Creating a Medical Imaging Workflow Based on FHIR, DICOMweb, and SVG.

This paper proposes a web-based workflow scheme for the organization of medical images using FHIR and DICOM servers equipped with standard RESTful APIs. In our integrated workflow, the client systems (including order placer, scheduler, imaging modality, viewer, and report creator) use standard FHIR and DICOMweb APIs. The proposed scheme also facilitates the creation of reports formatted as standard FHIR resources. This paper leverages W3C Scalable Vector Graphics (SVG) to record the image graphic annotations, and encapsulates the SVG image annotation in FHIR observation. FHIR DiagnosticReports and Observations are used to encapsulate reports, findings, and annotations, thereby facilitating the implementation and integration of the scheme within existing structures. The proposed scheme also provides the potential to make it possible to convert results of Computer Aided Detection/Diagnosis from medical images into FHIR DiagnosticReports and Observations to be stored on a FHIR server. The resulting web-based solution uses FHIR XML and/or JSON data to record and exchange information related to imaging workflow. It can also be used to store imaging reports, findings, and annotations linked to the images using the DICOM WADO-RS protocol. As a result, it is possible to integrate all information that is created in medical imaging workflow. Finally, the proposed scheme is easily integrated with other FHIR systems.

CineMol: a programmatically accessible direct-to-SVG 3D small molecule drawer.

Effective visualization of small molecules is paramount in conveying concepts and results in cheminformatics. Scalable vector graphics (SVG) are preferred for creating such visualizations, as SVGs can be easily altered in post-production and exported to other formats. A wide spectrum of software applications already exist that can visualize molecules, and customize these visualizations, in many ways. However, software packages that can output projected 3D models onto a 2D canvas directly as SVG, while being programmatically accessible from Python, are lacking. Here, we introduce CineMol, which can draw vectorized approximations of three-dimensional small molecule models in seconds, without triangulation or ray tracing, resulting in files of around 50-300 kilobytes per molecule model for compounds with up to 45 heavy atoms. The SVGs outputted by CineMol can be readily modified in popular vector graphics editing software applications. CineMol is written in Python and can be incorporated into any existing Python cheminformatics workflow, as it only depends on native Python libraries. CineMol also provides programmatic access to all its internal states, allowing for per-atom and per-bond-based customization. CineMol's capacity to programmatically create molecular visualizations suitable for post-production offers researchers and scientists a powerful tool for enhancing the clarity and visual impact of their scientific presentations and publications in cheminformatics, metabolomics, and related scientific disciplines.Scientific contributionWe introduce CineMol, a Python-based tool that provides a valuable solution for cheminformatics researchers by enabling the direct generation of high-quality approximations of two-dimensional SVG visualizations from three-dimensional small molecule models, all within a programmable Python framework. CineMol offers a unique combination of speed, efficiency, and accessibility, making it an indispensable tool for researchers in cheminformatics, especially when working with SVG visualizations.

Multi-Focal Laser Direct Writing through Spatial Light Modulation Guided by Scalable Vector Graphics.

Multi-focal laser direct writing (LDW) based on phase-only spatial light modulation (SLM) can realize flexible and parallel nanofabrication with high-throughput potential. In this investigation, a novel approach of combining two-photon absorption, SLM, and vector path-guided by scalable vector graphics (SVGs), termed SVG-guided SLM LDW, was developed and preliminarily tested for fast, flexible, and parallel nanofabrication. Three laser focuses were independently controlled with different paths, which were optimized according to the SVG to improve fabrication and promote time efficiency. The minimum structure width could be as low as 81 nm. Accompanied by a translation stage, a carp structure of 18.10 µm × 24.56 µm was fabricated. This method shows the possibility of developing LDW techniques toward fully electrical systems, and provides a potential way to efficiently engrave complex structures on nanoscales.

Quantification of Digital Body Maps for Pain: Development and Application of an Algorithm for Generating Pain Frequency Maps.

BACKGROUND: Pain is an unpleasant sensation that signals potential or actual bodily injury. The locations of bodily pain can be communicated and recorded by freehand drawing on 2D or 3D (manikin) surface maps. Freehand pain drawings are often part of validated pain questionnaires (eg, the Brief Pain Inventory) and use 2D templates with undemarcated body outlines. The simultaneous analysis of drawings allows the generation of pain frequency maps that are clinically useful for identifying areas of common pain in a disease. The grid-based approach (dividing a template into cells) allows easy generation of pain frequency maps, but the grid's granularity influences data capture accuracy and end-user usability. The grid-free templates circumvent the problem related to grid creation and selection and provide an unbiased basis for drawings that most resemble paper drawings. However, the precise capture of drawn areas poses considerable challenges in producing pain frequency maps. While web-based applications and mobile-based apps for freehand digital drawings are widely available, tools for generating pain frequency maps from grid-free drawings are lacking. OBJECTIVE: We sought to provide an algorithm that can process any number of freehand drawings on any grid-free 2D body template to generate a pain frequency map. We envisage the use of the algorithm in clinical or research settings to facilitate fine-grain comparisons of human pain anatomy between disease diagnosis or disorders or as an outcome metric to guide monitoring or discovery of treatments. METHODS: We designed a web-based tool to capture freehand pain drawings using a grid-free 2D body template. Each drawing consisted of overlapping rectangles (Scalable Vector Graphics elements) created by scribbling in the same area of the body template. An algorithm was developed and implemented in Python to compute the overlap of rectangles and generate a pain frequency map. The utility of the algorithm was demonstrated on drawings obtained from 2 clinical data sets, one of which was a clinical drug trial (ISRCTN68734605). We also used simulated data sets of overlapping rectangles to evaluate the performance of the algorithm. RESULTS: The algorithm produced nonoverlapping rectangles representing unique locations on the body template. Each rectangle carries an overlap frequency that denotes the number of participants with pain at that location. When transformed into an HTML file, the output is feasibly rendered as a pain frequency map on web browsers. The layout (vertical-horizontal) of the output rectangles can be specified based on the dimensions of the body regions. The output can also be exported to a CSV file for further analysis. CONCLUSIONS: Although further validation in much larger clinical data sets is required, the algorithm in its current form allows for the generation of pain frequency maps from any number of freehand drawings on any 2D body template.

BioInfograph: An Online Tool to Design and Display Multi-Panel Scientific Figure Interactively.

Many fit-for-purpose bioinformatics tools generate plots to interpret complex biological data and illustrate findings. However, assembling individual plots in different formats from various sources into one high-resolution figure in the desired layout requires mastery of commercial tools or even programming skills. In addition, it is a time-consuming and sometimes frustrating process even for a computationally savvy scientist who frequently takes a trial-and-error iterative approach to get satisfactory results. To address the challenge, we developed bioInfograph, a web-based tool that allows users to interactively arrange high-resolution images in diversified formats, mainly Scalable Vector Graphics (SVG), to produce one multi-panel publication-quality composite figure in both PDF and HTML formats in a user-friendly manner, requiring no programming skills. It solves stylesheet conflicts of coexisting SVG plots, integrates a rich-text editor, and allows creative design by providing advanced functionalities like image transparency, controlled vertical stacking of plots, versatile image formats, and layout templates. To highlight, the sharable interactive HTML output with zoom-in function is a unique feature not seen in any other similar tools. In the end, we make the online tool publicly available at https://baohongz.github.io/bioInfograph while releasing the source code at https://github.com/baohongz/bioInfograph under MIT open-source license.

Phylostat: a web-based tool to analyze paralogous clade divergence in phylogenetic trees.

Phylogenetic trees are useful tools to infer evolutionary relationships between genetic entities. Phylogenetics enables not only evolution-based gene clustering but also the assignment of gene duplication and deletion events to the nodes when coupled with statistical approaches such as bootstrapping. However, extensive gene duplication and deletion events bring along a challenge in interpreting phylogenetic trees and require manual inference. In particular, there has been no robust method of determining whether one of the paralog clades systematically shows higher divergence following the gene duplication event as a sign of functional divergence. Here, we provide Phylostat, a graphical user interface that enables clade divergence analysis, visually and statistically. Phylostat is a web-based tool built on phylo.io to allow comparative clade divergence analysis, which is available at https://phylostat.adebalilab.org under an MIT open-source licence.

Two-Dimensional Analysis of Digital Images through Vector Graphic Editors in Dentistry: New Calibration and Analysis Protocol Based on a Scoping Review.

This review was carried out to analyse the functions of three Vector Graphic Editor applications (VGEs) applicable to clinical or research practice, and through this we propose a two-dimensional image analysis protocol in a VGE. We adapted the review method from the PRISMA-ScR protocol. Pubmed, Embase, Web of Science, and Scopus were searched until June 2020 with the following keywords: Vector Graphics Editor, Vector Graphics Editor Dentistry, Adobe Illustrator, Adobe Illustrator Dentistry, Coreldraw, Coreldraw Dentistry, Inkscape, Inkscape Dentistry. The publications found described the functions of the following VGEs: Adobe Illustrator, CorelDRAW, and Inkscape. The possibility of replicating the procedures to perform the VGE functions was analysed using each study's data. The search yielded 1032 publications. After the selection, 21 articles met the eligibility criteria. They described eight VGE functions: line tracing, landmarks tracing, linear measurement recording, angular measurement recording, image calibration, image overlay, file transfer, and vector graphics development. The features offered by the VGEs bring great precision and objectivity to two-dimensional image analysis. The image analysis and editing procedures are currently not protocolised. Thus, a protocol for image calibration and measurement recording is proposed in order to guarantee the protocol's replication.

A Novel Method for Detection and Progress Assessment of Visual Distortion Caused by Macular Disorder: A Central Serous Chorioretinopathy (CSR) Case Study.

This paper presents a new mathematical model along with a measurement platform for accurate detection and monitoring of various visual distortions (VD) caused by macular disorders such as central serous chorioretinopathy (CSR) and age-related macular degeneration (AMD). This platform projects a series of graphical patterns on the patient's retina and calculates the severity of VDs accordingly. The accuracy of this technique relies on the accurate detection of distorted lines by the patient. We also propose a simple mathematical model to evaluate the VD created by CSR. The model is used as a control for the test results achieved from the proposed platform. The proposed platform consists of the required hardware and software for the generation and projection of patterns along with the collection and processing of patients against their standard optical coherence tomography (OCT) images. Based on these results, the OCT images agree with the VD test results, and the proposed platform can be used as an alternative home monitoring method for various macular disorders.

NGRID: A novel platform for detection and progress assessment of visual distortion caused by macular disorders.

This paper presents a new graphical macular interface system (GMIS) for accurate, rapid, and quantitative measurement of visual distortion (VD) in the central vision of patients suffering from macular disorders. In this system, a series of predefined graphical patterns or multiple grids (NGRID) are randomly selected from a library of patterns and visualized on the screen, then the VDs identified by the patient are recorded as binary codes using various control methods including speech recognition. Scalable Vector Graphics (SVG) is used to generate the patterns and save them into a central library. Based on the projected patterns and the patients' responses, a VD graph or so-called heatmap is generated for eye-care purposes. We demonstrate and discuss the functionality of the proposed system for the detection and progress assessment of a macular condition in patients suffering from Central Serous Chorioretinopathy (CSR). Also, we characterize the proposed technique to evaluate the systematic error and response time on healthy human subjects with normal vision. Based on these results, the voice recognition input method exhibits a lower error but a higher response time compared to other input devices. We run the proposed NGRID VD technique to evaluate the effect of CSR on the visual field of a CSR patient. The generated heatmaps are in agreement with standard Optical Coherence Tomography (OCT) images obtained at different times from both the left and right eyes. These results reveal the applicability of the proposed technique for the detection and assessment of macular disorders. Based on these results, the proposed NGRID platform shows great promise for use as an alternative solution for in-home monitoring of various macular disorders and as a means of forwarding responses to secured cloud facilities for future data analysis.

Raw data extraction from electrocardiograms with Portable Document Format.

During the last two decades there has been a thorough research and development of standards and protocols in order to cope with different electrocardiogram formats from heterogeneous acquisition systems. Despite the efforts of public and private consortiums on creating a standardized electrocardiogram (ECG) storage format, there is still not a single one. Indeed, there is also the necessity of access to raw data of the ECGs previously acquired. Most of these documents have been saved as Adobe PDF files, since for medical staff it is an easy format for later visualization. However, this format presents difficulties when trying to access original raw data for subsequent studies and signal analysis. In this manner, this paper presents an application that obtains plain numerical data from ECG files stored with PDF format. Data can also be exported to one of the most common file formats in existence, to be easily accessed thereafter.