Lecture

Image Filtering: Basics and Techniques

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In course

BIO-695: Image Processing for Life Science

Registration details will be announced via email. It takes place yearly from Sept./October to December & intends to teach image processing with a strong emphasis of applications in life sciences. The idea is to enable the participants to solve image-proces ...

Description

This lecture covers the fundamentals of image filtering, including linear and nonlinear filters, their applications in biological images, and techniques for artifact/noise removal, background subtraction, and feature enhancement. It explains spatial filtering, which manipulates pixel data to improve image aspects like contrast and feature enhancement. The lecture also discusses point operations for modifying pixel values without altering image structure, and provides examples of linear filters such as mean and Gaussian filters. Nonlinear filters like Gaussian and median kernels are explored, along with their applications. The instructor emphasizes the differences between linear and nonlinear filters, highlighting their advantages and performance characteristics.

In MOOC

Image Processing and Analysis for Life Scientists

Nowadays, image-based methods are indispensable for life scientists. Light microscopy especially, has evolved from sketched out observations by eye, to high throughput multi-plane, multi-channel, multi-position and multimode acquisitions that easily produce thousands of information-rich images that must be quantified somehow to answer biological questions. This course will teach you core concepts from image acquisition to image filtering and segmentation, to help you tackle simple image analysis workflows

Instructors (4)

Olivier Burri

Expertise Development of bioimage analysis workflows and algorithms to extract quantitative data from microscopy imagesTools & Software: ImageJ/Fiji, CellProfiler, ilastik, Imaris, Arivis, Matlab, RStudio, IntelliJ, Eclipse, Jupyter NotebooksProgramming languages:Java, Groovy, JavaScript, TypeScript, PHP, Python, R, C, C , Matlab, Bash Expertise Development of bioimage analysis workflows and algorithms to extract quantitative data from microscopy imagesTools & Software: ImageJ/Fiji, CellProfiler, ilastik, I

Arne Seitz

04/1996-06/2000 Scientific co-worker at Philipps-University of Marburg, Dep. of Physical Chemistry 07/2000-10/2002 Post Doc at Max-Planck Unit for Structural Molecular Biology in Hamburg 11/2002-11/2005 Post Doc at European Molecular Biolohy Laboratory (EMBL), Cell Biology and Cell Biophysics Programme 11/2005-03/2009 Staff Scientist at Advanced Light Microscopy Facility, EMBL 04/2009- Head of Bioimaging and Optics platforme (BIOP), Ecole Polytechnique Fédérale de Lausanne (EPFL)

Romain Guiet

Expertise Development of BioImage Analysis workflows and algorithms to extract quantitative data from microscopy images.BioSample Preparation : in vitro cell, organoid, time-lapse, fixation, staining strategies, actin, mitochondria, fluorescent protein expressionBioImage Acquisition : Widefield, Confocal, Whole Slide Imaging, Super-resolution (SIM, STORM, STED), FRET, FRAP, FLIMBioImage Analysis: Colocalisation analysis, Deconvolution, Time-lapse , Whole Slide ImagingTools & Software: ImageJ/Fiji, QuPath, i

Nicolas René Chiaruttini

Official source

Quiz

Ontological neighbourhood

Information engineering

Artificial intelligence: Computer vision

Related concepts (32)

Kalman filter

For statistics and control theory, Kalman filtering, also known as linear quadratic estimation (LQE), is an algorithm that uses a series of measurements observed over time, including statistical noise and other inaccuracies, and produces estimates of unknown variables that tend to be more accurate than those based on a single measurement alone, by estimating a joint probability distribution over the variables for each timeframe. The filter is named after Rudolf E. Kálmán, who was one of the primary developers of its theory.

Median filter

The median filter is a non-linear digital filtering technique, often used to remove noise from an image or signal. Such noise reduction is a typical pre-processing step to improve the results of later processing (for example, edge detection on an image). Median filtering is very widely used in digital because, under certain conditions, it preserves edges while removing noise (but see the discussion below), also having applications in signal processing.

Analogue filter

Analogue filters are a basic building block of signal processing much used in electronics. Amongst their many applications are the separation of an audio signal before application to bass, mid-range, and tweeter loudspeakers; the combining and later separation of multiple telephone conversations onto a single channel; the selection of a chosen radio station in a radio receiver and rejection of others.

Gaussian filter

In electronics and signal processing, mainly in digital signal processing, a Gaussian filter is a filter whose impulse response is a Gaussian function (or an approximation to it, since a true Gaussian response would have infinite impulse response). Gaussian filters have the properties of having no overshoot to a step function input while minimizing the rise and fall time. This behavior is closely connected to the fact that the Gaussian filter has the minimum possible group delay.

Digital filter

In signal processing, a digital filter is a system that performs mathematical operations on a sampled, discrete-time signal to reduce or enhance certain aspects of that signal. This is in contrast to the other major type of electronic filter, the analog filter, which is typically an electronic circuit operating on continuous-time analog signals. A digital filter system usually consists of an analog-to-digital converter (ADC) to sample the input signal, followed by a microprocessor and some peripheral components such as memory to store data and filter coefficients etc.

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