Lecture

From Intensities to Objects Introduction

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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 introduces segmentation techniques, including converting intensity images to binary, cleaning binary images, and labeling objects. Classic segmentation methods, morphological filters, and object measurements generation are explained, along with their pros and cons.

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

Related concepts (9)

Image segmentation

In and computer vision, image segmentation is the process of partitioning a into multiple image segments, also known as image regions or image objects (sets of pixels). The goal of segmentation is to simplify and/or change the representation of an image into something that is more meaningful and easier to analyze. Image segmentation is typically used to locate objects and boundaries (lines, curves, etc.) in images. More precisely, image segmentation is the process of assigning a label to every pixel in an image such that pixels with the same label share certain characteristics.

Mathematical morphology

Mathematical morphology (MM) is a theory and technique for the analysis and processing of geometrical structures, based on set theory, lattice theory, topology, and random functions. MM is most commonly applied to s, but it can be employed as well on graphs, surface meshes, solids, and many other spatial structures. Topological and geometrical continuous-space concepts such as size, shape, convexity, connectivity, and geodesic distance, were introduced by MM on both continuous and discrete spaces.

Erosion (morphology)

Erosion (usually represented by ⊖) is one of two fundamental operations (the other being dilation) in from which all other morphological operations are based. It was originally defined for s, later being extended to grayscale images, and subsequently to complete lattices. The erosion operation usually uses a structuring element for probing and reducing the shapes contained in the input image. In binary morphology, an image is viewed as a subset of a Euclidean space or the integer grid , for some dimension d.

Dilation (morphology)

Dilation (usually represented by ⊕) is one of the basic operations in mathematical morphology. Originally developed for , it has been expanded first to grayscale images, and then to complete lattices. The dilation operation usually uses a structuring element for probing and expanding the shapes contained in the input image. In binary morphology, dilation is a shift-invariant (translation invariant) operator, equivalent to Minkowski addition. A binary image is viewed in mathematical morphology as a subset of a Euclidean space Rd or the integer grid Zd, for some dimension d.

Object co-segmentation

In computer vision, object co-segmentation is a special case of , which is defined as jointly segmenting semantically similar objects in multiple images or video frames. It is often challenging to extract segmentation masks of a target/object from a noisy collection of images or video frames, which involves object discovery coupled with . A noisy collection implies that the object/target is present sporadically in a set of images or the object/target disappears intermittently throughout the video of interest.

Related lectures (18)

Morphological Operations MOOC: Image Processing and Analysis for Life Scientists

Covers basic to advanced morphological operations for image analysis workflows.

Image Processing in Fiji

Covers the basics of image processing using Fiji software, focusing on managing files and applying filters.

Image Processing I: Local Normalization and Morphological Operators

Introduces local normalization and morphological operators for shape analysis in image processing.

Image Processing in Python: Manipulation and Convolution Techniques

Introduces image processing techniques in Python, focusing on manipulation and convolution operations using NumPy and Pillow.

From Intensities To Objects: Summary MOOC: Image Processing and Analysis for Life Scientists