BS2010: Bioimaging
1
About
1.1
Usage
1.2
Render book
1.3
Preview book
2
History and Introduction of Light Microscopy
2.1
Brief History on Different Microscopes
2.1.1
Magnifying Glasses
2.1.2
Eyeglasses
2.1.3
First Compound Microscope
2.1.4
Galileo Gallei
2.2
Early Microscopists and their Microscopes
2.2.1
Robert Hooke (1653 - 1703)
2.2.2
Antoine van Leeuwenhoek (1632 - 1723)
2.2.3
Comparing Hooke’s and Leeuwenhoek’s Microscopes
2.3
Compound Microscopes as Scientific Instruments
2.3.1
Developments in Microscopes in the Past Century
2.4
Concepts on Light
2.4.1
Wave-Particle Duality of Light
2.4.2
Possible Light Sources in Microscopy
2.4.3
Refractive Indices
2.5
Geometrical Optics
2.5.1
Real versus Virtual Images
2.6
Microscope Principles and Parts
2.6.1
Finite and Infinite Systems
2.6.2
Parts of a Microscope
2.6.3
Optical Trains and Conjugate Plane Sets
2.6.4
Kohler Illumination
2.6.5
Inverted Microscopes
3
Image Formation and Bright-Field Microscopy
3.1
Objective Lens Specifications
3.1.1
Magnification
3.1.2
Aberrations
3.1.3
Other Specifications
3.2
Bright Field Microscopy
3.2.1
Preparing a Sample for Light Microscopy
3.2.2
H&E Staining
3.3
Phase Contrast Microscopy
3.4
Image Formation
3.4.1
Image of a Point Light Source
3.4.2
Rayleigh Criterion
3.4.3
Micoscope Spatial Resolution
3.4.4
Diffraction-Limited Objects
3.4.5
Convolution and Deconvolution
4
WIde-Field Flourescence Microscopy
4.1
What is Fluorescence?
4.1.1
Molecular Explanation of Fluorescence
4.2
Excitation and Emission Spectra
4.2.1
Small Molecule Fluorophores
4.2.2
Fluorescence Labelling Biological Samples
4.2.3
Pros and Cons of Fluorescence Microscopy
4.3
Wide-Field Microscopy
4.3.1
Filters in Epi-Fluorescence Microscopy
4.3.2
Kohler Illumination and Conjugate Planes
4.3.3
Resolution and Image Brightness
4.3.4
Multi-Colored Images
4.3.5
Advantages
5
Confocal and TIRF Microscopy
5.1
Charge Coupled Devices
5.1.1
How do CCDs Work?
5.1.2
CCD Parameters
5.1.3
Noises in CCD Images
5.2
Confocal Microscopes
5.2.1
Scanning Mechanisms of Confocal Microscopes
5.2.2
Features of the Confocal Microscope
5.2.3
Image Acquisition
5.2.4
Pros and Cons
5.3
Objective-Based TIRFM
5.3.1
Total Internal Reflection
5.3.2
Evanescent Field
5.3.3
Basic Approaches to TIRFM
6
Super-Resolution and F-Techniques
6.1
Approaches for Super-Resolution Microscopy
6.1.1
Concepts Behind Single Molecule Localization Super-Resolution Microscopy
6.1.2
Inner Workings of PALM and STORM
6.2
FRAP, FLIP, FRET, and FLIM
6.2.1
FRAP
6.2.2
FLIP
6.2.3
FRET
6.2.4
FLIM
7
Image Acquisition and Manipulations
7.1
Digital Imaging
7.1.1
Dyanmic Ranges in Imaging
7.1.2
Image Histograms
7.2
Image Acquisition Types
7.2.1
Storing Image in Right Formats
7.3
Digital Imaging
7.3.1
Nyquist Sampling Theorem
7.3.2
Basic Image Manipulation
7.4
Ethical Guidelines for Manipulating Images
8
Basic Image Analysis
8.1
Colocalization Studies (of Proteins)
8.2
Basic Morphometric Analysis
8.2.1
Measuring Length
8.2.2
Area and Volume
8.3
Image Sementation
8.3.1
Region of Interest (i.e., ROI)
8.4
Example: Image Analysis of Nulcei Using Hoechst33342
8.4.1
Analyzing Nuclei
8.4.2
Segmentation and Generating ROIs
8.4.3
Analyzing Nuclei Number, Size, and DNA Content
9
Electron Microscopy
9.1
SEM and TEM
9.2
Sample Preparation for Room-Temperature TEM
9.2.1
Sectioning
9.2.2
Other Sample Preparation Techniques for a Conventional TEM
9.2.3
Cryo-Fixation
9.3
Protein Localization in Conventional TEM
9.3.1
Immuno-gold EM
9.3.2
APEX2
9.3.3
Some Comparisons Between Immuno-Gold Labeling and Other Staining Techniques
10
Transmission Electron Microscopy
10.1
Missing Wedge Problem and Electron Tomography
10.1.1
Electron Tomography
10.2
3D EM Volume Imaging
10.2.1
Serial Section TEM / SEM
10.2.2
Summary
10.3
Cryo Electron Tomography
in situ
10.3.1
Comparing TEM and Cryo EM
10.4
Correlative Light and Electron Microscopy
10.4.1
3D TEM Imaging in Cell and Structural Biology
11
X-Rays and CT Scans
11.1
Medical Imaging
11.1.1
Imaging Types
11.1.2
Imaging Components and Terms
11.2
Imaging Modalities
11.2.1
X-Rays
11.2.2
X-Ray Computed Tomography (i.e., CT)
12
SPECT and PET Scans
12.1
Nuclear Medicine
12.1.1
Principles
12.1.2
Gamma Cameras
12.1.3
Radiopharmaceuticals
12.2
SPECT
12.2.1
How does SPECT Work?
12.2.2
Comparing SPECT and PET Scans
12.2.3
A Brief Overview on SPECT’s General Workings
12.2.4
SPECT Applications
12.3
PET
12.3.1
How Does a PET Scan Work?
12.3.2
How Does a PET Scan Work in Practice?
12.3.3
Radionuclides and Radiotracers
12.3.4
Chelating Agents
12.3.5
Uses of PET
12.3.6
Cons of PET Scans
13
Magnetic Resonance Imaging
13.1
Background Information for Performing MRI
13.1.1
Hydrogen Atoms
13.1.2
Magnetic Principles
13.1.3
Basic Physics of MRI
13.2
Performing MRI
13.2.1
Factors for Influencing MRI Quality
13.2.2
Kinds of Nuclei for NMR
13.2.3
Use Cases for MRI
13.2.4
Disadvantages of MRI
13.3
Types of MR Images
13.3.1
T
1
and T
2
Relaxation
13.3.2
T1 and T2 Relaxations
13.3.3
MR Image Construction
13.3.4
Contrast in MRI
13.4
MRI Weightings
13.4.1
T
1
Weighting
13.4.2
T
2
Weighting
13.4.3
Differences in T
1
and T
2
Weightings
13.4.4
Proton Density (i.e., PD) Weightings
13.5
Image Formation and Contrast Agents
13.5.1
k-Spaces
13.5.2
MRI Contrast Agents
14
Functional MRI
14.1
Setup of a fMRI
14.1.1
BOLD in fMRI
14.1.2
Hemodynamic Responses
14.2
Pros and Cons of BOLD
14.2.1
Advantages
14.2.2
Disadvantages
14.3
BOLD and Magnetic Susceptibility
14.3.1
Spatial vs. Temporal Resolution
14.3.2
T2* and fMRI
14.4
fMRI Image Acquisition
14.4.1
Shot Trajectories
14.4.2
Acquisition Stages
14.4.3
Limitations in Image Acquisition
14.5
fMRI Experiment Design
14.5.1
Blocked Designs
14.5.2
Event-Related Designs
14.5.3
Mixed Block Event
14.6
fMRI Applications
14.7
EEG fMRI
Published with bookdown
BS2010: Bioimaging
Topic 11
X-Rays and CT Scans