ECE 484 Digital Image Processing Lec 06 - Fourier Transform & Image Sampling
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An End-To-End System for Automatic Characterization of Iba1 Immunopositive Microglia in Whole Slide Imaging
Neuroinformatics (2019) 17:373–389 https://doi.org/10.1007/s12021-018-9405-x ORIGINAL ARTICLE An End-to-end System for Automatic Characterization of Iba1 Immunopositive Microglia in Whole Slide Imaging Alexander D. Kyriazis1 · Shahriar Noroozizadeh1 · Amir Refaee1 · Woongcheol Choi1 · Lap-Tak Chu1 · Asma Bashir2 · Wai Hang Cheng2 · Rachel Zhao2 · Dhananjay R. Namjoshi2 · Septimiu E. Salcudean3 · Cheryl L. Wellington2 · Guy Nir4 Published online: 8 November 2018 © Springer Science+Business Media, LLC, part of Springer Nature 2018 Abstract Traumatic brain injury (TBI) is one of the leading causes of death and disability worldwide. Detailed studies of the microglial response after TBI require high throughput quantification of changes in microglial count and morphology in histological sections throughout the brain. In this paper, we present a fully automated end-to-end system that is capable of assessing microglial activation in white matter regions on whole slide images of Iba1 stained sections. Our approach involves the division of the full brain slides into smaller image patches that are subsequently automatically classified into white and grey matter sections. On the patches classified as white matter, we jointly apply functional minimization methods and deep learning classification to identify Iba1-immunopositive microglia. Detected cells are then automatically traced to preserve their complex branching structure after which fractal analysis is applied to determine the activation states of the cells. The resulting system detects white matter regions with 84% accuracy, detects microglia with a performance level of 0.70 (F1 score, the harmonic mean of precision and sensitivity) and performs binary microglia morphology classification with a 70% accuracy. -
Discrete - Time Signals and Systems
Discrete - Time Signals and Systems Sampling – II Sampling theorem & Reconstruction Yogananda Isukapalli Sampling at diffe- -rent rates From these figures, it can be concluded that it is very important to sample the signal adequately to avoid problems in reconstruction, which leads us to Shannon’s sampling theorem 2 Fig:7.1 Claude Shannon: The man who started the digital revolution Shannon arrived at the revolutionary idea of digital representation by sampling the information source at an appropriate rate, and converting the samples to a bit stream Before Shannon, it was commonly believed that the only way of achieving arbitrarily small probability of error in a communication channel was to 1916-2001 reduce the transmission rate to zero. All this changed in 1948 with the publication of “A Mathematical Theory of Communication”—Shannon’s landmark work Shannon’s Sampling theorem A continuous signal xt( ) with frequencies no higher than fmax can be reconstructed exactly from its samples xn[ ]= xn [Ts ], if the samples are taken at a rate ffs ³ 2,max where fTss= 1 This simple theorem is one of the theoretical Pillars of digital communications, control and signal processing Shannon’s Sampling theorem, • States that reconstruction from the samples is possible, but it doesn’t specify any algorithm for reconstruction • It gives a minimum sampling rate that is dependent only on the frequency content of the continuous signal x(t) • The minimum sampling rate of 2fmax is called the “Nyquist rate” Example1: Sampling theorem-Nyquist rate x( t )= 2cos(20p t ), find the Nyquist frequency ? xt( )= 2cos(2p (10) t ) The only frequency in the continuous- time signal is 10 Hz \ fHzmax =10 Nyquist sampling rate Sampling rate, ffsnyq ==2max 20 Hz Continuous-time sinusoid of frequency 10Hz Fig:7.2 Sampled at Nyquist rate, so, the theorem states that 2 samples are enough per period. -
The Nyquist Sampling Rate for Spiraling Curves 11
THE NYQUIST SAMPLING RATE FOR SPIRALING CURVES PHILIPPE JAMING, FELIPE NEGREIRA & JOSE´ LUIS ROMERO Abstract. We consider the problem of reconstructing a compactly supported function from samples of its Fourier transform taken along a spiral. We determine the Nyquist sampling rate in terms of the density of the spiral and show that, below this rate, spirals suffer from an approximate form of aliasing. This sets a limit to the amount of under- sampling that compressible signals admit when sampled along spirals. More precisely, we derive a lower bound on the condition number for the reconstruction of functions of bounded variation, and for functions that are sparse in the Haar wavelet basis. 1. Introduction 1.1. The mobile sampling problem. In this article, we consider the reconstruction of a compactly supported function from samples of its Fourier transform taken along certain curves, that we call spiraling. This problem is relevant, for example, in magnetic resonance imaging (MRI), where the anatomy and physiology of a person are captured by moving sensors. The Fourier sampling problem is equivalent to the sampling problem for bandlimited functions - that is, functions whose Fourier transform are supported on a given compact set. The most classical setting concerns functions of one real variable with Fourier transform supported on the unit interval [ 1/2, 1/2], and sampled on a grid ηZ, with η > 0. The sampling rate η determines whether− every bandlimited function can be reconstructed from its samples: reconstruction fails if η > 1 and succeeds if η 6 1 [42]. The transition value η = 1 is known as the Nyquist sampling rate, and it is the benchmark for all sampling schemes: modern sampling strategies that exploit the particular structure of a certain class of signals are praised because they achieve sub-Nyquist sampling rates. -
2.161 Signal Processing: Continuous and Discrete Fall 2008
MIT OpenCourseWare http://ocw.mit.edu 2.161 Signal Processing: Continuous and Discrete Fall 2008 For information about citing these materials or our Terms of Use, visit: http://ocw.mit.edu/terms. MASSACHUSETTS INSTITUTE OF TECHNOLOGY DEPARTMENT OF MECHANICAL ENGINEERING 2.161 Signal Processing - Continuous and Discrete 1 Sampling and the Discrete Fourier Transform 1 Sampling Consider a continuous function f(t) that is limited in extent, T1 · t < T2. In order to process this function in the computer it must be sampled and represented by a ¯nite set of numbers. The most common sampling scheme is to use a ¯xed sampling interval ¢T and to form a sequence of length N: ffng (n = 0 : : : N ¡ 1), where fn = f(T1 + n¢T ): In subsequent processing the function f(t) is represented by the ¯nite sequence ffng and the sampling interval ¢T . In practice, sampling occurs in the time domain by the use of an analog-digital (A/D) converter. The mathematical operation of sampling (not to be confused with the physics of sampling) is most commonly described as a multiplicative operation, in which f(t) is multiplied by a Dirac comb sampling function s(t; ¢T ), consisting of a set of delayed Dirac delta functions: X1 s(t; ¢T ) = ±(t ¡ n¢T ): (1) n=¡1 ? We denote the sampled waveform f (t) as X1 ? f (t) = s(t; ¢T )f(t) = f(t)±(t ¡ n¢T ) (2) n=¡1 ? as shown in Fig. 1. Note that f (t) is a set of delayed weighted delta functions, and that the waveform must be interpreted in the distribution sense by the strength (or area) of each component impulse. -
Signal Sampling
FYS3240 PC-based instrumentation and microcontrollers Signal sampling Spring 2017 – Lecture #5 Bekkeng, 30.01.2017 Content – Aliasing – Sampling – Analog to Digital Conversion (ADC) – Filtering – Oversampling – Triggering Analog Signal Information Three types of information: • Level • Shape • Frequency Sampling Considerations – An analog signal is continuous – A sampled signal is a series of discrete samples acquired at a specified sampling rate – The faster we sample the more our sampled signal will look like our actual signal Actual Signal – If not sampled fast enough a problem known as aliasing will occur Sampled Signal Aliasing Adequately Sampled SignalSignal Aliased Signal Bandwidth of a filter • The bandwidth B of a filter is defined to be between the -3 dB points Sampling & Nyquist’s Theorem • Nyquist’s sampling theorem: – The sample frequency should be at least twice the highest frequency contained in the signal Δf • Or, more correctly: The sample frequency fs should be at least twice the bandwidth Δf of your signal 0 f • In mathematical terms: fs ≥ 2 *Δf, where Δf = fhigh – flow • However, to accurately represent the shape of the ECG signal signal, or to determine peak maximum and peak locations, a higher sampling rate is required – Typically a sample rate of 10 times the bandwidth of the signal is required. Illustration from wikipedia Sampling Example Aliased Signal 100Hz Sine Wave Sampled at 100Hz Adequately Sampled for Frequency Only (Same # of cycles) 100Hz Sine Wave Sampled at 200Hz Adequately Sampled for Frequency and Shape 100Hz Sine Wave Sampled at 1kHz Hardware Filtering • Filtering – To remove unwanted signals from the signal that you are trying to measure • Analog anti-aliasing low-pass filtering before the A/D converter – To remove all signal frequencies that are higher than the input bandwidth of the device. -
Lecture 12: Sampling, Aliasing, and the Discrete Fourier Transform Foundations of Digital Signal Processing
Lecture 12: Sampling, Aliasing, and the Discrete Fourier Transform Foundations of Digital Signal Processing Outline • Review of Sampling • The Nyquist-Shannon Sampling Theorem • Continuous-time Reconstruction / Interpolation • Aliasing and anti-Aliasing • Deriving Transforms from the Fourier Transform • Discrete-time Fourier Transform, Fourier Series, Discrete-time Fourier Series • The Discrete Fourier Transform Foundations of Digital Signal Processing Lecture 12: Sampling, Aliasing, and the Discrete Fourier Transform 1 News Homework #5 . Due this week . Submit via canvas Coding Problem #4 . Due this week . Submit via canvas Foundations of Digital Signal Processing Lecture 12: Sampling, Aliasing, and the Discrete Fourier Transform 2 Exam 1 Grades The class did exceedingly well . Mean: 89.3 . Median: 91.5 Foundations of Digital Signal Processing Lecture 12: Sampling, Aliasing, and the Discrete Fourier Transform 3 Lecture 12: Sampling, Aliasing, and the Discrete Fourier Transform Foundations of Digital Signal Processing Outline • Review of Sampling • The Nyquist-Shannon Sampling Theorem • Continuous-time Reconstruction / Interpolation • Aliasing and anti-Aliasing • Deriving Transforms from the Fourier Transform • Discrete-time Fourier Transform, Fourier Series, Discrete-time Fourier Series • The Discrete Fourier Transform Foundations of Digital Signal Processing Lecture 12: Sampling, Aliasing, and the Discrete Fourier Transform 4 Sampling Discrete-Time Fourier Transform Foundations of Digital Signal Processing Lecture 12: Sampling, Aliasing, -
Digital Image Processing
11/11/20 DIGITAL IMAGE PROCESSING Lecture 4 Frequency domain Tammy Riklin Raviv Electrical and Computer Engineering Ben-Gurion University of the Negev Fourier Domain 1 11/11/20 2D Fourier transform and its applications Jean Baptiste Joseph Fourier (1768-1830) ...the manner in which the author arrives at these A bold idea (1807): equations is not exempt of difficulties and...his Any univariate function can analysis to integrate them still leaves something be rewritten as a weighted to be desired on the score of generality and even sum of sines and cosines of rigour. different frequencies. • Don’t believe it? – Neither did Lagrange, Laplace, Poisson and Laplace other big wigs – Not translated into English until 1878! • But it’s (mostly) true! – called Fourier Series Legendre Lagrange – there are some subtle restrictions Hays 2 11/11/20 A sum of sines and cosines Our building block: Asin(wx) + B cos(wx) Add enough of them to get any signal g(x) you want! Hays Reminder: 1D Fourier Series 3 11/11/20 Fourier Series of a Square Wave Fourier Series: Just a change of basis 4 11/11/20 Inverse FT: Just a change of basis 1D Fourier Transform 5 11/11/20 1D Fourier Transform Fourier Transform 6 11/11/20 Example: Music • We think of music in terms of frequencies at different magnitudes Slide: Hoiem Fourier Analysis of a Piano https://www.youtube.com/watch?v=6SR81Wh2cqU 7 11/11/20 Fourier Analysis of a Piano https://www.youtube.com/watch?v=6SR81Wh2cqU Discrete Fourier Transform Demo http://madebyevan.com/dft/ Evan Wallace 8 11/11/20 2D Fourier Transform -
Adaptive Sub-Nyquist Spectrum Sensing for Ultra-Wideband Communication Systems †
S S symmetry Article Adaptive Sub-Nyquist Spectrum Sensing for Ultra-Wideband Communication Systems † Yong Lu , Shaohe Lv and Xiaodong Wang * Science and Technology on Parallel and Distributed Processing Laboratory, National University of Defense Technology, Changsha 410073, China; [email protected] (Y.L.); [email protected] (S.L.) * Correspondence: [email protected] † This paper is an extended version of our paper published in 2014 IEEE 17th International Conference on Computational Science and Engineering (CSE), Chengdu, China, 19–21 December 2014. Received: 14 January 2019; Accepted: 3 March 2019; Published: 7 March 2019 Abstract: With the ever-increasing demand for high-speed wireless data transmission, ultra-wideband spectrum sensing is critical to support the cognitive communication over an ultra-wide frequency band for ultra-wideband communication systems. However, it is challenging for the analog-to-digital converter design to fulfill the Nyquist rate for an ultra-wideband frequency band. Therefore, we explore the spectrum sensing mechanism based on the sub-Nyquist sampling and conduct extensive experiments to investigate the influence of sampling rate, bandwidth resolution and the signal-to-noise ratio on the accuracy of sub-Nyquist spectrum sensing. Afterward, an adaptive policy is proposed to determine the optimal sampling rate, and bandwidth resolution when the spectrum occupation or the strength of the existing signals is changed. The performance of the policy is verified by simulations. Keywords: ultra-wideband spectrum sensing; energy detection; cognitive radio; sub-Nyquist sensing; Chinese remainder theorem 1. Introduction After decades of rapid development, wireless technologies have been intensively applied to almost every field from daily communications to mobile medical and battlefield communications. -
Above the Nyquist Rate, Modulo Folding Does Not Hurt
1 Above the Nyquist Rate, Modulo Folding Does Not Hurt Elad Romanov and Or Ordentlich Abstract Q Q m −(R−1) —We consider the problem of recovering a continuous- choice will be xn . After all, xn xn < 2 2 , time bandlimited signal from the discrete-time signal obtained {res } | −m | −R · whereas xn xn can be as large as 2 (1 2 ). However, from sampling it every Ts seconds and reducing the result modulo somewhat| surprisingly,− | this letter shows that− the opposite is ∆, for some ∆ > 0. For ∆ = ∞ the celebrated Shannon- Nyquist sampling theorem guarantees that perfect recovery is true, provided that Ts < 1/2W . In particular, we improve possible provided that the sampling rate 1/Ts exceeds the so- upon the recent results of Bhandari et al. [1] and show called Nyquist rate. Recent work by Bhandari et al. has shown that whenever the sampling frequency exceeds the Shannon- ∆ 0 that for any > perfect reconstruction is still possible if the Nyquist frequency, for any R N, the signal xn can be sampling rate exceeds the Nyquist rate by a factor of πe. In perfectly reconstructed from x∈res . { } this letter we improve upon this result and show that for finite { n } energy signals, perfect recovery is possible for any ∆ > 0 and To be more concrete, the setup we consider is that of any sampling rate above the Nyquist rate. Thus, modulo folding sampling a modulo-reduced signal. For a given ∆ > 0, and does not degrade the signal, provided that the sampling rate a real number x R, we define x∗ = [x] mod ∆ as the exceeds the Nyquist rate. -
Can Compressed Sensing Beat the Nyquist Sampling Rate?
Can compressed sensing beat the Nyquist sampling rate? Leonid P. Yaroslavsky, Dept. of Physical Electronics, School of Electrical Engineering, Tel Aviv University, Tel Aviv 699789, Israel Data saving capability of “Compressed sensing (sampling)” in signal discretization is disputed and found to be far below the theoretical upper bound defined by the signal sparsity. On a simple and intuitive example, it is demonstrated that, in a realistic scenario for signals that are believed to be sparse, one can achieve a substantially larger saving than compressing sensing can. It is also shown that frequent assertions in the literature that “Compressed sensing” can beat the Nyquist sampling approach are misleading substitution of terms and are rooted in misinterpretation of the sampling theory. Keywords: sampling; sampling theorem; compressed sensing. Paper 150246C received Feb. 26, 2015; accepted for publication Jun. 26, 2015. This letter is motivated by recent OPN publications1,2 that Therefore, the inverse of the signal sparsity SPRS=K/N is the advertise wide use in optical sensing of “Compressed sensing” theoretical upper bound of signal dimensionality reduction (CS), a new method of digital image formation that has achievable by means of signal sparse approximation. This obtained considerable attention after publications3-7. This relationship is plotted in Fig. 1 (solid line). attention is driven by such assertions in numerous The upper bound of signal dimensionality reduction publications as “CS theory asserts that one can recover CSDRF of signals with sparsity SSP achievable by CS can be certain signals and images from far fewer samples or evaluated from the relationship: measurements than traditional methods use”6, “Beating 1/CSDRF>C(2SSPlogCSDRF) provided in Ref. -
9. Biomedical Imaging Informatics Daniel L
9. Biomedical Imaging Informatics Daniel L. Rubin, Hayit Greenspan, and James F. Brinkley After reading this chapter, you should know the answers to these questions: 1. What makes images a challenging type of data to be processed by computers, as opposed to non-image clinical data? 2. Why are there many different imaging modalities, and by what major two characteristics do they differ? 3. How are visual and knowledge content in images represented computationally? How are these techniques similar to representation of non-image biomedical data? 4. What sort of applications can be developed to make use of the semantic image content made accessible using the Annotation and Image Markup model? 5. Describe four different types of image processing methods. Why are such methods assembled into a pipeline when creating imaging applications? 6. Give an example of an imaging modality with high spatial resolution. Give an example of a modality that provides functional information. Why are most imaging modalities not capable of providing both? 7. What is the goal in performing segmentation in image analysis? Why is there more than one segmentation method? 8. What are two types of quantitative information in images? What are two types of semantic information in images? How might this information be used in medical applications? 9. What is the difference between image registration and image fusion? Given an example of each. 1 9.1. Introduction Imaging plays a central role in the healthcare process. Imaging is crucial not only to health care, but also to medical communication and education, as well as in research. -
Aliasing, Image Sampling and Reconstruction
https://youtu.be/yr3ngmRuGUc Recall: a pixel is a point… Aliasing, Image Sampling • It is NOT a box, disc or teeny wee light and Reconstruction • It has no dimension • It occupies no area • It can have a coordinate • More than a point, it is a SAMPLE Many of the slides are taken from Thomas Funkhouser course slides and the rest from various sources over the web… Image Sampling Imaging devices area sample. • An image is a 2D rectilinear array of samples • In video camera the CCD Quantization due to limited intensity resolution array is an area integral Sampling due to limited spatial and temporal resolution over a pixel. • The eye: photoreceptors Intensity, I Pixels are infinitely small point samples J. Liang, D. R. Williams and D. Miller, "Supernormal vision and high- resolution retinal imaging through adaptive optics," J. Opt. Soc. Am. A 14, 2884- 2892 (1997) 1 Aliasing Good Old Aliasing Reconstruction artefact Sampling and Reconstruction Sampling Reconstruction Slide © Rosalee Nerheim-Wolfe 2 Sources of Error Aliasing (in general) • Intensity quantization • In general: Artifacts due to under-sampling or poor reconstruction Not enough intensity resolution • Specifically, in graphics: Spatial aliasing • Spatial aliasing Temporal aliasing Not enough spatial resolution • Temporal aliasing Not enough temporal resolution Under-sampling Figure 14.17 FvDFH Sampling & Aliasing Spatial Aliasing • Artifacts due to limited spatial resolution • Real world is continuous • The computer world is discrete • Mapping a continuous function to a