@article {Ilina2018a, title = {3D Surface Scanning for Tumour Localization in Non-Melanoma Skin Cancer}, year = {2018}, month = {03/2018}, address = {Toronto, Canada}, author = {Anna Ilina and Csaba Pinter and Andras Lasso and Ingrid Lai and C.P. Joshi and Kevin Alexander and L. John Schreiner and Timothy Hanna and Gabor Fichtinger} } @article {Alexander2018, title = {Streamlined open-source gel dosimetry analysis in 3D slicer}, journal = {Biomedical Physics \& Engineering Express}, volume = {4}, number = {4}, year = {2018}, month = {07/2018}, pages = {045041}, abstract = {

Three dimensional dosimetry is being used in an increasingly wide variety of clinical applications as more gel and radiochromic plastic dosimeters become available. However, accessible 3D dosimetry analysis tools have not kept pace. 3D dosimetry data analysis is time consuming and laborious, creating a barrier to entry for busy clinical environments. To help in the adoption of 3D dosimetry, we have produced a streamlined, open-source dosimetry analysis system by developing a custom extension in 3D Slicer, called the Gel Dosimetry Analysis slicelet, which enables rapid and accurate data analysis. To assist those interested in adopting 3D dosimetry in their clinic or those unfamiliar with what is involved in a 3D dosimeter experiment, we first present the workflow of a typical gel dosimetry experiment. This is followed by the results of experiments used to validate, step-wise, each component of our software. Overall, our software has made a full 3D gel dosimeter analysis roughly 20 times faster than previous analysis systems.

}, keywords = {3d dosimetry, gel dosimetry, Radiation therapy}, doi = {https://doi.org/10.1088/2057-1976/aad0cf}, url = {http://stacks.iop.org/2057-1976/4/i=4/a=045041}, author = {Kevin Alexander and Csaba Pinter and Gabor Fichtinger and Tim Olding and L. John Schreiner} } @article {Ilina2018b, title = {Target Definition with 3D Surface Scanning for Orthovoltage Radiation Therapy Planning}, year = {2018}, address = {Berlin, Germany}, author = {Anna Ilina and Csaba Pinter and Andras Lasso and Ingrid Lai and C.P. Joshi and Kevin Alexander and L. John Schreiner and Timothy Hanna and Gabor Fichtinger} } @conference {Alexander2016, title = {Development of 3D Slicer Based Film Dosimetry Analysis}, booktitle = {IC3DDose (9th International Conference on 3D Radiation Dosimetry)}, volume = {847}, year = {2016}, month = {10/2016}, publisher = {IOP Science}, organization = {IOP Science}, address = {Houston, TX, USA}, abstract = {

Radiochromic film dosimetry has been widely adopted in the clinic as it is a convenient option for dose measurement and verification. Film dosimetry analysis is typically performed using expensive commercial software, or custom made scripts in Matlab. However, common clinical film analysis software is not transparent regarding what corrections/optimizations are running behind the scenes. An extension to the open-source medical imaging platform 3D Slicer has been designed and implemented in our centre for film dosimetry analysis. This extension enables importing treatment planning system dose and film imaging data, film calibration, registration, and comparison of 2D dose distributions, enabling greater accessibility to film analysis and higher reliability.

}, author = {Kevin Alexander and Alec Robinson and Csaba Pinter and Gabor Fichtinger and John Schreiner} } @conference {Alexander2015, title = {3D Slicer Gel Dosimetry Analysis: Validation of the Calibration Process}, booktitle = {World Congress on Medical Physics and Biomedical Engineering, June 7-12, 2015, Toronto, Canada}, volume = {51}, year = {2015}, month = {06/2015}, pages = {521-524}, publisher = {Springer International Publishing}, organization = {Springer International Publishing}, abstract = {

An extension tailored to dose data processing and analysis has been developed in the open source imaging application 3D Slicer to aid in routine clinical use of gel dosim-etry. This extension allows for registration, calibration, and comparison of 3D gel dosimeter data (imaged using an optical CT scanner) to treatment planning data. In this work, we present the accuracy and reproducibility of the gel dosimeter calibration component of the 3D Slicer extension. We examine the consistency of the calibration curves for a range of electron beam irradiations, and the inter-user variability of the gel dosimeter calibration process.

}, doi = {10.1007/978-3-319-19387-8_128}, url = {http://link.springer.com/chapter/10.1007\%2F978-3-319-19387-8_128}, author = {Kevin Alexander and Csaba Pinter and Jennifer Andrea and Gabor Fichtinger and John Schreiner} } @article {Alexander2015a, title = {Cross-Validation of 3D Gamma Comparison Tools}, volume = {42}, number = {15}, year = {2015}, month = {06/2015}, pages = {3385-3385}, publisher = {Medical Physics}, doi = {10.1118/1.4924592}, author = {Kevin Alexander and Christopher Jechel and Csaba Pinter and Greg Salomons and Andras Lasso and Gabor Fichtinger and L. John Schreiner} } @conference {Pinter2015, title = {Performing radiation therapy research using the open-source SlicerRT toolkit}, booktitle = {World Congress on Medical Physics and Biomedical Engineering}, year = {2015}, month = {07/2015}, publisher = {Springer}, organization = {Springer}, address = {Toronto}, abstract = {

Radiation therapy (RT) is a common treatment option for a wide variety of cancer types. Despite significant improvements in this technique over the past years, software tools for research in RT are limited to either expensive, closed, proprietary applications or heterogeneous sets of open-source software packages with limited scope, reliability, and user support. Our SlicerRT toolkit aspires to overcome these limitations by providing an extensive set of RT research tools leveraging the advanced visualization and image analysis features of its base platform 3D Slicer.

The SlicerRT toolkit comprises of a set of 3D Slicer extensions: SlicerRT core, Matlab Bridge, Multi-dimensional Data, and Gel Dosimetry. The SlicerRT core extension contains 26 modules, many of which provide common RT tools used in most RT research scenarios. Matlab Bridge provides a convenient way for connecting the researchers{\textquoteright} existing MATLAB algorithms to the SlicerRT ecosystem. Multi-dimensional Data offers a feature set for handling multi-dimensional datasets, such as longitudinal studies or 4D data. Finally, Gel Dosimetry facilitates gel dosimetry analysis workflows through a streamlined, workflow-based end-user application. It serves as an example and proof of concept for such applications implementing advanced clinical or research workflows.

Using these open-source software tools makes it possible to conduct cutting edge RT research without parallel development efforts. It acts as a medium into which researchers can integrate their methods into, and which they can use to perform comparative validation, develop novel RT techniques, or transition advanced methods into routine clinical practice.

}, doi = {10.1007/978-3-319-19387-8_152}, author = {Csaba Pinter and Andras Lasso and An Wang and Gregory C Sharp and Kevin Alexander and David Jaffray and Gabor Fichtinger} } @conference {Alexander2014, title = {Implementation of an efficient workflow process for gel dosimetry using 3D Slicer}, booktitle = {IC3DDose}, year = {2014}, abstract = {

One challenge in gel dosimetry is the manipulation and analysis of complex data sets from different systems. In this paper, we describe a simple and fast gel dosimetry analysis tool for radiation therapy dose deliveries. Using the open source medical imaging software 3D Slicer, an extension was designed and implemented for the purpose of importing treatment planning system dose, CT imaging from simulation and at treatment, and optical CT gel dosimeter data. The extension also allows for calibration of gel dosimeter data, registration, and comparison of 3D dose distributions. The development of an open source gel dosimetry processing environment may help adoption of gels in the clinic.

}, author = {Kevin Alexander and Csaba Pinter and Jennifer Andrea and Gabor Fichtinger and John Schreiner} } @article {Lasso2014b, title = {Running Matlab functions in 3D Slicer using MatlabBridge}, year = {2014}, month = {03/2014}, pages = {78}, address = {Toronto, ON, Canada, March 24-25, 2014}, url = {http://www.imno.ca/sites/default/files/2014Proceedings.pdf}, author = {Andras Lasso and Kevin Alexander and Christopher Jechel and Kevin Wang and John Schreiner and Gabor Fichtinger} } @article {Andrea2014a, title = {Slicelet implementation for gel dosimetry analysis}, year = {2014}, month = {03/2014}, pages = {63}, address = {Toronto, Canada}, url = {http://www.imno.ca/sites/default/files/2014Proceedings.pdf}, author = {Jennifer Andrea and Mattea Welch and Csaba Pinter and Kevin Alexander and John Schreiner and Gabor Fichtinger} }