Studierfenster or StudierFenster (SF) is a free, non-commercial open science client/server-based medical imaging processing online framework. It offers capabilities, like viewing medical data ( computed tomography (CT),

magnetic resonance imaging Magnetic resonance imaging (MRI) is a medical imaging technique used in radiology to form pictures of the anatomy and the physiological processes of the body. MRI scanners use strong magnetic fields, magnetic field gradients, and radio wave ...

(MRI), etc.) in two- and three-dimensional space directly in standard

web browser A web browser is application software for accessing websites. When a user requests a web page from a particular website, the browser retrieves its files from a web server and then displays the page on the user's screen. Browsers are used on ...

s, like Google Chrome, Mozilla Firefox, Safari, and Microsoft Edge. Other functionalities are the calculation of medical metrics ( dice score and

Hausdorff distance In mathematics, the Hausdorff distance, or Hausdorff metric, also called Pompeiu–Hausdorff distance, measures how far two subsets of a metric space are from each other. It turns the set of non-empty compact subsets of a metric space into a metric ...

), manual slice-by-slice outlining of structures in medical images ( segmentation Linda G. Shapiro and George C. Stockman (2001): “Computer Vision”, pp 279–325, New Jersey, Prentice-Hall, ), manual placing of (anatomical) landmarks in medical image data, viewing medical data in

virtual reality Virtual reality (VR) is a simulated experience that employs pose tracking and 3D near-eye displays to give the user an immersive feel of a virtual world. Applications of virtual reality include entertainment (particularly video games), educ ...

, a facial reconstruction and registration of medical data for

augmented reality Augmented reality (AR) is an interactive experience that combines the real world and computer-generated content. The content can span multiple sensory modalities, including visual, auditory, haptic, somatosensory and olfactory. AR can be de ...

, one click showcases for COVID-19 and veterinary scans, and a Radiomics module. Other features of Studierfenster are the automatic cranial implant design with a

neural network A neural network is a network or circuit of biological neurons, or, in a modern sense, an artificial neural network, composed of artificial neurons or nodes. Thus, a neural network is either a biological neural network, made up of biological ...

, the inpainting of

aortic dissection Aortic dissection (AD) occurs when an injury to the innermost layer of the aorta allows blood to flow between the layers of the aortic wall, forcing the layers apart. In most cases, this is associated with a sudden onset of severe chest or ...

s with a

generative adversarial network A generative adversarial network (GAN) is a class of machine learning frameworks designed by Ian Goodfellow and his colleagues in June 2014. Two neural networks contest with each other in the form of a zero-sum game, where one agent's gain is a ...

, an automatic aortic landmark detection with

deep learning Deep learning (also known as deep structured learning) is part of a broader family of machine learning methods based on artificial neural networks with representation learning. Learning can be supervised, semi-supervised or unsupervised. De ...

in computed tomography angiography scans, and a GrowCut algorithm implementation for image segmentation. Studierfenster is currently hosted on an server at the

Graz University of Technology Graz University of Technology (german: link=no, Technische Universität Graz, short ''TU Graz'') is one of five universities in Styria, Austria. It was founded in 1811 by Archduke John of Austria and is the oldest science and technology research ...

in Austria, and expanded jointly with the Institute for Artificial Intelligence in Medicine (IKIM) in Essen, Germany.

History

Studierfenster was initiated within two bachelor theses during the summer bachelor program of the Institute of Computer Graphics and Vision (ICG) at Graz University of Technology, Austria, in cooperation with the Medical University of Graz, Austria, in 2018/2019. The name Studierfenster (or StudierFenster) is German and can be translated to 'StudyWindow', whereby window refers here to a browser window. The word ''Studierfenster'' is an adaption from the word ('study room'), which was an augmented reality project at the

Vienna University of Technology TU Wien (TUW; german: Technische Universität Wien; still known in English as the Vienna University of Technology from 1975–2014) is one of the major universities in Vienna, Austria. The university finds high international and domestic recogn ...

in Austria.

Architecture

Studierfenster is set up as a distributed application via a client–server model. The client side (front-end) consists of HTML and JavaScript with

WebGL WebGL (Short for Web Graphics Library) is a JavaScript API for rendering interactive 2D and 3D graphics within any compatible web browser without the use of plug-ins. WebGL is fully integrated with other web standards, allowing GPU-accelerated ...

to enable 2D and 3D visualization, rendered on the client. The server side (back-end) handles client requests via C, C++ and Python. It interfaces to common open source libraries and software tools like the Insight Toolkit, the Visualization Toolkit (

VTK The Visualization Toolkit (VTK) is an open-source software system for 3D computer graphics, image processing and scientific visualization.''Visualization Handbook'', Academic Press, 2005, Chapter 30: the Visualization Toolkit/ref> VTK is distrib ...

), the X Toolkit (XTK) and Slice:Drop. The server communication is handled by AJAX requests were needed. Studierfenster employs a

Flask Flask may refer to: Container * Hip flask, a small container used to carry a small amount of liquid * Laboratory flask, laboratory glassware for holding larger volumes than simple test tubes ** Erlenmeyer flask, a common laboratory flask wit ...

server.

Features

Dicom browser

This allows client-side parsing a local folder with

DICOM Digital Imaging and Communications in Medicine (DICOM) is the standard for the communication and management of medical imaging information and related data. DICOM is most commonly used for storing and transmitting medical images enabling the integ ...

(Digital Imaging and Communications in Medicine) files. Afterwards, the whole folder can be converted to compressed (nearly raw raster data) files and downloaded as a single file. Nrrd is a library and

file format A file format is a standard way that information is encoded for storage in a computer file. It specifies how bits are used to encode information in a digital storage medium. File formats may be either proprietary or free. Some file formats ...

for the representation and processing of n-dimensional

raster Raster may refer to: * Raster graphics, graphical techniques using arrays of pixel values * Raster graphics editor, a computer program * Raster scan, the pattern of image readout, transmission, storage, and reconstruction in television and compu ...

data. It is intended to support scientific visualization and (medical)

image processing An image is a visual representation of something. It can be two-dimensional, three-dimensional, or somehow otherwise feed into the visual system to convey information. An image can be an artifact, such as a photograph or other two-dimensiona ...

applications. With the "Dicom Browser" of Studierfenster, it is possible to select specific Studies or Series, and only convert these.

File converter

The file converter converts a medical volume file (e.g. a non-compressed file) to a compressed/binary file. After the conversion, the compressed file can be downloaded and used with the "Medical 3D Viewer" for 2D and 3D visualization, and further image processing.

Metrics module

This can calculate the Dice similarity coefficient and Hausdorff distance between two segmentation masks (in format) in a standard web browser. The resulting table has seven columns: the file names for both files used in the calculation, the calculated Dice similarity coefficient, the calculated Hausdorff distance, the calculated directed HD for both directions and the information if image spacing was used in the calculation. The table can be sorted, is searchable and can be exported as a simple copy, an Excel spreadsheet, a comma-separated values file or as a portable document format. The Metrics Module has been used to compare manual anatomical segmentations of brain tumors

VR viewer

The VR Viewer (or Medical VR Viewer) enables viewing (medical) data in Virtual Reality (VR) with devices like the Google Cardboard or the

HTC Vive VIVE, sometimes referred to as HTC Vive, is a virtual reality brand of HTC Corporation. It consists of hardware like its titular virtual reality headsets and accessories, virtual reality software and services, and initiatives that promote appl ...

(via the WebVR App). For viewing the data in VR, it needs to be converted to the VTI (.vti) format, which can be done with open-source, multi-platform data analysis and visualization application ParaView

Critics

Studierfenster is not a certified medical product; it can only be used for educational, research, and informational purposes.

References

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External links

Studierfenster
2018 software Open science Software frameworks Medical imaging Free health care software Free DICOM software Free software programmed in C++ Free software programmed in Python Computer vision software Image processing software Data visualization software Free 3D graphics software Software that uses VTK