ImageJ2: ImageJ for the next generation of scientific image data

ImageJ is an image analysis program extensively used in the biological sciences and beyond. Due to its ease of use, recordable macro language, and extensible plug-in architecture, ImageJ enjoys contributions from non-programmers, amateur programmers, and professional developers alike. Enabling such a diversity of contributors has resulted in a large community that spans the biological and physical sciences. However, a rapidly growing user base, diverging plugin suites, and technical limitations have revealed a clear need for a concerted software engineering effort to support emerging imaging paradigms, to ensure the software's ability to handle the requirements of modern science. Due to these new and emerging challenges in scientific imaging, ImageJ is at a critical development crossroads. We present ImageJ2, a total redesign of ImageJ offering a host of new functionality. It separates concerns, fully decoupling the data model from the user interface. It emphasizes integration with external applications to maximize interoperability. Its robust new plugin framework allows everything from image formats, to scripting languages, to visualization to be extended by the community. The redesigned data model supports arbitrarily large, N-dimensional datasets, which are increasingly common in modern image acquisition. Despite the scope of these changes, backwards compatibility is maintained such that this new functionality can be seamlessly integrated with the classic ImageJ interface, allowing users and developers to migrate to these new methods at their own pace. ImageJ2 provides a framework engineered for flexibility, intended to support these requirements as well as accommodate future needs

Apical invasion of intestinal epithelial cells by salmonella typhimurium requires villin to remodel the brush border actin cytoskeleton

Funding Information: We thank R. Friedman, C. Mulet and T. Pedron for technical help. We thank T. Marlovits for antibodies, H.D. Hardt and J. Galan for Salmonella strains, and D. Zhou and V. Koronakis for plasmids. We acknowledge France-BioImaging infrastructure supported by the French National Research Agency (ANR-10-INSB-04-01, «Investments for the future»). This work was supported by the ERC (P.S. Advanced Grant HOMEOEPITH, number 232798). P.J.S. is an HHMI senior foreign scholar. The authors declare no conflict of interest. Publisher Copyright: © 2015 Elsevier Inc.Salmonella invasion of intestinal epithelial cells requires extensive, though transient, actin modifications at the site of bacterial entry. The actin-modifying protein villin is present in the brush border where it participates in the constitution of microvilli and in epithelial restitution after damage through its actin-severing activity. We investigated a possible role for villin in Salmonella invasion. The absence of villin, which is normally located at the bacterial entry site, leads to a decrease in Salmonella invasion. Villin is necessary for early membrane-associated processes and for optimal ruffle assembly by balancing the steady-state level of actin. The severing activity of villin is important for Salmonella invasion in vivo. The bacterial phosphatase SptP tightly regulates villin phosphorylation, while the actin-binding effector SipA protects F-actin and counterbalances villin-severing activity. Thus, villin plays an important role in establishing the balance between actin polymerization and actin severing to facilitate the initial steps of Salmonella entry.publishersversionpublishe

Apical invasion of intestinal epithelial cells by salmonella typhimurium requires villin to remodel the brush border actin cytoskeleton

Funding Information: We thank R. Friedman, C. Mulet and T. Pedron for technical help. We thank T. Marlovits for antibodies, H.D. Hardt and J. Galan for Salmonella strains, and D. Zhou and V. Koronakis for plasmids. We acknowledge France-BioImaging infrastructure supported by the French National Research Agency (ANR-10-INSB-04-01, «Investments for the future»). This work was supported by the ERC (P.S. Advanced Grant HOMEOEPITH, number 232798). P.J.S. is an HHMI senior foreign scholar. The authors declare no conflict of interest. Publisher Copyright: © 2015 Elsevier Inc.Salmonella invasion of intestinal epithelial cells requires extensive, though transient, actin modifications at the site of bacterial entry. The actin-modifying protein villin is present in the brush border where it participates in the constitution of microvilli and in epithelial restitution after damage through its actin-severing activity. We investigated a possible role for villin in Salmonella invasion. The absence of villin, which is normally located at the bacterial entry site, leads to a decrease in Salmonella invasion. Villin is necessary for early membrane-associated processes and for optimal ruffle assembly by balancing the steady-state level of actin. The severing activity of villin is important for Salmonella invasion in vivo. The bacterial phosphatase SptP tightly regulates villin phosphorylation, while the actin-binding effector SipA protects F-actin and counterbalances villin-severing activity. Thus, villin plays an important role in establishing the balance between actin polymerization and actin severing to facilitate the initial steps of Salmonella entry.publishersversionpublishe

Metrics for optimising the multi-dimensional value of resources recovered from waste in a circular economy: A critical review

© 2017 The Authors - Established assessment methods focusing on resource recovery from waste within a circular economy context consider few or even a single domain/s of value, i.e. environmental, economic, social and technical domains. This partial approach often delivers misleading messages for policy- and decision-makers. It fails to accurately represent systems complexity, and obscures impacts, trade-offs and problem shifting that resource recovery processes or systems intended to promote circular economy may cause. Here, we challenge such partial approaches by critically reviewing the existing suite of environmental, economic, social and technical metrics that have been regularly observed and used in waste management and resource recovery systems' assessment studies, upstream and downstream of the point where waste is generated. We assess the potential of those metrics to evaluate ‘complex value’ of materials, components and products, i.e., the holistic sum of their environmental, economic, social and technical benefits and impacts across the system. Findings suggest that the way resource recovery systems are assessed and evaluated require simplicity, yet must retain a suitable minimum level of detail across all domains of value, which is pivotal for enabling sound decision-making processes. Criteria for defining a suitable set of metrics for assessing resource recovery from waste require them to be simple, transparent and easy to measure, and be both system- and stakeholder-specific. Future developments must focus on providing a framework for the selection of metrics that accurately describe (or at least reliably proxy for) benefits and impacts across all domains of value, enabling effective and transparent analysis of resource recovery form waste in circular economy systems.We gratefully acknowledge support of the UK Natural Environ-ment Research Council (NERC) and the UK Economic and SocialResearch Council (ESRC) who funded this work in the context of‘Complex Value Optimisation for Resource Recovery’(CVORR)project (Grant No. NE/L014149/1)

Salmonella enterica serovar Typhimurium infection of the gallbladder : a novel in vivo epithelial cell infection model

The gallbladder has long been recognized as a site of infection during systemic salmonellosis; yet little is known regarding bacterial pathogenesis in this organ. My PhD research constitutes the first detailed characterization of a bacterial infection of the gallbladder, focusing on the local biology, pathology, and immunology of Salmonella infection. Using a murine model of acute typhoid fever, it was found that Salmonella in the gallbladder show a unique behavior, as they remained confined to gallbladder epithelial cells without translocating to the mucosa. Moreover, they replicated within these cells instead of phagocytes. These findings add yet another functional significance to the invasion phenotype in vivo, and together with the presence of high numbers of extracellular, luminal bacteria, put forward the concept that acute infection of the gallbladder may be important for later events in the bacterial life cycle. A murine model of persistent typhoid infection revealed that gallbladder colonization occurs intermittently during chronic infection and that colonization may result in pathological damage. The in vivo work described here validates some of the paradigms of Salmonella infection, but also shows that Salmonella accumulation in vivo does no exclusively occur in the canonical intra-macrophage niche. This research also established a new system for the study of Salmonella Typhimurium’s biology, and a way to probe the biological function of individual gene products in a meaningful in vivo infection model. The model was validated in a screen of Salmonella mutants of known virulence factors involved in intracellular survival and replication within host cells. Novel phenotypes were described within this more natural host:pathogen environment, which highlighted potentially new biological functions for several Salmonella genes. This is the first study of its kind, which reveals the usefulness of the in vivo gallbladder epithelial cell infection model. It is hoped that future studies using this system shall continue to impact the field of Salmonella pathogenesis.Science, Faculty ofMicrobiology and Immunology, Department ofGraduat

Scientific Community Image Forum: A discussion forum for scientific image software.

Forums and email lists play a major role in assisting scientists in using software. Previously, each open-source bioimaging software package had its own distinct forum or email list. Although each provided access to experts from various software teams, this fragmentation resulted in many scientists not knowing where to begin with their projects. Thus, the scientific imaging community lacked a central platform where solutions could be discussed in an open, software-independent manner. In response, we introduce the Scientific Community Image Forum, where users can pose software-related questions about digital image analysis, acquisition, and data management