Image Segmentation, Registration and Characterization in R with Simpleitk
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Navigating the R Package Universe by Julia Silge, John C
CONTRIBUTED RESEARCH ARTICLES 558 Navigating the R Package Universe by Julia Silge, John C. Nash, and Spencer Graves Abstract Today, the enormous number of contributed packages available to R users outstrips any given user’s ability to understand how these packages work, their relative merits, or how they are related to each other. We organized a plenary session at useR!2017 in Brussels for the R community to think through these issues and ways forward. This session considered three key points of discussion. Users can navigate the universe of R packages with (1) capabilities for directly searching for R packages, (2) guidance for which packages to use, e.g., from CRAN Task Views and other sources, and (3) access to common interfaces for alternative approaches to essentially the same problem. Introduction As of our writing, there are over 13,000 packages on CRAN. R users must approach this abundance of packages with effective strategies to find what they need and choose which packages to invest time in learning how to use. At useR!2017 in Brussels, we organized a plenary session on this issue, with three themes: search, guidance, and unification. Here, we summarize these important themes, the discussion in our community both at useR!2017 and in the intervening months, and where we can go from here. Users need options to search R packages, perhaps the content of DESCRIPTION files, documenta- tion files, or other components of R packages. One author (SG) has worked on the issue of searching for R functions from within R itself in the sos package (Graves et al., 2017). -
Other Departments and Institutes Courses 1
Other Departments and Institutes Courses 1 Other Departments and Institutes Courses About Course Numbers: 02-250 Introduction to Computational Biology Each Carnegie Mellon course number begins with a two-digit prefix that Spring: 12 units designates the department offering the course (i.e., 76-xxx courses are This class provides a general introduction to computational tools for biology. offered by the Department of English). Although each department maintains The course is divided into two halves. The first half covers computational its own course numbering practices, typically, the first digit after the prefix molecular biology and genomics. It examines important sources of biological indicates the class level: xx-1xx courses are freshmen-level, xx-2xx courses data, how they are archived and made available to researchers, and what are sophomore level, etc. Depending on the department, xx-6xx courses computational tools are available to use them effectively in research. may be either undergraduate senior-level or graduate-level, and xx-7xx In the process, it covers basic concepts in statistics, mathematics, and courses and higher are graduate-level. Consult the Schedule of Classes computer science needed to effectively use these resources and understand (https://enr-apps.as.cmu.edu/open/SOC/SOCServlet/) each semester for their results. Specific topics covered include sequence data, searching course offerings and for any necessary pre-requisites or co-requisites. and alignment, structural data, genome sequencing, genome analysis, genetic variation, gene and protein expression, and biological networks and pathways. The second half covers computational cell biology, including biological modeling and image analysis. It includes homework requiring Computational Biology Courses modification of scripts to perform computational analyses. -
Introduction to Ggplot2
Introduction to ggplot2 Dawn Koffman Office of Population Research Princeton University January 2014 1 Part 1: Concepts and Terminology 2 R Package: ggplot2 Used to produce statistical graphics, author = Hadley Wickham "attempt to take the good things about base and lattice graphics and improve on them with a strong, underlying model " based on The Grammar of Graphics by Leland Wilkinson, 2005 "... describes the meaning of what we do when we construct statistical graphics ... More than a taxonomy ... Computational system based on the underlying mathematics of representing statistical functions of data." - does not limit developer to a set of pre-specified graphics adds some concepts to grammar which allow it to work well with R 3 qplot() ggplot2 provides two ways to produce plot objects: qplot() # quick plot – not covered in this workshop uses some concepts of The Grammar of Graphics, but doesn’t provide full capability and designed to be very similar to plot() and simple to use may make it easy to produce basic graphs but may delay understanding philosophy of ggplot2 ggplot() # grammar of graphics plot – focus of this workshop provides fuller implementation of The Grammar of Graphics may have steeper learning curve but allows much more flexibility when building graphs 4 Grammar Defines Components of Graphics data: in ggplot2, data must be stored as an R data frame coordinate system: describes 2-D space that data is projected onto - for example, Cartesian coordinates, polar coordinates, map projections, ... geoms: describe type of geometric objects that represent data - for example, points, lines, polygons, ... aesthetics: describe visual characteristics that represent data - for example, position, size, color, shape, transparency, fill scales: for each aesthetic, describe how visual characteristic is converted to display values - for example, log scales, color scales, size scales, shape scales, .. -
Sharing and Organizing Research Products As R Packages Matti Vuorre1 & Matthew J
Sharing and organizing research products as R packages Matti Vuorre1 & Matthew J. C. Crump2 1 Oxford Internet Institute, University of Oxford, United Kingdom 2 Department of Psychology, Brooklyn College of CUNY, New York USA A consensus on the importance of open data and reproducible code is emerging. How should data and code be shared to maximize the key desiderata of reproducibility, permanence, and accessibility? Research assets should be stored persistently in formats that are not software restrictive, and documented so that others can reproduce and extend the required computations. The sharing method should be easy to adopt by already busy researchers. We suggest the R package standard as a solution for creating, curating, and communicating research assets. The R package standard, with extensions discussed herein, provides a format for assets and metadata that satisfies the above desiderata, facilitates reproducibility, open access, and sharing of materials through online platforms like GitHub and Open Science Framework. We discuss a stack of R resources that help users create reproducible collections of research assets, from experiments to manuscripts, in the RStudio interface. We created an R package, vertical, to help researchers incorporate these tools into their workflows, and discuss its functionality at length in an online supplement. Together, these tools may increase the reproducibility and openness of psychological science. Keywords: reproducibility; research methods; R; open data; open science Word count: 5155 Introduction package standard, with additional R authoring tools, provides a robust framework for organizing and sharing reproducible Research projects produce experiments, data, analyses, research products. manuscripts, posters, slides, stimuli and materials, computa- Some advances in data-sharing standards have emerged: It tional models, and more. -
Rkward: a Comprehensive Graphical User Interface and Integrated Development Environment for Statistical Analysis with R
JSS Journal of Statistical Software June 2012, Volume 49, Issue 9. http://www.jstatsoft.org/ RKWard: A Comprehensive Graphical User Interface and Integrated Development Environment for Statistical Analysis with R Stefan R¨odiger Thomas Friedrichsmeier Charit´e-Universit¨atsmedizin Berlin Ruhr-University Bochum Prasenjit Kapat Meik Michalke The Ohio State University Heinrich Heine University Dusseldorf¨ Abstract R is a free open-source implementation of the S statistical computing language and programming environment. The current status of R is a command line driven interface with no advanced cross-platform graphical user interface (GUI), but it includes tools for building such. Over the past years, proprietary and non-proprietary GUI solutions have emerged, based on internal or external tool kits, with different scopes and technological concepts. For example, Rgui.exe and Rgui.app have become the de facto GUI on the Microsoft Windows and Mac OS X platforms, respectively, for most users. In this paper we discuss RKWard which aims to be both a comprehensive GUI and an integrated devel- opment environment for R. RKWard is based on the KDE software libraries. Statistical procedures and plots are implemented using an extendable plugin architecture based on ECMAScript (JavaScript), R, and XML. RKWard provides an excellent tool to manage different types of data objects; even allowing for seamless editing of certain types. The objective of RKWard is to provide a portable and extensible R interface for both basic and advanced statistical and graphical analysis, while not compromising on flexibility and modularity of the R programming environment itself. Keywords: GUI, integrated development environment, plugin, R. -
An Introduction to Image Analysis Using Imagej
An introduction to image analysis using ImageJ Mark Willett, Imaging and Microscopy Centre, Biological Sciences, University of Southampton. Pete Johnson, Biophotonics lab, Institute for Life Sciences University of Southampton. 1 “Raw Images, regardless of their aesthetics, are generally qualitative and therefore may have limited scientific use”. “We may need to apply quantitative methods to extrapolate meaningful information from images”. 2 Examples of statistics that can be extracted from image sets . Intensities (FRET, channel intensity ratios, target expression levels, phosphorylation etc). Object counts e.g. Number of cells or intracellular foci in an image. Branch counts and orientations in branching structures. Polarisations and directionality . Colocalisation of markers between channels that may be suggestive of structure or multiple target interactions. Object Clustering . Object Tracking in live imaging data. 3 Regardless of the image analysis software package or code that you use….. • ImageJ, Fiji, Matlab, Volocity and IMARIS apps. • Java and Python coding languages. ….image analysis comprises of a workflow of predefined functions which can be native, user programmed, downloaded as plugins or even used between apps. This is much like a flow diagram or computer code. 4 Here’s one example of an image analysis workflow: Apply ROI Choose Make Acquisition Processing to original measurement measurements image type(s) Thresholding Save to ROI manager Make binary mask Make ROI from binary using “Create selection” Calculate x̄, Repeat n Chart data SD, TTEST times and interpret and Δ 5 A few example Functions that can inserted into an image analysis workflow. You can mix and match them to achieve the analysis that you want. -
R Generation [1] 25
IN DETAIL > y <- 25 > y R generation [1] 25 14 SIGNIFICANCE August 2018 The story of a statistical programming they shared an interest in what Ihaka calls “playing academic fun language that became a subcultural and games” with statistical computing languages. phenomenon. By Nick Thieme Each had questions about programming languages they wanted to answer. In particular, both Ihaka and Gentleman shared a common knowledge of the language called eyond the age of 5, very few people would profess “Scheme”, and both found the language useful in a variety to have a favourite letter. But if you have ever been of ways. Scheme, however, was unwieldy to type and lacked to a statistics or data science conference, you may desired functionality. Again, convenience brought good have seen more than a few grown adults wearing fortune. Each was familiar with another language, called “S”, Bbadges or stickers with the phrase “I love R!”. and S provided the kind of syntax they wanted. With no blend To these proud badge-wearers, R is much more than the of the two languages commercially available, Gentleman eighteenth letter of the modern English alphabet. The R suggested building something themselves. they love is a programming language that provides a robust Around that time, the University of Auckland needed environment for tabulating, analysing and visualising data, one a programming language to use in its undergraduate statistics powered by a community of millions of users collaborating courses as the school’s current tool had reached the end of its in ways large and small to make statistical computing more useful life. -
Bio-Formats Documentation Release 4.4.9
Bio-Formats Documentation Release 4.4.9 The Open Microscopy Environment October 15, 2013 CONTENTS I About Bio-Formats 2 1 Why Java? 4 2 Bio-Formats metadata processing 5 3 Help 6 3.1 Reporting a bug ................................................... 6 3.2 Troubleshooting ................................................... 7 4 Bio-Formats versions 9 4.1 Version history .................................................... 9 II User Information 23 5 Using Bio-Formats with ImageJ and Fiji 24 5.1 ImageJ ........................................................ 24 5.2 Fiji .......................................................... 25 5.3 Bio-Formats features in ImageJ and Fiji ....................................... 26 5.4 Installing Bio-Formats in ImageJ .......................................... 26 5.5 Using Bio-Formats to load images into ImageJ ................................... 28 5.6 Managing memory in ImageJ/Fiji using Bio-Formats ................................ 32 5.7 Upgrading the Bio-Formats importer for ImageJ to the latest trunk build ...................... 34 6 OMERO 39 7 Image server applications 40 7.1 BISQUE ....................................................... 40 7.2 OME Server ..................................................... 40 8 Libraries and scripting applications 43 8.1 Command line tools ................................................. 43 8.2 FARSIGHT ...................................................... 44 8.3 i3dcore ........................................................ 44 8.4 ImgLib ....................................................... -
Ilastik: Interactive Machine Learning for (Bio)Image Analysis
ilastik: interactive machine learning for (bio)image analysis Stuart Berg1, Dominik Kutra2,3, Thorben Kroeger2, Christoph N. Straehle2, Bernhard X. Kausler2, Carsten Haubold2, Martin Schiegg2, Janez Ales2, Thorsten Beier2, Markus Rudy2, Kemal Eren2, Jaime I Cervantes2, Buote Xu2, Fynn Beuttenmueller2,3, Adrian Wolny2, Chong Zhang2, Ullrich Koethe2, Fred A. Hamprecht2, , and Anna Kreshuk2,3, 1HHMI Janelia Research Campus, Ashburn, Virginia, USA 2HCI/IWR, Heidelberg University, Heidelberg, Germany 3European Molecular Biology Laboratory, Heidelberg, Germany We present ilastik, an easy-to-use interactive tool that brings are computed and passed on to a powerful nonlinear algo- machine-learning-based (bio)image analysis to end users with- rithm (‘the classifier’), which operates in the feature space. out substantial computational expertise. It contains pre-defined Based on examples of correct class assignment provided by workflows for image segmentation, object classification, count- the user, it builds a decision surface in feature space and ing and tracking. Users adapt the workflows to the problem at projects the class assignment back to pixels and objects. In hand by interactively providing sparse training annotations for other words, users can parametrize such workflows just by a nonlinear classifier. ilastik can process data in up to five di- providing the training data for algorithm supervision. Freed mensions (3D, time and number of channels). Its computational back end runs operations on-demand wherever possible, allow- from the necessity to understand intricate algorithm details, ing for interactive prediction on data larger than RAM. Once users can thus steer the analysis by their domain expertise. the classifiers are trained, ilastik workflows can be applied to Algorithm parametrization through user supervision (‘learn- new data from the command line without further user interac- ing from training data’) is the defining feature of supervised tion. -
Simpleitk Tutorial Image Processing for Mere Mortals
SimpleITK Tutorial Image processing for mere mortals Insight Software Consortium Sept 23, 2011 (Insight Software Consortium) SimpleITK - MICCAI 2011 Sept 2011 1 / 142 This presentation is copyrighted by The Insight Software Consortium distributed under the Creative Commons by Attribution License 3.0 http://creativecommons.org/licenses/by/3.0 What this Tutorial is about Provide working knowledge of the SimpleITK platform (Insight Software Consortium) SimpleITK - MICCAI 2011 Sept 2011 3 / 142 Program Virtual Machines Preparation (10min) Introduction (15min) Basic Tutorials I (45min) Short Break (10min) Basic Tutorials II (45min) Co↵ee Break (30min) Intermediate Tutorials (45min) Short Break (10min) Advanced Topics (40min) Wrap-up (10min) (Insight Software Consortium) SimpleITK - MICCAI 2011 Sept 2011 4 / 142 Tutorial Goals Gentle introduction to ITK Introduce SimpleITK Provide hands-on experience Problem solving, not direction following ...but please follow directions! (Insight Software Consortium) SimpleITK - MICCAI 2011 Sept 2011 13 / 142 ITK Overview How many are familiar with ITK? (Insight Software Consortium) SimpleITK - MICCAI 2011 Sept 2011 14 / 142 Ever seen code like this? 1 // Setup image types. 2 typedef float InputPixelType ; 3 typedef float OutputPixelType ; 4 typedef itk ::Image<InputPixelType ,2> InputImageType ; 5 typedef itk ::Image<OutputPixelType,2> OutputImageType ; 6 // Filter type 7 typedef itk ::DiscreteGaussianImageFilter< 8 InputImageType , OutputImageType > 9 FilterType ; 10 // Create a filter 11 FilterType ::Pointer filter = FilterType ::New (); 12 // Create the pipeline 13 filter >SetInput( reader >GetOutput () ); 14 filter−>SetVariance(1.0);− 15 filter−>SetMaximumKernelWidth(5); 16 filter−>Update (); 17 OutputImageType− ::Pointer blurred = filter >GetOutput (); − (Insight Software Consortium) SimpleITK - MICCAI 2011 Sept 2011 15 / 142 We are here to tell you that you can.. -
Modelling of the Effects of Entrainment Defects on Mechanical Properties in Al-Si-Mg Alloy Castings
MODELLING OF THE EFFECTS OF ENTRAINMENT DEFECTS ON MECHANICAL PROPERTIES IN AL-SI-MG ALLOY CASTINGS By YANG YUE A dissertation submitted to University of Birmingham for the degree of DOCTOR OF PHILOSOPHY School of Metallurgy and Materials University of Birmingham June 2014 University of Birmingham Research Archive e-theses repository This unpublished thesis/dissertation is copyright of the author and/or third parties. The intellectual property rights of the author or third parties in respect of this work are as defined by The Copyright Designs and Patents Act 1988 or as modified by any successor legislation. Any use made of information contained in this thesis/dissertation must be in accordance with that legislation and must be properly acknowledged. Further distribution or reproduction in any format is prohibited without the permission of the copyright holder. Abstract Liquid aluminium alloy is highly reactive with the surrounding atmosphere and therefore, surface films, predominantly surface oxide films, easily form on the free surface of the melt. Previous researches have highlighted that surface turbulence in liquid aluminium during the mould-filling process could result in the fold-in of the surface oxide films into the bulk liquid, and this would consequently generate entrainment defects, such as double oxide films and entrapped bubbles in the solidified casting. The formation mechanisms of these defects and their detrimental e↵ects on both mechani- cal properties and reproducibility of properties of casting have been studied over the past two decades. However, the behaviour of entrainment defects in the liquid metal and their evolution during the casting process are still unclear, and the distribution of these defects in casting remains difficult to predict. -
Book of Abstracts
Book of Abstracts June 27, 2015 1 Conference Sponsors Diamond Sponsor Platinum Sponsors Gold Sponsors Silver Sponsors Open Analytics Bronze Sponsors Media Sponsors 2 Conference program Time Tuesday Wednesday Thursday Friday 08:00 Registration opens Registration opens Registration opens Registration opens 08:30 – 09:00 Opening session (by Rector peR! M. Johansen, Aalborg University) Aalborghallen 09:00 – 10:00 Romain François Di Cook Thomas Lumley Aalborghallen Aalborghallen Aalborghallen 10:00 – 10:30 Coffee break Coffee break Coffee break (15 min) ee break Sponsored by Quantide Sponsored by Alteryx ff Session 1 Session 4 10:30 – 12:00 Sponsor session (10:15) Kaleidoscope 1 Kaleidoscope 4 Aalborghallen Aalborghallen Aalborghallen incl. co Morning Tutorials DataRobot Ecology Medicine Gæstesalen Gæstesalen RStudio Teradata Networks Regression Musiksalen Musiksalen Revolution Analytics Reproducibility Commercial Offerings alteryx Det Lille Teater Det Lille Teater TIBCO H O Interfacing Interactive graphics 2 Radiosalen Radiosalen HP 12:00 – 13:00 Sandwiches Lunch (standing buffet) Lunch (standing buffet) Break: 12:00 – 12:30 Sponsored by Sponsored by TIBCO ff Revolution Analytics Ste en Lauritzen (12:30) Aalborghallen Session 2 Session 5 13:00 – 14:30 13:30: Closing remarks Kaleidoscope 2 Kaleidoscope 5 Aalborghallen Aalborghallen 13:45: Grab ’n go lunch 14:00: Conference ends Case study Teaching 1 Gæstesalen Gæstesalen Clustering Statistical Methodology 1 Musiksalen Musiksalen ee break Data Management Machine Learning 1 ff Det Lille Teater Det Lille