MITK-ModelFit: A generic open-source framework for model fits and their exploration in medical imaging -- design, implementation and application on the example of DCE-MRI

Many medical imaging techniques utilize fitting approaches for quantitative parameter estimation and analysis. Common examples are pharmacokinetic modeling in DCE MRI/CT, ADC calculations and IVIM modeling in diffusion-weighted MRI and Z-spectra analysis in chemical exchange saturation transfer MRI. Most available software tools are limited to a special purpose and do not allow for own developments and extensions. Furthermore, they are mostly designed as stand-alone solutions using external frameworks and thus cannot be easily incorporated natively in the analysis workflow. We present a framework for medical image fitting tasks that is included in MITK, following a rigorous open-source, well-integrated and operating system independent policy. Software engineering-wise, the local models, the fitting infrastructure and the results representation are abstracted and thus can be easily adapted to any model fitting task on image data, independent of image modality or model. Several ready-to-use libraries for model fitting and use-cases, including fit evaluation and visualization, were implemented. Their embedding into MITK allows for easy data loading, pre- and post-processing and thus a natural inclusion of model fitting into an overarching workflow. As an example, we present a comprehensive set of plug-ins for the analysis of DCE MRI data, which we validated on existing and novel digital phantoms, yielding competitive deviations between fit and ground truth. Providing a very flexible environment, our software mainly addresses developers of medical imaging software that includes model fitting algorithms and tools. Additionally, the framework is of high interest to users in the domain of perfusion MRI, as it offers feature-rich, freely available, validated tools to perform pharmacokinetic analysis on DCE MRI data, with both interactive and automatized batch processing workflows.Comment: 31 pages, 11 figures URL: http://mitk.org/wiki/MITK-ModelFi

Reducing the Barrier to Entry of Complex Robotic Software: a MoveIt! Case Study

Developing robot agnostic software frameworks involves synthesizing the disparate fields of robotic theory and software engineering while simultaneously accounting for a large variability in hardware designs and control paradigms. As the capabilities of robotic software frameworks increase, the setup difficulty and learning curve for new users also increase. If the entry barriers for configuring and using the software on robots is too high, even the most powerful of frameworks are useless. A growing need exists in robotic software engineering to aid users in getting started with, and customizing, the software framework as necessary for particular robotic applications. In this paper a case study is presented for the best practices found for lowering the barrier of entry in the MoveIt! framework, an open-source tool for mobile manipulation in ROS, that allows users to 1) quickly get basic motion planning functionality with minimal initial setup, 2) automate its configuration and optimization, and 3) easily customize its components. A graphical interface that assists the user in configuring MoveIt! is the cornerstone of our approach, coupled with the use of an existing standardized robot model for input, automatically generated robot-specific configuration files, and a plugin-based architecture for extensibility. These best practices are summarized into a set of barrier to entry design principles applicable to other robotic software. The approaches for lowering the entry barrier are evaluated by usage statistics, a user survey, and compared against our design objectives for their effectiveness to users

mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking.

Mock communities are an important tool for validating, optimizing, and comparing bioinformatics methods for microbial community analysis. We present mockrobiota, a public resource for sharing, validating, and documenting mock community data resources, available at http://caporaso-lab.github.io/mockrobiota/. The materials contained in mockrobiota include data set and sample metadata, expected composition data (taxonomy or gene annotations or reference sequences for mock community members), and links to raw data (e.g., raw sequence data) for each mock community data set. mockrobiota does not supply physical sample materials directly, but the data set metadata included for each mock community indicate whether physical sample materials are available. At the time of this writing, mockrobiota contains 11 mock community data sets with known species compositions, including bacterial, archaeal, and eukaryotic mock communities, analyzed by high-throughput marker gene sequencing. IMPORTANCE The availability of standard and public mock community data will facilitate ongoing method optimizations, comparisons across studies that share source data, and greater transparency and access and eliminate redundancy. These are also valuable resources for bioinformatics teaching and training. This dynamic resource is intended to expand and evolve to meet the changing needs of the omics community

Land surface Verification Toolkit (LVT)

LVT is a framework developed to provide an automated, consolidated environment for systematic land surface model evaluation Includes support for a range of in-situ, remote-sensing and other model and reanalysis products. Supports the analysis of outputs from various LIS subsystems, including LIS-DA, LIS-OPT, LIS-UE. Note: The Land Information System Verification Toolkit (LVT) is a NASA software tool designed to enable the evaluation, analysis and comparison of outputs generated by the Land Information System (LIS). The LVT software is released under the terms and conditions of the NASA Open Source Agreement (NOSA) Version 1.1 or later. Land Information System Verification Toolkit (LVT) NOSA

SpaceTx: A Roadmap for Benchmarking Spatial Transcriptomics Exploration of the Brain

Mapping spatial distributions of transcriptomic cell types is essential to understanding the brain, with its exceptional cellular heterogeneity and the functional significance of its spatial organization. Spatial transcriptomics techniques are hoped to accomplish these measurements, but each method uses different experimental and computational protocols, with different trade-offs and optimizations. In 2017, the SpaceTx Consortium was formed to compare these methods and determine their suitability for large-scale spatial transcriptomic atlases. SpaceTx work included progress in tissue processing, taxonomy development, gene selection, image processing and data standardization, cell segmentation, cell type assignments, and visualization. Although the landscape of experimental methods has changed dramatically since the beginning of SpaceTx, the need for quantitative and detailed benchmarking of spatial transcriptomics methods in the brain is still unmet. Here, we summarize the work of SpaceTx and highlight outstanding challenges as spatial transcriptomics grows into a mature field. We also discuss how our progress provides a roadmap for benchmarking spatial transcriptomics methods in the future. Data and analyses from this consortium, along with code and methods are publicly available at https://spacetx.github.io/

1st INCF Workshop on Sustainability of Neuroscience Databases

The goal of the workshop was to discuss issues related to the sustainability of neuroscience databases, identify problems and propose solutions, and formulate recommendations to the INCF. The report summarizes the discussions of invited participants from the neuroinformatics community as well as from other disciplines where sustainability issues have already been approached. The recommendations for the INCF involve rating, ranking, and supporting database sustainability

uTHCD: A New Benchmarking for Tamil Handwritten OCR

Handwritten character recognition is a challenging research in the field of document image analysis over many decades due to numerous reasons such as large writing styles variation, inherent noise in data, expansive applications it offers, non-availability of benchmark databases etc. There has been considerable work reported in literature about creation of the database for several Indic scripts but the Tamil script is still in its infancy as it has been reported only in one database [5]. In this paper, we present the work done in the creation of an exhaustive and large unconstrained Tamil Handwritten Character Database (uTHCD). Database consists of around 91000 samples with nearly 600 samples in each of 156 classes. The database is a unified collection of both online and offline samples. Offline samples were collected by asking volunteers to write samples on a form inside a specified grid. For online samples, we made the volunteers write in a similar grid using a digital writing pad. The samples collected encompass a vast variety of writing styles, inherent distortions arising from offline scanning process viz stroke discontinuity, variable thickness of stroke, distortion etc. Algorithms which are resilient to such data can be practically deployed for real time applications. The samples were generated from around 650 native Tamil volunteers including school going kids, homemakers, university students and faculty. The isolated character database will be made publicly available as raw images and Hierarchical Data File (HDF) compressed file. With this database, we expect to set a new benchmark in Tamil handwritten character recognition and serve as a launchpad for many avenues in document image analysis domain. Paper also presents an ideal experimental set-up using the database on convolutional neural networks (CNN) with a baseline accuracy of 88% on test data.Comment: 30 pages, 18 figures, in IEEE Acces