Collaborations
Huygens Remote Manager
Huygens Remote Manager (HRM), is an open source task manager that acts as a web-interface to Huygens Core. It can be used with any web-browser, and is therefore ideally suited for scheduling many image processing (high content/throughput) jobs and serving many different users from any location. The user-friendly HRM interface accepts templates from Huygens Essential and Professional, and facilitates an optimized connection to OMERO (open source) image data servers for data import and export.
HRM is an open-source application developed by the Montpellier Rio Imaging facility, the Facility for Advanced Imaging and Microscopy at the Friedrich Miescher Institute (FMI, Basel), the BioImaging and Optics Platform at the Ecole Polytechnique Fédérale de Lausanne, and Scientific Volume Imaging.
Research Projects
Scientific Volume Imaging has supported many grant applications of international projects involving high quality optical imaging, restoration and analysis, and a long track record of succesful collaborations with universities and research universities worldwide. You find here a short description of these projects.
NWO Talent Programme – Veni scheme: ‘‘Illuminating the microstructure of the human brain in health and disease: 3D histology by tissue clearing and light-sheet microscopy’’ (2020 - present)
Although our brain is 3-dimensional, it is currently investigated with small 2D tissue sections. In this research project novel microscopy approaches are developed for 3D imaging of large human brain samples, at cellular and sub-cellular resolution. This will set new standards for brain research and histology protocols in disease pathology investigations. SVI will collaborate with setting up an extensive pipeline for data processing with stitching and deconvolution of large data sets with the Huygens Software. Collaboration with Dr. A.K.D. Schueth (Maastricht University).
ProMiSe: Tackling defective Prefrontal development in Mendelian Syndromes - a compelling (pre-)clinical integrative approach”. NWA–ORC 2018. (2019 - present)
This project aims at improving our understanding of biological mechanisms underpinning psychiatric and cognitive aspects in Mendelian syndromes, and based on this, develop tailored intervention strategies targeted at the severe behavior and psychiatric problems that are frequently encountered. SVI contributes with the Huygens software to the restoration (deconvolution), visualization, and analysis of micropscopy data. This data is produced by the participating groups that are imaging biological cells (molecular networks) and tissue (cellular networks e.g., brain organoids). SVI imaging experts will provide training and help with the analysis of the image data on high-end servers. Collaboration with Prof.Dr. S.M. Kolk (Donders Institute for Brain, Cognition and Behaviour, Radboud University)
MUSIQ - Multiphoton Microscopy and Ultrafast Spectroscopy: Imaging meets Quantum - EU, H2020 MSCA-ITN-2018 (2019 - 2023)
SVI acts is involved as a partner in Innovative Training Network with the acronym “MUSIQ”, which is being funded by the European Union under its Horizon 2020 Programme. Goal of this network is to recruit 15 Early Stage Researchers to work toward the central ambitious goal of developing the next-generation optical microscopy exploiting quantum coherent nonlinear phenomena. The network brings together a unique team of 7 world-leading academics and 6 high tech companies at the forefront of optical microscopy and ultrafast laser technology developments merged with fundamental understanding of coherent light-matter interaction phenomena, development of quantitative image analysis tools, and biomedical/pharmaceutical real-world applications. Registered office of the consortium is based at Cardiff University.
PolarNet - Principles of Polarity - EU, H2020 MSCA-ITN-2015 (2015 - 2019)
The ability of cells to polarize underlies the most basic biological functions such as motility and response to external challenges, but also the formation and maintenance of tissues in a multicellular organism. The importance of cell polarity is underscored by the fact that cell polarity is essential for animal development and is perturbed in disease states such as cancer. PolarNet brings together academic and private partners from 7 European countries to establish a multidisciplinary, intersectoral training and research programme that will study the basic principles of cell polarity. The research will combine complementary model systems, and employ a broad set of approaches such as advanced genetics, protein biochemistry, high-resolution live imaging and image analysis, biophysics and theoretical modelling. The tight collaboration with non-academic partners (like SVI) will strengthen the technological base of different projects and provide early stage researchers with insights into the translation potential of the performed studies and the career development opportunities in biomedical industry.
Scaled Gradient Projection (SGP) algorithm – In collaboration with University Genoa, Italy (2014 and 2015)
This collaboration included the implementation of the SGP algorithm in the Huygens software.
Huygens remote Manager Project (2004-present)
To facilitate the restoration of increasing volumes of microscopy data, researchers at the Montpellier RIO Imaging (CNRS, France) started in 2004 developing the open-source, multi-user, web-based Remote Manager (HRM) for the Huygens software (www.svi.nl/Huygens). Soon after, several other research institutes among which the EPFL Lausanne (Switzerland), and Scientific Volume Imaging b.v. joined this open-source project. The HRM project is a succesful ongoing project with nowadays more than 10 academic institutes involved (see https://hrm.svi.nl/), and yearly hackatons organized by SVI). The HRM web interface has proven to be useful in the large-scale automation and optimization of the image processing pipelines at a growing number of facilities worldwide.
SVI imaging partner in leading-edge Nanoscope Science Project (2012-2016)
The Dutch Technology Foundation (STW) awarded a consortium of scientists and companies in The Netherlands among them Huygens SVI with an "STW-perspectief programme". The aim of this program is to make modern nanoscopy technology broadly applicable in biomedical research. Nanoscopy is also known as super-resolution microscopy as it defeats the 'Von Abbe' limit allowing no better resolution than around 250 nm.
With the Huygens deconvolution software the 'Von Abbe' limit is already challenged as three- or fourfold resolution increases are normal. In a sub-standard situation 22 nm was easily obtained with the new superresolution microscope, STED 22 nm deconvolution,and the Huygens software.
The aim is to develop new technologies that enable full implementation of nanoscopy in biomedical research. Program leader Prof. Erik Manders (Leeuwenhoek Centre for Advanced Microscopy, Amsterdam) believes that within 10 years nanoscopy will become the standard technique with important consequences for biomedical research, health care and the high-tech industry. Huygens SVI is involved to monitor the quality of the imaging environment.
In this program, 12 positions are available for enthusiastic and talented PhD students and post-docs who like to contribute to the next step in advanced microscopy: "biomedical nanoscopy". Candidates with a background ranging from engineering, physics and (bio)chemistry to cell biology and molecular biology are encouraged to send their CV, motivation-letter according to the directions mentioned on the website STW-nanoscopy.nl (external link) . (Source Prof. Dr. Erik Manders)
Find great traineeships with SVI at Internships
EU Framework 6 projects
Scientific Volume Imaging not only develops software applications but also participates in research of scientific projects. SVI worked with various scientific institutes in these FP6 research projects between 2002 and 2006:
Automation (Completed)
Major research topic: research into diminishing one critical constraint of established techniques namely that samples must be stabilised by attachment to an optically transparent surface.Non-adherent cell types therefore fall outside this range.
The severity of this limitation becomes clear when one considers that for basic- and biomedical-research, cell-based assay and cell-diagnostic applications some of the most important targets are non-adherent cells, for example, stem cells, systemic cancer cells and lymphocytes. The aim of the project was to built a completely new 3D imaging strategy targeted specifically at live, non-adherent cells.
The core technology combines proprietary state of the art hardware for suspended cell manipulation with super high-speed dynamic imaging methods. Around this, our consortium draws together unique expertise from four SME and three academic teams providing the necessary critical-mass to industrialize this methodology as 1) a routine research-bench tool, and 2) a high-throughput, high-content imaging device AUTOMATION (automated tomographic analysis station).
See also the Micro Rotation Workbench to learn more about the methods developed.
3DGenome (Completed)
Our knowledge about gene regulation at the single gene and the epigenetic levelhasrapidly expanded. However, at the turn of the millenium our understanding of the role in gene control of the three-dimensional folding of the genome in the cell nucleus, was poorly understood; this despite the fact that considerable evidence was available showing that large-scale chromatin organization played an important role in gene control in higher eukaryotes.
The 3Dgenome consortium members developd state-of-the-art 3D light microscopy techniques, along with image processing and analysis tools to visualise DNA inside the cell. They correlated the genome's 3D structure with the expression of specific genes in human, mice and drosophila cells. Using this range of model systems helped establish which aspects of the 3D genome structure have been conserved through evolution and which are most likely to play an important role in gene regulation.