Image Analysis PDF

Image Analysis Oriol Gallego: [email protected] Where to find me: PRBB, lab 367 (3rd floor) Image Analysis Goals of the course: - Fundamental concepts in optical microscopy - Introduction to the main principles of fluorescence micros...

Image Analysis Oriol Gallego: [email protected] Where to find me: PRBB, lab 367 (3rd floor) Image Analysis Goals of the course: - Fundamental concepts in optical microscopy - Introduction to the main principles of fluorescence microscopy - Introduction to the main principles of bioimage - Computational image analysis: FIJI software - Be able to critically design microscopy experiments and ANALYSIS Image Analysis Theoretical classes (6h): Oriol Gallego Include “Integration of concepts” classes: Kahoot (10% final mark) + discussion Seminars (8h): Trifone Pastore ([email protected]) 6h of content, 2h of troubleshooting and 10’ individual presentation Exercises of image analysis (recommended to bring your laptop) Software for automated image analysis: Download Fiji: https://fiji.sc Deadline: 24th November: Practicals (4h): Xavi Sanjuan ([email protected]) Image Analysis Evaluation Cell Biology (Berta Alsina): 60% Image Analysis (Oriol Gallego): 40% Kahoot (No reassessment possible): 10% Final assessment: Final exam 20% ≥4 ≥5 Macro (No reassessment possible): 70% “Macro grade” = “group”(30%) + “individual defense”(40%) + “individual contribution”(30%) Image Analysis Theme 1: the bioimage Light: Refraction It is a good trick to play with small (or not that small) kids! Image Analysis Theme 1: the bioimage Light What is light? Light is and electromagnetic wave (radiation) A wave is a periodic oscillation by which energy is transmitted through space. Waves can be defined by:  Amplitude Wavelength (=1/f) Phase (fraction of the cycle covered) Phase Image Analysis Theme 1: the bioimage Light What is light? Visible light is the range of wavelength that human eye can detect Image Analysis Theme 1: the bioimage Light What is a photon? Massless particle that carry the smallest unit of energy from a given electromagnetic wave: wave-particle duality As they are massless, photons can propagate in vacuum at 300,000,000 m/s (other waves such as sound cannot do that!) A photon can transfer its energy to another particle such as molecules during an interaction. Depending on the photon’s energy (determined by its wavelength) interaction with atoms will be different Image Analysis Theme 1: the bioimage Light Image Analysis Theme 1: the bioimage Light Which is the light that we detect? Image Analysis Theme 1: the bioimage Light How we capture light from a single point Refraction Source of light (reflected or transmited) Without refraction, waves would excite different points in the retina = No image reconstructed Image Analysis Theme 1: the bioimage Light: Refraction Refraction depends on: Change in the velocity of propagation Angle Wavelength Image Analysis Theme 2: the (optical) microscope How we can use lens Image Analysis Theme 1: the bioimage Visualizing objects: more than one point of light Refraction Reconstructed Image Image Analysis Theme 1: the bioimage Light: Refraction in water What happened to the pen? Broken Magnified Image Analysis Theme 1: the bioimage Light: Refraction Why a magnified flower Glass of water acts as a convex lense Image Analysis Theme 1: the bioimage Light: Refraction Glass of water acts as a convex lense Image Analysis Theme 1: the bioimage Light: Refraction More about light and refractive lenses used in the microscope (not mandatory): https://www.youtube.com/watch?v=vlxMSz7XRys&feature=emb_rel_pause Image Analysis Theme 1: the bioimage Light: Refraction If we move away the eye from the lense, the observed object is inverted Image Analysis Theme 1: the bioimage Myopia: cannot see far objects Source of light (reflected or transmited) Image Analysis Theme 1: the bioimage Hyperopia: cannot see nearby objects Source of light (reflected or transmited)