 09:00–09:30 IMARIS presentation
- 09:30–10:00 IMARIS presentation
- 10:00–10:15 Coffee Break
- 10:15–12:00 IMARIS hands on
- 12:15–13:00 Lunch Break
- 13:15–14:15 IMARIS hands on
- 14:15–14:45 IMARIS hands on
- 14:45–15:00 Coffee Break
- 15:00–16:00 IMARIS hands on
- 16:00–17:00 IMARIS hands on
Thursday, December 4
- 09:00–09:45 AIVIA introduction
- 09:45–10:10 Modules and Visualization, AI integration, etc.
- 10:10–10:30 Coffee Break
- 10:30–11:45 AIVIA training with basic data sets, session I (User Interface, Loading data, AI training with Machine Learning Pixel Classifier)
- 12:00–13:00 Lunch Break
- 13:15–15:15 AVIA training with your data sets, session II (CellPose for 2D and 3D segmentation, Charts and Color-Coded views)
- 15:15–15:45 Coffee Break
- 15:45–17:00 Session III: Combine AI with STELLARIS powerful functionalities (TauSense, Rare Event Detection)
- 19:00 Social Dinner
Friday, December 5
Peter Walczysko, OME team
- 09:00–10:00 OMERO introduction
- 10:00–10:30 Coffee Break
- 10:30–11:30 OMERO training session I
- 12:00–13:00 Lunch Break at Campus River
- 13:15–15:15 OMERO training session II
- 15:15–15:45 Coffee Break
- 15:45–17:00 OMERO training session III
Closing remarks, END of the course.
Registration fees
Academic users: 3500 without VAT
Others: 8500 without VAT
Additional information about registration fees will be provided upon confirmation of registration by Tereza Kopřivová (Tereza.Koprivova@ceitec.muni.cz).
