What are obstacles in the analysis of biological images (compared to other CV)?
nature soft -> no straight lines or harsh corners -> difficult to use SIFT
but images produced for specific purpose -> settings can be easily adjusted
Name image analysis programs with/without GUI, open source/commercial
What is the fourier transformation?
image representation in frequency space
theory: every curve is representable as the integral of several sinus-curves
What is convolution?
most common operation for filter application
pixel-wise calculate sum of pointwise multiplication of filter (kernel) with i mage matrix of surrounding neighboorhoud
What is the Gaussian filter?
suppress unwanted structure -> low pass filter
image appears smoother/blurry
2D sx = sy; 3D sx = sy != sz
What is the Median filter?
for each pixel, pick median value in neighborhood
conserves shaprness
Name reversible and irreversible operations.
reversible - given filtered image and operation applied, original image can be restored
Converting 8-bit image to 16-bit
Changing color space
Gaussian filter
irreversible - Image can not be restored even with exact details of operation
Converting 16-bit image to 8-bit
Decreasing resolution
Median filter
(Almost) Anything you do on the microscope
What is the theory behind deconvolution in microscopy?
image given by microscope is convolution between original object and point spread function
deconvolution = restoration technique
FFT for numerical approximation of PSF
What is the output of intensity transformation?
saturate percentage of pixels by stretching histogram -> contrast enhancement
What is the principle of histogram qualization?
flatten histogram -> enhance hidden structures
CLAHE: clip peaks and distribute it evenly
How does basic edge detection work?
find boundaries based on local intensity change
magnitude: sqrt(dI/dx²+dI/dy²)
gradient direction: arg(dI/dx,dI/dy)
What is image registration?
sample might move or deform between images -> map onto each other
image-based -> minimize error between images
feature-based -> position of given features (ladnmarks) matched
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