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

The Virtual Insect Brain protocol: creating and comparing standardized neuroanatomy

BACKGROUND: In the fly Drosophila melanogaster, new genetic, physiological, molecular and behavioral techniques for the functional analysis of the brain are rapidly accumulating. These diverse investigations on the function of the insect brain use gene expression patterns that can be visualized and provide the means for manipulating groups of neurons as a common ground. To take advantage of these patterns one needs to know their typical anatomy. RESULTS: This paper describes the Virtual Insect Brain (VIB) protocol, a script suite for the quantitative assessment, comparison, and presentation of neuroanatomical data. It is based on the 3D-reconstruction and visualization software Amira, version 3.x (Mercury Inc.) [1]. Besides its backbone, a standardization procedure which aligns individual 3D images (series of virtual sections obtained by confocal microscopy) to a common coordinate system and computes average intensities for each voxel (volume pixel) the VIB protocol provides an elaborate data management system for data administration. The VIB protocol facilitates direct comparison of gene expression patterns and describes their interindividual variability. It provides volumetry of brain regions and helps to characterize the phenotypes of brain structure mutants. Using the VIB protocol does not require any programming skills since all operations are carried out at an intuitively usable graphical user interface. Although the VIB protocol has been developed for the standardization of Drosophila neuroanatomy, the program structure can be used for the standardization of other 3D structures as well. CONCLUSION: Standardizing brains and gene expression patterns is a new approach to biological shape and its variability. The VIB protocol provides a first set of tools supporting this endeavor in Drosophila. The script suite is freely available at [2

There is no such thing as ‘undisturbed’ soil and sediment sampling: sampler-induced deformation of salt marsh sediments revealed by 3D X-ray computed tomography

Purpose: Within most environmental contexts, the collection of 'undisturbed' samples is widely relied-upon in studies of soil and sediment properties and structure. However, the impact of sampler-induced disturbance is rarely acknowledged, despite the potential significance of modification to sediment structure for the robustness of data interpretation. In this study, 3D-computed X-ray microtomography (μCT) is used to evaluate and compare the disturbance imparted by four commonly-used sediment sampling methods within a coastal salt-marsh. Materials and methods: Paired sediment core samples from a restored salt-marsh at Orplands Farm, Essex, UK were collected using four common sampling methods (push, cut, hammer and gouge methods). Sampling using two different area-ratio cores resulted in a total of 16 cores that were scanned using 3D X-Ray computed tomography, to identify and evaluate sediment structural properties of samples that can be attributed to sampling method. Results and discussion: 3D qualitative analysis identifies a suite of sampling-disturbance structures including gross-scale changes to sediment integrity and substantial modification of pore-space, structure and distribution, independent of sediment strength and stiffness. Quantitative assessment of changes to pore-space and sediment density arising from the four sampling methods offer a means of direct comparison between the impact of depth-sampling methods. Considerable disturbance to samples result from use of push, hammer and auguring samplers, whilst least disturbance is found in samples recovered by cutting and advanced trimming approaches. Conclusions: It is evident that with the small-bore tubes and samplers commonly used in environmental studies, all techniques result in disturbance to sediment structure to a far greater extent than previously reported, revealed by μCT. This work identifies and evaluates for the first time the full nature, extent and significance of internal sediment disturbance arising from common sampling methods

Stability, affinity, and chromatic variants of the glutamate sensor iGluSnFR

International audienceSingle-wavelength fluorescent reporters allow visualization of specific neurotransmitters with high spatial and temporal resolution. We report variants of intensity-based glutamate-sensing fluorescent reporter (iGluSnFR) that are functionally brighter; detect submicromolar to millimolar amounts of glutamate; and have blue, cyan, green, or yellow emission profiles. These variants could be imaged in vivo in cases where original iGluSnFR was too dim, resolved glutamate transients in dendritic spines and axonal boutons, and allowed imaging at kilohertz rates