FAFF20: Multispectral Imaging From astronomy to microscopy Stefan Kröll, Johan Axelsson Atomic Physics, LTH
Multispectral = many spectral bands Each pixel contains a spectrum
Spectral bands from the electromagnetic spectrum
Aim The aim of the course is to provide theoretical and practical knowledge on the generation of and information extraction from multi-spectral images in different wavelength regions and on different spatial scales. Basic knowledge on image processing should be attained.
Learning outcomes Knowledge and understanding For a passing grade the student must understand how techniques, common to all fields can be used to extract physical and chemical information from images have a basic knowledge on how spectroscopy allows to characterize materials and phenomena have basic knowledge on image analysis and multi-variate methods
Learning outcomes Competences and skills For a passing grade the student must be able to assess which spectral region is useful for a particular task be able to assess which characteristics are useful for a definite characterization of an image pixel be able to work with image analysis tools have an increased competence for presenting in writing an accomplished project have an increased experience in working in groups of two or four persons towards a common goal have improved knowledge on how to extract relevant data from literature references (project).
Learning outcomes Judgement and approach For a passing grade the student must be able to judge the power of multispectral imaging techniques to extract physical and chemical information from images recorded in different wavelength bands.
Examination Written exam, graded 0-6 where the requirement for pass is the grade 3. Compulsory laboratory exercises Digital Imaging Fluorescence Imaging Microscopy computer exercise Optional home assignments where each assignment can award up to 0.15 credit on the final exam. There are four assignments.
Course schedule
Spectral bands from the electromagnetic spectrum
Interactions between electromagnetic radiation and sample Electromagnetic radiation transfers energy Sample is composed of atoms, molecules By examining the resulting electromagnetic radiation after it has intracted with the sample - conclusions can be drawn about the object under study
Interactions between energy levels Absorption E 2 E 1 Emission E 2 E 1 Stimulated emission E 2 E 1
Basic arrangement for Multispectral imaging Source Sample Analyzer Detector Sun Lamps Lasers LEDs Synchrotron X-ray tube Plants Forests Tissue Cells Flames Chemical compounds etc. etc. Filters Spectrometers Monochromators Photodiodes Photomultiplier tubes CCD cameras CMOS cameras Image intensifiers
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Microscopic imaging Example: Zebra fish brain with Light Sheet Microscope
Microscopic imaging: computer exercise
Microscopic imaging: computer exercise
Course schedule
PIXE Particle Induced X-ray Emission or Proton Induced X-ray Emission X-ray production crosssection is high for protons with a few MeV (~3 MeV). By directing a proton beam towards a sample very sensitive elemental analysis can be performed.
PIXE Particle Induced X-ray Emission or Proton Induced X-ray Emission
PIXE Hair follicle from Tycho Brahe
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Combustion diagnostics: Laser-induced fluorescence Energy S 2 S 1 5 4 3 2 1 0 5 4 3 2 1 0 Absorption Vibrational relaxation Fluorescence S 0 5 4 3 2 1 0
Combustion diagnostics: Laser-induced fluorescence
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Medical optical imaging: UV-VIS-IR
Medical imaging: Optical imaging absorption of light
Optical tomography of tissue chromophores 25 40 74 82 50 80 0 1000 0.5E15 4E15 Hemoglobin SO2 Water Scatter size Scatter dens.
Medical imaging: Contrast based on fluorescence Energy S 2 S 1 5 4 3 2 1 0 5 4 3 2 1 0 Absorption Vibrational relaxation Fluorescence S 0 5 4 3 2 1 0
Fluorescence guided cervical tumor resection
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Active remote sensing
Active remote sensing
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Supernova 1604 Multispectral (X-ray, optical and infrared) representation of the last supervova and the Milky Way in 1604
Coronal temperature diagnostics derived from multilayer observations with the multi-spectral solar telescope array Paul Boerner Dissertation thesis Stanford University July 2004 Image from the 211 Å Ritchey-Chrétien telescope Image from the 1216 Å Ritchey-Chrétien telescope
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Animal vision
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MRI
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Google Earth
Reflectance from fresh or dry oak leaf Reflectance spectra of leaves will be different dependent on its state
Satellite imaging of forests Photosynthetic activity Average rainfall University of Arizona Terrestial Biophysics and Remote Sensing Lab
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Multivariate analysis Microscopic imaging Microscopy of red blood cells Find which red blood cells that are infected with the malaria parasite
Microscopic imaging R S T
Multivariate analysis PC1 PC2 PC3
Microscopic imaging
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Scanning Probe Microscopy Example: Scanning Tunneling Microscopy
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Home assignments Four home assignments Contrast function (Data analysis lecture) Noise (Data aquisition lecture) Satellite imaging (Satellite imaging lecture) PET/SPECT/X-ray imaging (High-energy imaging lecture)
Laboratory exercises Sign up for the labs during lectures on paper! Hand in lab reports (afterwards) Lab reports should be approved before written exam
Multispectral imaging from radiowaves to gammarays
Multispectral imaging from astronomy to microscopy