Imagining the Future of Bioimage Analysis
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Bioimage Analysis Tools
Bioimage Analysis Tools Kota Miura, Sébastien Tosi, Christoph Möhl, Chong Zhang, Perrine Paul-Gilloteaux, Ulrike Schulze, Simon Norrelykke, Christian Tischer, Thomas Pengo To cite this version: Kota Miura, Sébastien Tosi, Christoph Möhl, Chong Zhang, Perrine Paul-Gilloteaux, et al.. Bioimage Analysis Tools. Kota Miura. Bioimage Data Analysis, Wiley-VCH, 2016, 978-3-527-80092-6. hal- 02910986 HAL Id: hal-02910986 https://hal.archives-ouvertes.fr/hal-02910986 Submitted on 3 Aug 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. 2 Bioimage Analysis Tools 1 2 3 4 5 6 Kota Miura, Sébastien Tosi, Christoph Möhl, Chong Zhang, Perrine Pau/-Gilloteaux, - Ulrike Schulze,7 Simon F. Nerrelykke,8 Christian Tischer,9 and Thomas Penqo'" 1 European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany National Institute of Basic Biology, Okazaki, 444-8585, Japan 2/nstitute for Research in Biomedicine ORB Barcelona), Advanced Digital Microscopy, Parc Científic de Barcelona, dBaldiri Reixac 1 O, 08028 Barcelona, Spain 3German Center of Neurodegenerative -
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. -
A Call for Public Archives for Biological Image Data Public Data Archives Are the Backbone of Modern Biological Research
comment A call for public archives for biological image data Public data archives are the backbone of modern biological research. Biomolecular archives are well established, but bioimaging resources lag behind them. The technology required for imaging archives is now available, thus enabling the creation of the frst public bioimage datasets. We present the rationale for the construction of bioimage archives and their associated databases to underpin the next revolution in bioinformatics discovery. Jan Ellenberg, Jason R. Swedlow, Mary Barlow, Charles E. Cook, Ugis Sarkans, Ardan Patwardhan, Alvis Brazma and Ewan Birney ince the mid-1970s it has been possible image data to encourage both reuse and in automation and throughput allow this to analyze the molecular composition extraction of knowledge. to be done in a systematic manner. We Sof living organisms, from the individual Despite the long history of biological expect that, for example, super-resolution units (nucleotides, amino acids, and imaging, the tools and resources for imaging will be applied across biological metabolites) to the macromolecules they collecting, managing, and sharing image and biomedical imaging; examples in are part of (DNA, RNA, and proteins), data are immature compared with those multidimensional imaging8 and high- as well as the interactions among available for sequence and 3D structure content screening9 have recently been these components1–3. The cost of such data. In the following sections we reported. It is very likely that imaging data measurements has decreased remarkably outline the current barriers to progress, volume and complexity will continue to over time, and technological development the technological developments that grow. Second, the emergence of powerful has widened their scope from investigations could provide solutions, and how those computer-based approaches for image of gene and transcript sequences (genomics/ infrastructure solutions can meet the interpretation, quantification, and modeling transcriptomics) to proteins (proteomics) outlined need. -
3 on the Nature of Biological Data
ON THE NATURE OF BIOLOGICAL DATA 35 3 On the Nature of Biological Data Twenty-first century biology will be a data-intensive enterprise. Laboratory data will continue to underpin biology’s tradition of being empirical and descriptive. In addition, they will provide confirming or disconfirming evidence for the various theories and models of biological phenomena that researchers build. Also, because 21st century biology will be a collective effort, it is critical that data be widely shareable and interoperable among diverse laboratories and computer systems. This chapter describes the nature of biological data and the requirements that scientists place on data so that they are useful. 3.1 DATA HETEROGENEITY An immense challenge—one of the most central facing 21st century biology—is that of managing the variety and complexity of data types, the hierarchy of biology, and the inevitable need to acquire data by a wide variety of modalities. Biological data come in many types. For instance, biological data may consist of the following:1 • Sequences. Sequence data, such as those associated with the DNA of various species, have grown enormously with the development of automated sequencing technology. In addition to the human genome, a variety of other genomes have been collected, covering organisms including bacteria, yeast, chicken, fruit flies, and mice.2 Other projects seek to characterize the genomes of all of the organisms living in a given ecosystem even without knowing all of them beforehand.3 Sequence data generally 1This discussion of data types draws heavily on H.V. Jagadish and F. Olken, eds., Data Management for the Biosciences, Report of the NSF/NLM Workshop of Data Management for Molecular and Cell Biology, February 2-3, 2003, Available at http:// www.eecs.umich.edu/~jag/wdmbio/wdmb_rpt.pdf. -
Visualization of Biomedical Data
Visualization of Biomedical Data Corresponding author: Seán I. O’Donoghue; email: [email protected] • Data61, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Eveleigh NSW 2015, Australia • Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney NSW 2010, Australia • School of Biotechnology and Biomolecular Sciences, UNSW, Kensington NSW 2033, Australia Benedetta Frida Baldi; email: [email protected] • Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney NSW 2010, Australia Susan J Clark; email: [email protected] • Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney NSW 2010, Australia Aaron E. Darling; email: [email protected] • The ithree institute, University of Technology Sydney, Ultimo NSW 2007, Australia James M. Hogan; email: [email protected] • School of Electrical Engineering and Computer Science, Queensland University of Technology, Brisbane QLD, 4000, Australia Sandeep Kaur; email: [email protected] • School of Computer Science and Engineering, UNSW, Kensington NSW 2033, Australia Lena Maier-Hein; email: [email protected] • Div. Computer Assisted Medical Interventions (CAMI), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany Davis J. McCarthy; email: [email protected] • European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, CB10 1SD, Hinxton, Cambridge, UK • St. Vincent’s Institute of Medical Research, Fitzroy VIC 3065, Australia William -
When Biology Gets Personal: Hidden Challenges of Privacy and Ethics in Biological Big Data
Pacific Symposium on Biocomputing 2019 When Biology Gets Personal: Hidden Challenges of Privacy and Ethics in Biological Big Data Gamze Gürsoy* Computational Biology and Bioinformatics Program, Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, 06511, USA Email: [email protected] Arif Harmanci Center for Precision Health, School of Biomedical Informatics, University of Texas Health Science Center, Houston, TX, 77030, USA Email: [email protected] Haixu Tang† School of Informatics, Computing and Engineering, Indiana University Bloomington, Bloomington, IN, 47405, USA Email: [email protected] Erman Ayday Department of Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, OH, 44106, USA Email: [email protected] Steven E. Brenner# University of California Berkeley, CA, 94720-3012, USA Email: [email protected] High-throughput technologies for biological data acquisition are advancing at an increasing pace. Most prominently, the decreasing cost of DNA sequencing has led to an exponential growth of sequence information, including individual human genomes. This session of the 2019 Pacific Symposium on Biocomputing presents the distinctive privacy and ethical challenges related to the generation, storage, processing, study, and sharing of individuals’ biological data generated by multitude of technologies including but not limited to genomics, proteomics, metagenomics, bioimaging, biosensors, and personal health trackers. The mission is to bring together computational biologists, experimental biologists, computer scientists, ethicists, and policy and lawmakers to share ideas, discuss the challenges related to biological data and privacy. Keywords: biological data privacy, genomics, genetic testing * This work is partially supported by NIH grant U01EB023686. † This work is partially supported by NIH grant U01EB023685 and NSF grant CNS-1408874. -
From Big Data Analysis to Personalized Medicine for All: Challenges and Opportunities Akram Alyass1, Michelle Turcotte1 and David Meyre1,2*
Alyass et al. BMC Medical Genomics (2015) 8:33 DOI 10.1186/s12920-015-0108-y REVIEW Open Access From big data analysis to personalized medicine for all: challenges and opportunities Akram Alyass1, Michelle Turcotte1 and David Meyre1,2* Abstract Recent advances in high-throughput technologies have led to the emergence of systems biology as a holistic science to achieve more precise modeling of complex diseases. Many predict the emergence of personalized medicine in the near future. We are, however, moving from two-tiered health systems to a two-tiered personalized medicine. Omics facilities are restricted to affluent regions, and personalized medicine is likely to widen the growing gap in health systems between high and low-income countries. This is mirrored by an increasing lag between our ability to generate and analyze big data. Several bottlenecks slow-down the transition from conventional to personalized medicine: generation of cost-effective high-throughput data; hybrid education and multidisciplinary teams; data storage and processing; data integration and interpretation; and individual and global economic relevance. This review provides an update of important developments in the analysis of big data and forward strategies to accelerate the global transition to personalized medicine. Keywords: Big data, Omics, Personalized medicine, High-throughput technologies, Cloud computing, Integrative methods, High-dimensionality Introduction of biology and medicine [5, 6]. The use of deterministic Access to large omics (genomics, transcriptomics, proteo- networks for normal and abnormal phenotypes are mics, epigenomic, metagenomics, metabolomics, nutrio- thought to allow for the proactive maintenance of wellness mics, etc.) data has revolutionized biology and has led to specific to the individual, that is predictive, preventive, the emergence of systems biology for a better understand- personalized, and participatory medicine (P4, or more ing of biological mechanisms. -
Bioimage Informatics
Bioimage Informatics Lecture 22, Spring 2012 Empirical Performance Evaluation of Bioimage Informatics Algorithms Image Database; Content Based Image Retrieval Emerging Applications: Molecular Imaging Lecture 22 April 23, 2012 1 Outline • Empirical performance evaluation of bioimage Informatics algorithm • Image database; content-based image retrieval • Introduction to molecular imaging 2 • Empirical performance evaluation of bioimage Informatics algorithm • Image database; content-based image retrieval • Introduction to molecular imaging 3 Overview of Algorithm Evaluation (I) • Two sets of data are required - Input data - Corresponding correct output (ground truth) • Sources of input data - Actual/experimental data, often from experiments - Synthetic data, often from computer simulation • Actual/experimental data - Essential for performance evaluation - May be costly to acquire - May not be representative - Ground truth often is unknown Overview of Algorithm Evaluation (II) • What exactly is ground truth? Ground truth is a term used in cartography, meteorology, analysis of aerial photographs, satellite imagery and a range of other remote sensing techniques in which data are gathered at a distance. Ground truth refers to information that is collected "on location." - http://en.wikipedia.org/wiki/Ground_truth • Synthetic (simulated) data Advantages - Ground truth is known - Usually low-cost Disadvantages - Difficult to fully represent the original data 5 Overview of Algorithm Evaluation (III) • Simulated data Advantages - Ground truth is known - Usually low-cost Disadvantages - Difficult to fully represent the original data • Realistic synthetic data - To use as much information from real experimental data as possible • Quality control of manual analysis Test Protocol Development (I) • Implementation - Source codes are not always available and often are on different platforms. • Parameter setting - This is one of the most challenging issues. -
Personalized Medicine in Big Data
INTERNATIONAL JOURNAL FOR RESEARCH IN EMERGING SCIENCE AND TECHNOLOGY E-ISSN: 2349-7610 Personalized Medicine in Big Data Mr.A.Kesavan, M.C.A., M.Phil., Dr.C.Jayakumari, M.C.A., Ph.D., Mr.A.Kesavan, M.C.A, M.Phil., Research Scholar, Bharathiar University, India. [email protected] Dr.C.Jayakumari, M.C.A, Ph.D., Associate Professor, Middle East College, Oman, [email protected] ABSTRACT The rapid and ongoing digitalization of society leads to an exponential growth of both structured and unstructured data, so-called Big Data. This wealth of information opens the door to the development of more advanced personalized medicine technologies. The analysis of log data from such applications and wearables provide the opportunity to personalize and to improve their strength and long-term use. Personalized medicine is the use of a patient’s genomic information to form individualized prevention, diagnosis, and treatment plans to combat disease. Keywords: Big Data, Personalized Medicine, Omics Data, High-throughput technologies, Integrative methods, High- dimensionality. 1. INTRODUCTION Big Data refers to the practice of combining huge volumes of The overarching goal of “Personalized Medicine” is to create a diversely sourced information and analyzing them, using more framework that leverage patient EHRs and Omics data to sophisticated algorithms to inform decisions. Big Data relies facilitate clinical decision-making that is predictive, not only on the increasing ability of technology to support the personalized, preventive and participatory [4]. The emphasis is collection and storage of large amounts of data, but also on its to customize medical treatment based on the individual ability to analyses, understand and take advantage of the full characteristics of patients and nature of their disease, value of data. -
Bioimage Informatics 2019
BioImage Informatics 2019 Co-hosted by: October 2-4, 2019 Allen Institute 615 Westlake Avenue N Seattle, WA 98109 alleninstitute.org/bioimage-informatics twitter #bioimage19 THANKS TO OUR SPONSORS BioImage Informatics 2019 Wednesday, October 2 8:00-9:00am Registration and continental breakfast 9:00-9:15am Welcome and introductory remarks, BioImage Informatics Local Planning Committee • Michael Hawrylycz, Ph.D., Allen Institute for Brain Science (co-chair) • Winfried Wiegraebe, Ph.D., Allen Institute for Cell Science (co-chair) • Forrest Collman, Ph.D., Allen Institute for Brain Science • Greg Johnson, Ph.D., Allen Institute for Cell Science • Lydia Ng, Ph.D., Allen Institute for Brain Science • Kaitlyn Casimo, Ph.D., Allen Institute 9:15-10:15am Opening keynote Gaudenz Danuser, UT Southwestern Medical Center “Inference of causality in molecular pathways from live cell images” Defining cause-effect relations among molecular components is the holy grail of every cell biological study. It turns out that for many of the molecular pathways this task is far from trivial. Many of the pathways are characterized by functional overlap and nonlinear interactions between components. In this configuration, perturbation of one component may result in a measureable shift of the pathway output – commonly referred to as a phenotype – but it is strictly impossible to interpret the phenotype in terms of the roles the targeted component plays in the unperturbed system. This caveat of perturbation approaches applies equally to genetic perturbations, which lead to long-term adaptation, and more acute pharmacological and optogenetic approaches, which often induce short-term adaptation. For nearly two decades my lab has been devoted to circumventing this problem by exploiting basal fluctuations of unperturbed systems to establish cause-and-effect cascades between pathway components. -
A Bioimage Informatics Platform for High-Throughput Embryo Phenotyping James M
Briefings in Bioinformatics, 19(1), 2018, 41–51 doi: 10.1093/bib/bbw101 Advance Access Publication Date: 14 October 2016 Paper A bioimage informatics platform for high-throughput embryo phenotyping James M. Brown, Neil R. Horner, Thomas N. Lawson, Tanja Fiegel, Simon Greenaway, Hugh Morgan, Natalie Ring, Luis Santos, Duncan Sneddon, Lydia Teboul, Jennifer Vibert, Gagarine Yaikhom, Henrik Westerberg and Ann-Marie Mallon Corresponding author: James Brown, MRC Harwell Institute, Harwell Campus, Oxfordshire, OX11 0RD. Tel. þ44-0-1235-841237; Fax: +44-0-1235-841172; E-mail: [email protected] Abstract High-throughput phenotyping is a cornerstone of numerous functional genomics projects. In recent years, imaging screens have become increasingly important in understanding gene–phenotype relationships in studies of cells, tissues and whole organisms. Three-dimensional (3D) imaging has risen to prominence in the field of developmental biology for its ability to capture whole embryo morphology and gene expression, as exemplified by the International Mouse Phenotyping Consortium (IMPC). Large volumes of image data are being acquired by multiple institutions around the world that encom- pass a range of modalities, proprietary software and metadata. To facilitate robust downstream analysis, images and metadata must be standardized to account for these differences. As an open scientific enterprise, making the data readily accessible is essential so that members of biomedical and clinical research communities can study the images for them- selves without the need for highly specialized software or technical expertise. In this article, we present a platform of soft- ware tools that facilitate the upload, analysis and dissemination of 3D images for the IMPC. -
View of Above Observations and Arguments, the Fol- Scopy Environment) [9]
Loyek et al. BMC Bioinformatics 2011, 12:297 http://www.biomedcentral.com/1471-2105/12/297 SOFTWARE Open Access BioIMAX: A Web 2.0 approach for easy exploratory and collaborative access to multivariate bioimage data Christian Loyek1*, Nasir M Rajpoot2, Michael Khan3 and Tim W Nattkemper1 Abstract Background: Innovations in biological and biomedical imaging produce complex high-content and multivariate image data. For decision-making and generation of hypotheses, scientists need novel information technology tools that enable them to visually explore and analyze the data and to discuss and communicate results or findings with collaborating experts from various places. Results: In this paper, we present a novel Web2.0 approach, BioIMAX, for the collaborative exploration and analysis of multivariate image data by combining the webs collaboration and distribution architecture with the interface interactivity and computation power of desktop applications, recently called rich internet application. Conclusions: BioIMAX allows scientists to discuss and share data or results with collaborating experts and to visualize, annotate, and explore multivariate image data within one web-based platform from any location via a standard web browser requiring only a username and a password. BioIMAX can be accessed at http://ani.cebitec. uni-bielefeld.de/BioIMAX with the username “test” and the password “test1” for testing purposes. Background key challenge of bioimage informatics is to present the In the last two decades, innovative biological and biome- large amount of image data in a way that enables them dical imaging technologies greatly improved our under- to be browsed, analyzed, queried or compared with standing of structures of molecules, cells and tissue and other resources [2].