IT’IS and ZMT release open source version of the medical image segmentation and modeling toolkit iSEG
The Medical Image Segmentation Tool Set iSEG, originally developed by IT'IS as an in-house solution for the creation of computational anatomical phantoms such as our widely used Virtual Population, is now open source. This important step will facilitate the further improvement, extension, and eventual re-purposing of the iSEG platform for communities beyond its original scope.
The iSEG medical-image segmentation and modeling toolkit is now open source. Watch the introductory tutorial here.
Compared to alternative software, iSEG is able to handle enormous 3D image datasets and manage large numbers of different tissues or complex tissue hierarchies, making it the ideal toolbox for the efficient, fast, and flexible generation of anatomical phantoms from various types of imaging data. Ever since its development, iSEG has been licensed to Z43 partner ZMT for integration into ZMT’s Sim4Life simulation platform as an image-modeling module that allows users to create patient-specific anatomical geometries for dosimetry, hyperthermia, neuro-stimulation, and other life science applications.
The decision to make iSEG open source was made in recognition of the multitude of diverse questions that arise in medical-image segmentation, with powerful problem-specific algorithms and workflows. iSEG is released under the very permissive MIT license on GitHub, which enables users to create their own extensions. To support this feature, we implemented an easy-to-use plugin mechanism to allow the addition of new algorithms with simple user interfaces without having to modify the iSEG core.
We hope this approach will encourage a growing community of researchers and developers to use and extend iSEG for their individual projects. Instructions for building from the source code and tutorials for first-time users are available on our GitHub page.
IT'IS and ZMT remain committed to maintaining and extending iSEG in the future.
Ilaria Liorni, Bryn Lloyd, Silvia Farcito, and Niels Kuster, in Computational Anatomical Animal Models: Methodological developments and research applications, Edited by Habib Zaidi, Pages 11-1 – 11-18, online December 2018
Esra Neufeld, Bryn Lloyd, Beatrice Schneider, Wolfgang Kainz, and Niels Kuster, Frontiers in Physiology, section Computational Physiology and Medicine, online 16 November 2018, doi: 10.3389/fphys.2018.01594
Professor Dr. Philippe Cattin of the University of Basel Department of Biomedical Engineering was a guest speaker in the BBL seminar series with a presentation on "Volume Rendering in Virtual Reality (VR²)".
National Toxicology Program (NTP) Technical Reports: Toxicology and Carcinogenesis Studies in Hsd:Sprague Dawley SD Rats Exposed to Whole-Body Radio Frequency Radiation at a Frequency (900 MHz) and Modulations (GSM and CDMA) Used by Cell Phones (TR595) and Toxicology and Carcinogenesis Studies in B6C3F1/N Mice Exposed to Whole-Body Radio Frequency Radiation at a Frequency (1,900 MHz) and Modulations (GSM and CDMA) Used by Cell Phones (TR596)
IT’IS in Nature: Our in silico neurostimulation tools are being used in groundbreaking research, but we don’t stop there ‒ we are pleased to announce the first neuro-functionalized computational anatomical model Yoon-sun V4.0.
A paper – co-authored by Esra Neufeld and Niels Kuster – published 31 October 2018 in Nature, on the results of a study in which three paraplegic patients recovered the ability to walk after years of paralysis, has been widely covered in the popular press worldwide.
Esra Neufeld, Eduardo Carrasco, Manuel Murbach, Quirino Balzano, Andreas Christ, and Niels Kuster, Bioelectromagnetics, December 2018, Volume 39, Issue 8, pp. 617–630; online 01 November 2018; doi: https://doi.org/10.1002/bem.22147
Fabien B. Wagner, Jean-Baptiste Mignardot, Camille G. Le Goff-Mignardot, Robin Demesmaeker, Salif Komi, Marco Capogrosso, Andreas Rowald, Ismael Seáñez, Miroslav Caban, Elvira Pirondini, Molywan Vat, Laura McCracken, Roman Heimgartner, Isabelle Fodor, Anne Watrin, Perrine Seguin, Edorardo Paoles, Katrien Van Den Keybus, Grégoire Eberle, Brigitte Schurch, Etienne Pralong, Fabio Becce, John Prior, Nicholas Buse, Rik Buschman, Esra Neufeld, Niels Kuster, Stefano Carda, Joachim von Zitzewitz, Vincent Delattre, Tim Denison, Hendrik Lambert, Karen Minassian, Jocelyne Bloch, and Grégoire Courtine, Nature, Volume 563, Issue 7729, pages 65–71, online 31 October 2018, doi: https://doi.org/10.1038/s41586-018-0649-2
Professor Dr. Angelo Iollo of INRIA and Dr. Haysam Telib of Optimad Engineering were guest speakers in the BBL seminar series with a presentation on “Convergence Between Data and High-Fidelity Numerical Models”.
Professor Dr. Klaas Enno Stephan of the Institute for Biomedical Engineering, University of Zurich and ETH Zurich, was a guest speaker in the BBL seminar series with a presentation on "Translational Neuromodeling for Psychiatry and Psychosomatics".
Professor Theodoros Samaras of the Aristotle University of Thessaloniki in Greece was a special guest presenter in the IT'IS Brown-Bag-Lunch (BBL) seminar series on Tuesday 28 August 2018 with a presentation on "Magnetic Nanoparticles as Therapeutic Agents: Focusing on the Role of a Scientist and Engineer".
IT’IS Director Niels Kuster was an international expert speaker at the Standards Regulations Testing Certifications (SRTC) 2018 Engineering Seminar in New Delhi, India. The two-day seminar-workshop, held 25 – 26 July 2018, featured presentations by representatives of the Indian government to introduce its program for mandatory testing and certification of telecommunications equipment. BNNSPEAG participated with a booth, with live demonstrations of cSAR3D and advice on state-of-the-art test facilities the newly formulated Mandatory Testing and Certification of Telecom Equipment (MTCTE) test protocols.
IT’IS is proud to announce the release of the first Asian member of our ViP, the Korean female computational anatomical model “Yoon-sun cV3.1”! The new phantom is based on high-quality images with a resolution of 0.1 x 0.1 x 0.2 mm and provides unmatched details from head to toe.
On Wednesday July 11, Dr. Jeffrey Fong of the National Institute of Standards & Technology (NIST) in Gaithersburg MD, USA, visited IT'IS as a guest speaker in the Brown Bag Lunch Seminar series with a talk on "Uncertainty Quantification Tools for Brain Metrology and an Application to the Multimodal Imaging-Based Detailed Anatomical (MIDA) Head-Neck Model."
IT'IS Director Niels Kuster presented presented keynote lectures on “EM Evaluation and Optimization of IoT Systems: Standards, Software and Instrumentations” and “Workflow for Demonstration of Compliance of Transmitters Operating above 10 GHz” at a symposium on IoT co-organized by the AUDEN Group and the IEEE EMC Chapter in Taipei on July 4, 2018.
Sean Hill, Professor at the University of Toronto Faculty of Medicine visited IT'IS as a guest speaker in the Brown Bag Lunch Seminar series with a talk on "The Multiscale Brain: Linking Genes, Brain States, Behavior and the Clinic."
A paper co-authored by several researchers of the IT’IS Foundation, “Novel hyperthermia applicator system allows adaptive treatment planning: Preliminary clinical results in tumour-bearing animal”, is on the cover of the June 2018 issue of the June 2018 issue of the journal.