Studierfenster

Studierfenster is a free, non-commercial Open Science client/server-based Medical Imaging Processing (MIP) online framework. It offers capabilities, like viewing medical data (Computed Tomography (CT), Magnetic Resonance Imaging (MRI), etc.) in two-dimensional (2D) and three-dimensional space (3D) directly in a standard web browser, like Google Chrome, Mozilla Firefox, Safari or Microsoft Edge. Other functionalities are the calculation of Medical Metrics (Dice Score and Hausdorff distance), manual slice-by-slice outlining of structures in medical images (segmentation), manual placing of (anatomical) landmarks in medical image data, viewing medical data in Virtual Reality (VR) and a facial reconstruction and registration of medical data for Augmented Reality (AR).
Other features of Studierfenster are the automatic Cranial Implant Design with a neural network, the inpainting of Aortic Dissections with a Generative Adversarial Network(GAN) and an automatic aortic landmark detection with Deep Learning in Computed Tomography Angiography (CTA) scans.
Studierfenster is currently hosted on an server at the Graz University of Technology (TU Graz) in Styria, Austria.
History.
Studierfenster (SF) was initiated within two Bachelor theses during the Summer Bachelor (SB) program of the Institute of Computer Graphics and Vision (ICG) at the Graz University of Technology, Austria, in cooperation with the Medical University of Graz (MedUni 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 Studierstube (Study Room), which was an Augmented Reality project at the Vienna University of Technology in Austria.
Architecture.
Studierfenster is setup as a distributed application via a client–server model. The client side (front-end) consists of Hypertext Markup Language (HTML) and JavaScript. The front-end also uses the Web Graphics Library (WebGL) that is a Javascript Application Programming Interface (API) descending from the Open Graphics Library (OpenGL) ES 2.0 specification, which it still closely resembles. In contrast to OpenGL, WebGL allows for the rendering of 2D and 3D graphics in web browsers. This enables the use of graphics features known from stand-alone programs directly in web applications, supported by the processing power of the client-side Graphics Processing Unit (GPU).
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 (ITK), the Visualization Toolkit (VTK), the X Toolkit (XTK) and Slice:Drop. The server communication is handled by AJAX requests were needed.
Studierfenster employs a Flask server. Coincidentally, Flask was created by Armin Ronacher an alumnus of the Graz University of Technology in Austria.
Features.
Dicom Browser.
This allows client-side parsing a local folder with DICOM (Digital Imaging and Communications in Medicine) files. Afterwards, the whole folder can be converted to compressed .Nrrd (nearly raw raster data) files and downloaded as a single .zip file.
Nrrd is a library and file format for the representation and processing of n-dimensional raster data. It is intended to support scientific visualization and (medical) image processing 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 .Nrrd file) to a compressed/binary .Nrrd file. After the conversion, the compressed .Nrrd 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 (DSC) and Hausdorff Distance (HD) between two segmentation masks (in .nrrd format) in a standard web browser. 
The resulting table has seven columns: the file names for both files used in the calculation, the calculated DSC, the calculated HD, 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 export, a Comma-Separated Values (CSV) file or as a Portable Document Format (PDF).
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 (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.