2022/23
336 - Faculty of Medicine and Life Sciences
3362 - Bachelor's Degree in Human Biology
20427 - Diagnostic Imaging
Oriol Gallego Moli, Pablo Guerra Lahoz, Anna Oddone , Xavier Sanjuan Samarra
Contents
Lectures. Duration: 20 hours. All sessions are programmed to have duration equivalent to 50 minutes and will be in-person when possible, otherwise it will be online.
Theme 1. The principle of magnification. (Oriol)
Intro to the subject. Refraction and magnification.
Theme 2. The microscope. (Oriol)
History of the microscopy. Main parts of the microscope and types. Optical aberrations. Limits of light microscopy and biological relevance.
Theme 3. Light microscopy. (Oriol)
Optical lenses, physical principles and functioning. Focal distance and numerical aperture. Contrast: chemical contrast, dyes, and optical contrast.
Theme 4. Fluorescence microscopy I. (Oriol)
Physical principles of the fluorescence. Properties of fluorochromes and fluorescent proteins. Bleaching. Fluorescence microscope and filters.
Theme 5. Resolution. (Oriol)
Resolution: waves diffraction, PSF, Abbe’s formula and numerical aperture.
Theme 6: Integration of concepts I. (Oriol)
Scientific discussion to consolidate theoretical concepts and Kahoot (or similar) test.
Theme 7: From qualitative imaging to quantitative measurements. (Oriol)
The concept of bioimage. ImageJ and Fiji. Bit depth. Brightness and contrast. Look-up tables. Object segmentation.
Theme 8: Image analysis (Oriol)
Pre-processing. Filters. Background subtraction. Automatization.
Theme 9. Optical sectioning I. (Xavi)
Focal plane and confocal microscopy.
Theme 10. Optical sectioning II. (Xavi)
Other techniques for optical sectioning: spinning disk and TIRF/HILO.
Theme 11. Fluorescence microscopy II. (Xavi)
Inverted microscope. Comparative analysis of live-cell imaging and imaging of fixed cells. Time (time-lapse and time scale). Particle tracking.
Theme 12. Fluorescence microscopy III. (Xavi)
X + Y (Automated microscopy/screening microscopy). Depth (Z-stacks, projections, 3D rendering). Colocalization.
Theme 13. Fluorescence microscopy in tissues and animals. (Xavi)
2-photon microscopy. Optical clearing and light-sheet microscopy.
Theme 14. Super-resolution I. (Xavi)
Diffraction limit. PSF engineering and STED microscopy.
Theme 15. Super-resolution II. (Anna)
Photoactivation Light Microscopy and Single Molecule Localization Microscopy (PALM and STORM).
Theme 16. Integration of concepts. (Anna)
Scientific discussion to consolidate theoretical concepts Scientific discussion to consolidate theoretical concepts and Kahoot (or similar) test.
Theme 17. Electron Microscopy. (Pablo)
Structural biology. Comparison of structural biology techniques. Transmission electron microscopy: basic principles. Processing of samples for electron microscopy. Applications of transmission electron microscopy in biomedical sciences.
Theme 18. Cryo-Electron Microscopy. (Pablo)
Basic principles. Single Particles Approximation (SPA):sample preparation and data processing. Cryo-Electron Tomography (cryoET): sample preparation and data processing. Sub-tomogram averaging. Outstanding examples.
Theme 19. Cryo-Electron Microscopy (Pablo). Limitations to high-resolution structure determination. The resolution revolution: instrumental and software improvements. In-cell cryo-electron microscopy. Outstanding examples.
Theme 20. Correlative Microscopy. (Oriol)
Electron microscopy Vs optical microscopy: Correlative Light-Electron microscopy. Main methods of correlative microscopy and examples of applications.
Seminars.
Duration: 8 hours. All seminars will be carried in two sessions of 50 minutes, will be online (synchronic) if necessary and they will be performed in groups of 30 students.
Seminar 1. Pre-processing and Automatization.
Introduction to the project. Group presentation of filters and other pre-processing tools. Automatization of measurements. Discussion of strategies to tackle the project.
Seminar 2. Macro design.
Answering questions and discussion of strategies. Problems solving using computational image analysis.
Seminar 3. Macro troubleshooting
Discussion about problems encountered during the coding of the groups software for automate image analysis.
Seminar 4. Macro presentation
Presentation of the projects developed.
Practices.
Duration: 16 hours. Practices will be in the campus, in groups of about 12 students that will work individually.
Practice 1.1 Microscope manipulation and sample observation.
Duration: 2 hours. Location: Microscopy room.
Goal: Introduction to the employment of optical microscopes.
Development: Each student will have a light microscope to observe histological samples. We will use laser pointers of different wavelength to discuss the functioning of fluorescence filters. At the end of the practice, the student will acquire the skills to design an optimal imaging.
Practice 1.2. Frugal microscopy to study Barcelona’s plankton
Duration: 4 hours. Location: teaching room.
Goal: Learn the basic principles of frugal microscopy and plankton biology
Development: Students, in 2-3 people group, will construct their own microscope Curiosity, a frugal microscope designed for citizen science in the study of plankton. They will collect and analyze plankton samples from Barcelona’s beach.
Practice 2.1. Advanced Imaging.
Duration: 4 hours. Location: Microscopy room. The group of 15 students will be divided into groups of 3 people and visit the Laboratory of Live-cell structural biology.
Goal: Learn the specificities of an advanced fluorescence microscope and to design an imaging experiment.
Development: Students will visit the live-cell structural biology lab, equipped with one of an advanced fluorescence microscope capable of doing live-cell imaging and super resolution microscopy.
Practice 2.2. Computational image analysis.
Duration: 4 hours. Location: Informatics room.
Goal: Quantitative analysis of bioimages using Fiji and iLastik.
Development: Students will use different computational tools to analyze the images obtained in the practices, including Fiji macro language and machine learning.
Practice 3. Electronic microscopy.
Duration: 2 hours. Location: Informatics room
Goal: Cryo-electron microscopy data processing using Relion
Development: Students will carry out an introduction to the use of Relion for cryo-EM structure determination, covering the first steps of single-particle analysis workflow.
Evaluation
The activity is assessed solely on the basis of specific objectives.
Assessment will be by means of multiple choice tests, essay tests, mostly of short answers with objective correction criteria.
Type and number of assessments
During the course assessment will be followed with the Kahoot tool in the theoretical lessons.
Seminars on bioimage analysis will be evaluated as the result of a macro for image analysis to quantify biological features of the sample such as protein expression levels, colocalization, etc. The macro will be developed in small groups. During the last seminar session, each group will present their macro and defend the strategy used. Evaluation will take into account performance of the macro (group mark), the consolidation of concepts by each student (individual defense) and the contribution according to members of the group (individual contribution). “Seminars mark” = Average (“group mark”, “individual defense”, “individual contribution”).
At the end of the teaching process, a final evaluation of the theory will take place, consisting of a multiple choice test with questions on all the subjects covered and an essay test with short questions.
Impact of the various types of assessment on the final accreditive mark
Final assessment: MCT 35%
Test 30%
Assessment during course:
Kahoot 10%
Seminars 25%
Pass criteria and qualitative grades
Student must participate in the programmed activities and obtain a mark of 4 or higher in final assessment (MCT + Test) and 5 or higher in global mark to pass the subject.
Recovery process criteria
Students that after the evaluation process have not passed the subject, have the option of a recovery test of the final evaluation in July. Under no circumstances, the continuous evaluation can be recovered. The student undergoing recovery will keep the mark of the continuous evaluation and this will be computed with the new mark of July with the contingencies described before.