3D Slicer as an image computing platform for the Quantitative Imaging Network.

Diffusion Tensor Imaging (DTI) studies are increasingly popular among clinicians and researchers as they provide unique insights into brain network connectivity. However, in order to optimize the use of DTI, several technical and methodological aspects must be factored in. These include decisions on: acquisition protocol, artifact handling, data quality control, reconstruction algorithm, and visualization approaches, and quantitative analysis methodology. Furthermore, the researcher and/or clinician also needs to take into account and decide on the most suited software tool(s) for each stage of the DTI analysis pipeline. Herein, we provide a straightforward hitchhiker's guide, covering all of the workflow's major stages. Ultimately, this guide will help newcomers navigate the most critical roadblocks in the analysis and further encourage the use of DTI.

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A hitchhiker's guide to diffusion tensor imaging

Semantic segmentation of medical images aims to associate a pixel with a label in a medical image without human initialization. The success of semantic segmentation algorithms is contingent on the availability of high-quality imaging data with corresponding labels provided by experts. We sought to create a large collection of annotated medical image datasets of various clinically relevant anatomies available under open source license to facilitate the development of semantic segmentation algorithms. Such a resource would allow: 1) objective assessment of general-purpose segmentation methods through comprehensive benchmarking and 2) open and free access to medical image data for any researcher interested in the problem domain. Through a multi-institutional effort, we generated a large, curated dataset representative of several highly variable segmentation tasks that was used in a crowd-sourced challenge - the Medical Segmentation Decathlon held during the 2018 Medical Image Computing and Computer Aided Interventions Conference in Granada, Spain. Here, we describe these ten labeled image datasets so that these data may be effectively reused by the research community.

A large annotated medical image dataset for the development and evaluation of segmentation algorithms

Representative members of the bioimage informatics community review the computational steps and some of the primary software tools available to biologists who are acquiring and analyzing microscopy-based digital image data, with a focus on open-source options. Few technologies are more widespread in modern biological laboratories than imaging. Recent advances in optical technologies and instrumentation are providing hitherto unimagined capabilities. Almost all these advances have required the development of software to enable the acquisition, management, analysis and visualization of the imaging data. We review each computational step that biologists encounter when dealing with digital images, the inherent challenges and the overall status of available software for bioimage informatics, focusing on open-source options.

Biological imaging software tools

Currently, examination of the cellular structure of plant organs and the gene expression therein largely relies on the production of tissue sections. Here, we present a staining technique that can be used to image entire plant organs using confocal laser scanning microscopy. This technique produces high-resolution images that allow three-dimensional reconstruction of the cellular organization of plant organs. Importantly, three-dimensional domains of gene expression can be analyzed with single-cell precision. We used this technique for a detailed examination of phloem cells in the wild type and mutants. We were also able to recognize phloem sieve elements and their differentiation state in any tissue type and visualize the structure of sieve plates. We show that in the altered phloem development mutant, a hybrid cell type with phloem and xylem characteristics develops from initially normally differentiated protophloem cells. The simplicity of sieve element data collection allows for the statistical analysis of structural parameters of sieve plates, essential for the calculation of phloem conductivity. Taken together, this technique significantly improves the speed and accuracy of the investigation of plant growth and development.

High-Resolution Whole-Mount Imaging of Three-Dimensional Tissue Organization and Gene Expression Enables the Study of Phloem Development and Structure in Arabidopsis

A multidimensional image navigation and display software was designed for display and interpretation of large sets of multidimensional and multimodality images such as combined PET-CT studies. The software is developed in Objective-C on a Macintosh platform under the MacOS X operating system using the GNUstep development environment. It also benefits from the extremely fast and optimized 3D graphic capabilities of the OpenGL graphic standard widely used for computer games optimized for taking advantage of any hardware graphic accelerator boards available. In the design of the software special attention was given to adapt the user interface to the specific and complex tasks of navigating through large sets of image data. An interactive jog-wheel device widely used in the video and movie industry was implemented to allow users to navigate in the different dimensions of an image set much faster than with a traditional mouse or on-screen cursors and sliders. The program can easily be adapted for very specific tasks that require a limited number of functions, by adding and removing tools from the program’s toolbar and avoiding an overwhelming number of unnecessary tools and functions. The processing and image rendering tools of the software are based on the open-source libraries ITK and VTK. This ensures that all new developments in image processing that could emerge from other academic institutions using these libraries can be directly ported to the OsiriX program. OsiriX is provided free of charge under the GNU open-source licensing agreement at http://homepage.mac.com/rossetantoine/osirix.

OsiriX: An Open-Source Software for Navigating in Multidimensional DICOM Images

The display and interpretation of images obtained by combining three-dimensional data acquired with two different modalities (eg, positron emission tomography and computed tomography) in the same subject require complex software tools that allow the user to adjust the image parameters. With the current fast imaging systems, it is possible to acquire dynamic images of the beating heart, which add a fourth dimension of visual information—the temporal dimension. Moreover, images acquired at different points during the transit of a contrast agent or during different functional phases add a fifth dimension—functional data. To facilitate real-time image navigation in the resultant large multidimensional image data sets, the authors developed a Digital Imaging and Communications in Medicine–compliant software program. The open-source software, called OsiriX, allows the user to navigate through multidimensional image series while adjusting the blending of images from different modalities, image contrast and inten...

Informatics in radiology (infoRAD): navigating the fifth dimension: innovative interface for multidimensional multimodality image navigation.

OsiriX: a new generation of multidimensional DICOM viewer based on new imaging standards

This paper reports the application of an innovative technique of image fusion of color-coded fluid-sensitive MRI images with high-resolution anatomical images. Image fusion of corresponding slices from two imaging sequences is obtained in real time allowing the user to navigate interactively through large image sets. This technique was applied and evaluated in cases of a variety of musculoskelettal diseases. A color image, overlaying conspicuous findings of fluid-sensitive images, on high resolution spin-echo images, providing accurate anatomical localization were obtained. Compared with traditional side-by-side reviews of these images, this interactive technique it was found to facilitates the correlation of information of different imaging sequences. Furthermore the color images that are generated greatly facilitate the communication of the diagnostic findings to referring physicians.

Luca Spadola

Papers

OsiriX: An Open-Source Software for Navigating in Multidimensional DICOM Images

Informatics in radiology (infoRAD): navigating the fifth dimension: innovative interface for multidimensional multimodality image navigation.

OsiriX: a new generation of multidimensional DICOM viewer based on new imaging standards

Color fusion MRI: an effective technique for image visualization in a variety of clinical applications