4,660 research outputs found
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
A Factor Graph Approach to Automated Design of Bayesian Signal Processing Algorithms
The benefits of automating design cycles for Bayesian inference-based
algorithms are becoming increasingly recognized by the machine learning
community. As a result, interest in probabilistic programming frameworks has
much increased over the past few years. This paper explores a specific
probabilistic programming paradigm, namely message passing in Forney-style
factor graphs (FFGs), in the context of automated design of efficient Bayesian
signal processing algorithms. To this end, we developed "ForneyLab"
(https://github.com/biaslab/ForneyLab.jl) as a Julia toolbox for message
passing-based inference in FFGs. We show by example how ForneyLab enables
automatic derivation of Bayesian signal processing algorithms, including
algorithms for parameter estimation and model comparison. Crucially, due to the
modular makeup of the FFG framework, both the model specification and inference
methods are readily extensible in ForneyLab. In order to test this framework,
we compared variational message passing as implemented by ForneyLab with
automatic differentiation variational inference (ADVI) and Monte Carlo methods
as implemented by state-of-the-art tools "Edward" and "Stan". In terms of
performance, extensibility and stability issues, ForneyLab appears to enjoy an
edge relative to its competitors for automated inference in state-space models.Comment: Accepted for publication in the International Journal of Approximate
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Modelling and simulation framework for reactive transport of organic contaminants in bed-sediments using a pure java object - oriented paradigm
Numerical modelling and simulation of organic contaminant reactive transport in the environment is being increasingly
relied upon for a wide range of tasks associated with risk-based decision-making, such as prediction of contaminant
profiles, optimisation of remediation methods, and monitoring of changes resulting from an implemented remediation
scheme. The lack of integration of multiple mechanistic models to a single modelling framework, however, has
prevented the field of reactive transport modelling in bed-sediments from developing a cohesive understanding of
contaminant fate and behaviour in the aquatic sediment environment. This paper will investigate the problems involved
in the model integration process, discuss modelling and software development approaches, and present preliminary
results from use of CORETRANS, a predictive modelling framework that simulates 1-dimensional organic contaminant
reaction and transport in bed-sediments
Verifying Safety Properties With the TLA+ Proof System
TLAPS, the TLA+ proof system, is a platform for the development and
mechanical verification of TLA+ proofs written in a declarative style requiring
little background beyond elementary mathematics. The language supports
hierarchical and non-linear proof construction and verification, and it is
independent of any verification tool or strategy. A Proof Manager uses backend
verifiers such as theorem provers, proof assistants, SMT solvers, and decision
procedures to check TLA+ proofs. This paper documents the first public release
of TLAPS, distributed with a BSD-like license. It handles almost all the
non-temporal part of TLA+ as well as the temporal reasoning needed to prove
standard safety properties, in particular invariance and step simulation, but
not liveness properties
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