Ran Klein profile picture

Contact Information

Ran Klein, PhD


ORCID logo https://orcid.org/0000-0002-4357-3779


Matlab Source Code

Image Perception and Lesion Synthesis

Two separate, but related, tools used in our image perception and limits-of-detection (LOD) work in PET/CT.

  • The lesion synthesis toolbox is an integrated workflow for generating well characterized and realistic lesions in PET and CT data. While the tool was designed with the intention of being vendor neutral, for the time being it was only implemented and tested on General Electric Healthcare products and relies on the PET Duetto image reconstruction toolbox available from GE through a research collaboration agreement. Functionality includes a graphical user interface (GUI) for data retrieval from the scanner console, PET image reconstruction, definition and batch generation of user defined lesions and building of an image database of synthetic lesion and their ground truth.
  • The image perception suite enables a researcher to conduct and analyze an image perception study. A library of images and ground truth data (e.g. synthetic lesions) is used to run the study, collect user responses and then perform initial analysis such as deriving performance metrics (e.g. LOD).

The work was first described in ***Manuscript under review***. Both tools may be run as an application on a personal computer or as a web-hosted service. The latter enables to host the service on a single server computer that is accessible on the network, reducing setup and maintenance time and leveraging computing power to process data in the cloud.

Bland-Altman and Correlation Analysis

Open source tool for plotting Bland-Altman and Correlation plots and performing statistical analysis.


An interactive image viewer for 3D and 4D data. It is intended for visualization and interaction with tomographic medical images. The 4th dimension can represent time, phase, energy or any other image component. Time-activity curves of the user selected pixel are displayed and the plot can be used specify the time range to summarize and display. Fused image overlay with a second volume (3D) image and mesh intersection contours are optional features.
Input argument can be used to customize/initialize the display. Callback function can used to integrate the viewer into custom applications. The viewer can be called in wait-for-close or continue-execution mode.
Demo call functions and data are included in the package along with instructions.


Similar to View4D in many ways, but uses a single display of intersecting slices through a volume. Produces prettier images, but is typically less functional than View4D. This interactive image viewer is intended to explore multi-frame tomographic medical image data consisting of 3 spatial domains and a 4th domain (e.g. time, phase, energy). Input argument can be used to initialize the display. A callback function can be specified to trigger on pixel selection and it can be run in wait-for-close mode, in which the user can select a cropped volume, 2D slices, and a range of time frames (4th dimension). So it is simple to integrate into other programs.

DICOM Convert Server

Reading DICOM image series into Matlab can be challenging due to a lack of standardized format among vendors and can be slow. The DICOM Convert Server is a free executable that monitors an incoming directory and converts DICOM series into a single matlab (.mat) file containing the image volume and header information. Detailed instruction are included in the accompanying manual.

Other Contributions

Glomerular Filtration Rate Electronic Worksheet Template

The GFR spreadsheet incorporates quality control indicators as described in NMC 2019:40(1):30-40. It is designed to be used in a routine clinical setting to calculate GFR and generate a printed report as part of a complete patient workup. The spreadsheet can be tailored to site's needs. Important note: By using our tool, you agree to these terms and conditions, made between you and the Ottawa Hospital Research Institute and the Ottawa Hospital. The template should be tailored to a clinic's needs and is provided solely as a guidance template. The template is provided as is, with no guarantees or warranties, and its use is at your own risk. It is not a licensed medical device in any jurisdiction.
The Ottawa Hospital Research Institute, the Ottawa Hospital, and its researchers, including Ran Klein, expressly disclaim all warranties of any kind regarding this tool, either express or implied, including, without limitation, warranties of title, non-infringement, and implied warranties of merchantability or fitness for a particular purpose. The Ottawa Hospital Research Institute, the Ottawa Hospital, and its researchers, including Ran Klein, will have no liability for any damages, injury or any other loss whatsoever suffered as a result of use of, or reliance upon, this tool. In the case of loss, injury or damage of any kind to a person resulting from your use of this tool, you agree to indemnify and hold harmless the Ottawa Hospital Research Institute, the Ottawa Hospital, and its researchers, including Ran Klein, from any and all claims arising therefrom.

Commercial Medical Products

RUBY-FILL® (Rubidium Rb82 Generator and Infuser)

Developed as during my Master's thesis work, the infuser delivers a controlled activity profile to the patient which is optimized for dynamic cardiac imaging on 3D PET scanners, to avoid saturation of the detectors at early phases of the scan and ensuring ample activity for late phases of the scan. Hence both high quality myocardial perfusion images generated and precise myocardial blood flow measurements can be made from a single acquisition, increasing clinical throughput, reducing radiation exposure, and providing encompassing diagnostic information. The system also offers unique quality and safety features that enforce rigorous radiation protection while extending the useful life of the 82Rb/82Sr generator.

4DM Myocardial Blood Flow Quantification Software

Dynamic image analysis algorithms developed and validated at the during my PhD and Research Associate day at the University of Ottawa Heart Institute, National Cardiac PET Centre, have been implemented and commercialized by INVIA Medical Imaging Solutions. The Coronary Flow Reserve (CFR) package processed dynamic PET and SPECT images to measure regional myocardial blood flow and coronary flow reserve to improve diagnosis of ischemic disease that may be missed by conventional imaging technology.