Lecture15 Flashcards
(107 cards)
1
Q
What is the focus of the first part of the lecture?
A
Crossover between optical instruments, microscopes, and computation
2
Q
What is the second part of the lecture about?
A
Visualization techniques, specifically 3D visualization and stereo images
3
Q
What are integrated density measurements used for?
A
To focus on density through two moments, inertia moments
4
Q
What is ratio imaging a form of?
A
Texture analysis
5
Q
What does time lapse imaging add to the analysis?
A
A new dimension
6
Q
What does the overlap coefficient measure?
A
How much channels overlap and share information
7
Q
What are the two types of sampling mentioned for 3D images?
A
- Isotropic sampling
- Anisotropic sampling
8
Q
What are the two strategies for dry field 3D imaging discussed?
A
- Control imaging
- Transmission electron microscopy
9
Q
What technique is used to improve images in computational microscopy?
A
Deconvolution
10
Q
What is the purpose of reconstruction in imaging?
A
To recreate a complete signal from corrupted samples
11
Q
What is the difference between plan parallel sections and axial images?
A
- Plan parallel sections involve cutting samples into thin slices
- Axial images follow the old views in tomography
12
Q
What is the main challenge with serial sectioning?
A
Loss of coherence and potential deformation of the signal
13
Q
What does 3D voxel image represent?
A
A volumetric representation reconstructed from images
14
Q
What is the main difference between optical tomography and electron tomography?
A
Optical tomography can do a full 360-degree rotation while electron tomography cannot
15
Q
What is required for successful registration in image reconstruction?
A
Minimization of translation and rotation variances
16
Q
What is implicit knowledge in the context of reconstruction?
A
Knowledge that is assumed based on the sequence or order of images
17
Q
What role does the point spread function play in deconvolution?
A
It helps to estimate and improve the representation of the image
18
Q
What can cause deformation in samples during sectioning?
A
- Thickness of the slice
- Preparation techniques
19
Q
What is the outcome of proper registration of section images?
A
A volume image composed of registered section images
20
Q
What is a common model system used for imaging in this context?
A
Zebrafish
21
Q
Fill in the blank: The main output of a series of images is a _______.
A
3D image
22
Q
True or False: Deconvolution can be performed without any prior knowledge about the noise.
A
False
23
Q
What is the significance of annotations in volumetric models?
A
They allow for detailed analysis and labeling of structures within the model
24
Q
What is the age of the zebrafish mentioned?
A
48 hours old
25
What model is started with in the annotation process?
Gray value voxel model
26
What kind of model is obtained after annotations?
Annotated labeled voxel model
27
What is one downside of serial sectioning?
It is invasive and may cause deformation
28
What does serial sectioning require in terms of skill?
Manual dexterity
29
What should not be done before performing serial sectioning?
Do not do it after a weekend of partying
30
What is the older strategy mentioned for imaging?
Tomography
31
What type of microscopy is discussed as being non-invasive?
Light microscopy
32
Who was the Czech mathematician related to the mathematical foundation of tomography?
Johan Radon
33
What technique is related to the mathematical foundation for tomography?
Radon transformation
34
Which two individuals worked on the development of CAT scans?
Cormack and Hounsfield
35
What does the radon transformation relate to in mathematical terms?
Fourier transform
36
What is the discrete form of the radon transformation called?
Cynogram
37
What is the purpose of back projection in imaging?
To reconstruct a 3D image from projections
38
What is the effect of the number of projections on image reconstruction?
More projections lead to better reconstruction
39
What type of projection is used in optical projection tomography?
Optical projection using visible light
40
What is the purpose of using a stepper motor in the imaging setup?
To rotate the sample for projections
41
What is the benefit of using fluorescent channels in imaging?
To analyze gene expression
42
What must be matched to ensure effective imaging?
Refraction of the solution and embedding material
43
What is the typical size range for specimens in optical projection tomography?
Half a millimeter to one centimeter
44
What is important for achieving good projections in imaging?
Transparency of the sample
45
What happens to the image quality with smaller angular steps in projections?
Image quality improves with smaller angular steps
46
What is the primary purpose of creating a cynogram from projections?
To compute the back projection for visualization
47
Fill in the blank: The integration of projections is part of the _______ process.
Reconstruction
48
True or False: Serial sectioning is non-invasive.
False
49
What is produced from a tomogram?
Cynogram
## Footnote
A cynogram is a representation used in back projection from a tomogram.
50
How many images are produced from a full revolution with 400 views at 0.8 degrees each?
400 images
51
What determines the number of cynograms?
Height of the OPD images
52
What is the relationship between the width of the cynogram and OPD images?
The width of the cynogram is the width of the OPD images.
53
What is a voxel image?
A representation of a 3D volume in imaging.
54
What is the significance of the delta phi in the cynogram?
It represents the consistent angle steps during the imaging process.
55
What is the camera specification mentioned?
1000 by 3200, 16 bit image
56
What is the purpose of back projection in this context?
To reconstruct a slice from multiple projections.
57
What is a typical example of a reconstructed image mentioned?
A reconstructed 3D volume of a zebrafish.
58
What does single particle analysis involve?
Sorting orientations of particles for reconstruction.
59
What is a typical tilt range for electron tomography?
Plus and minus 70 degrees.
60
What does cryo-EM stand for?
Cryo-electron microscopy.
61
What does the acronym 'LPT' refer to in imaging contexts?
Optical Projection Tomography.
62
Fill in the blank: The technique used to analyze macromolecular complexes and organelles is called _______.
Electron tomography.
63
What is a common application of magnetic resonance microscopy?
Imaging small animals.
64
What is the function of the swim bladder in the zebrafish?
It is filled with air and serves buoyancy.
65
What is the importance of deconvolution in computational microscopy?
To improve image resolution and clarity.
66
What does the term 'whole slide imaging' refer to?
A method to capture high-resolution images of entire histological slides.
67
True or False: Optical tomography is generally non-invasive.
True
68
What is the main difference between Optical tomography and Electron microscopy?
Optical tomography is non-invasive, while Electron microscopy is invasive.
69
What is the role of software like Eman in structural biology?
To assist in sorting orientations and performing back projections.
70
What does the term 'projection' mean in the context of tomography?
A 2D representation derived from a 3D structure.
71
What imaging technique is described as having a strong magnetic field for small animal imaging?
Magnetic Resonance Microscopy.
72
What kind of reconstruction is performed from plant parallel sections?
3D volume models.
73
What is deconvolution in microscopy?
Deconvolution is the process used to reverse the effects of convolution in imaging, aiming to restore the original image from a blurred one.
74
What is the purpose of whole slide imaging?
Whole slide imaging allows pathologists to view entire biopsies at once, facilitating simultaneous examination by multiple observers.
75
How does deconvolution improve microscopy images?
Deconvolution enhances image quality by correcting blurriness and noise, enabling clearer visualization of details.
76
What is convolution in the context of microscopy?
Convolution refers to the process of combining an image with a point spread function to produce a blurred output.
77
What is a point spread function?
A point spread function characterizes how a lens captures light from a point source, affecting the resulting image quality.
78
What types of microscopy commonly use deconvolution?
Deconvolution is typically used in fluorescent microscopy, wide field, confocal, and two-photon microscopy.
79
What is the modulation transfer function?
The modulation transfer function describes the response of an imaging system to different spatial frequencies, indicating its resolution capabilities.
80
True or False: Deconvolution can be performed simultaneously across multiple channels in microscopy.
False. Deconvolution is performed channel by channel.
81
Fill in the blank: Deconvolution is often used to correct _______ and _______ in microscopy images.
[blur], [noise]
82
What does a good point spread function look like in the xy and z planes?
A good point spread function appears as a clear diffraction pattern in the xy plane and two cones in the z direction.
83
What is the significance of the signal-to-noise ratio in microscopy?
A high signal-to-noise ratio is crucial for obtaining clear images and effective deconvolution.
84
What happens if the signal-to-noise ratio is poor?
A poor signal-to-noise ratio can lead to suboptimal deconvolution results, making it difficult to distinguish features in the image.
85
What is the Nyquist criterion in microscopy?
The Nyquist criterion states that sampling frequency must be at least twice the highest frequency present in the image to avoid aliasing.
86
What technology has improved the deconvolution process in microscopy?
The availability of GPUs has significantly enhanced the speed and efficiency of the deconvolution process.
87
What is the iterative process in deconvolution?
The iterative process in deconvolution involves making successive approximations to improve the quality of the image until a convergence criterion is met.
88
What is the role of scientific volume imaging in deconvolution?
Scientific volume imaging develops software for performing deconvolution on confocal images, facilitating improved image analysis.
89
What does the term 'blur' refer to in microscopy?
Blur refers to the loss of detail in an image caused by optical limitations or improper focus.
90
What are some challenges in dealing with glare and scatter in microscopy?
Glare and scatter are difficult to correct and can significantly impact the quality of the acquired images.
91
What is the advantage of confocal microscopy compared to biofield microscopy?
Confocal microscopy provides an improved signal and better image quality
## Footnote
It allows for clearer separation of different spots in the image.
92
What is simulated emission depletion microscopy known for?
It offers even better separation of different spots in the image compared to confocal microscopy
## Footnote
The preparation and imaging setup are different but achieve similar outcomes.
93
What is the purpose of deconvolution in microscopy?
Deconvolution improves image quality by reducing noise and enhancing the signal
## Footnote
It can be applied to various microscopy techniques.
94
How is a whole slide image created in high-resolution microscopy?
By scanning the whole slide at different magnifications and stitching together multiple images
## Footnote
This process results in a single high-resolution image.
95
What role do pathologists play in utilizing high-resolution monitors?
They assess scanned images of tissues, such as hearts, to identify abnormalities
## Footnote
This often involves using two monitors for detailed analysis.
96
What is the significance of scanning at different levels of resolution?
It allows for detailed examination of tissue sections at various scales
## Footnote
This includes full resolution and reduced resolutions for comparative analysis.
97
What is histology and how does it relate to microscopy?
Histology involves making tissue sections for microscopic examination
## Footnote
It is invasive and requires staining to obtain useful information.
98
What is the purpose of using different stains in histological analysis?
To identify specific cells or abnormalities, such as carcinogenic cells
## Footnote
Pathologists often use various probes for targeted analysis.
99
What is the importance of 3D visualization in microscopy?
It helps in understanding the spatial relationships and structures within tissues
## Footnote
Visualization techniques include intensity projections and volume rendering.
100
What are isosurfaces in 3D imaging?
They represent surfaces connecting points of equal value in a 3D space
## Footnote
Typically obtained using the marching cubes algorithm.
101
How does maximum intensity projection work in microscopy?
It retains the highest value from multiple slices to create a composite image
## Footnote
This technique enhances depth perception in the resulting image.
102
What is the purpose of using simulation in fluorescence microscopy?
To visualize the excitation and emission characteristics of fluorophores
## Footnote
This includes accounting for shadowing effects from light direction.
103
What does the term 'volume rendering' refer to?
A technique used to visualize 3D volumes by representing data in three dimensions
## Footnote
It combines various imaging data for comprehensive analysis.
104
What are the typical visualization strategies used in microscopy?
Intensity projections, volume rendering, isosurfaces, and stereo visualization
## Footnote
Each method provides unique insights into the sample being analyzed.
105
What is the role of annotation in microscopy imaging?
To highlight specific features or areas of interest within the image
## Footnote
This aids in better understanding and communication of findings.
106
What is the significance of high-resolution imaging in studying infections?
It allows researchers to observe the effects of infections on tissues in detail
## Footnote
For example, observing granulomas in infected zebrafish.
107
Fill in the blank: The whole slide imaging process requires _______ to create a single high-resolution image.
multiple images
