The final results and impact

1. Potential impact

The socio-economic impact of cancer in the European Union is immense and puts a huge burden on society, with an estimated cost of 126 billion euro in 2009 (Luengo-Fernandez R et al., 2013). A census and in depth understanding of molecular players regulating different aspects of progression through the cell cycle as well as cell migration is of crucial importance for the development of cancer treatments. A major challenge in the clinical treatment of hyperproliferative disorders such as cancer is that the treatment should specifically target cells that undergo uncontrolled proliferation, but should not harm normal, healthy cells.

The field of systems microscopy is still just emerging, but has proven its impact in being able to powerfully combine systems biology with detailed visual analysis of cellular processes. Thus, the Systems Microscopy NoE took on the task to enable systems biology of complex cellular processes by developing and providing common technical and computational tools for systems microscopy, experimental and theoretical resources to carry out systems experiments and model their results, thus providing a generic approach for next generation systems biology.  

At the beginning of this project experimental methods for systems biology to analyze biological processes in space and time were limited in the ability to resolve this spatiotemporal complexity during certain biological processes. During the course of this project, Systems Microscopy NoE consortium was able to successfully develop technologies that cannot only capture data and build models in four dimensions, three-dimensional space and time, but as well address dynamic events in single living cells. The developed technologies can be used for a wide field of research including the investigation of various cellular processes and protein networks, drug screens, and discovery of cancer biomarkers. Moreover, new knowledge about cell division and cell migration is at the basis of many key processes of normal human physiology and disease, such as infertility and cancer, and will therefore be an important value for society and future medical applications.

Cutting edge mathematical methods and computational software are essential for systems microscopy in order to tackle the tremendous amount of data to be analyzes as well as the complexity of it. Thus, we developed computational tools that were made available to the public as open source software. These technologies have been disseminated through several international workshops on biological computer vision and machine learning, and it has been widely used by the Systems Microscopy consortium members, as well as by outside researchers. This has also contributed to the training of a generation of researchers that are highly qualified to work in small biotech companies as well as large pharmaceutical companies, in light of an increasing demand for high-content screening technology. Further, we applied the computer vision technology to elucidate molecular mechanisms underlying cell division, thus providing fundamental insights into the regulation of cell division by phosphatases, which might provide candidate targets for future developments of anti-cancer therapeutics. On the data analysis side, much of the theoretical groundwork existed already at the start of this project but not particularly applicable for systems microscopy. We focused our research to develop and improve already existing tools such as classification algorithms for recognition of phenotype of interest from dynamic image features or to define and navigate phenotype clusters and (dis)similarity landscapes and relate them to protein interactions and pathway network.

We have been actively working in the development of algorithms and bioinformatics' processes to determine novel functional and phenotypic associations using IT technologies and public database repositories. Our work has been intensive in the implementation of effective gene selection strategies, by integrating and exploiting several heterogeneous biological graphs. A standard genome-wide time-lapse imaging study easily reaches several hundred thousand euros, a sum which goes beyond the budget of most laboratories. We demonstrated that the in silico selection of genes allows investigators to focus experimental screens on the most likely candidates, reducing dramatically the complexity and cost associated to high-resolution time-lapse imaging assays. This work has been disseminated by different publications, and it is accessible to the general society by mean of the web tool Fun-L (http://funl.org).

Like most high-throughput methodologies, systems microscopy generates vast amounts of raw data, typically digital images, which come in different formats and undergo several data processing steps before meaningful biological information can be extracted. To maximize this benefit to society, we have focused on the establishment of standards and protocols for Systems Microscopy experiments and created a prototype database for systems microscopy data. Notably, we established a set of standards for outlining the minimal information about a Systems Microscopy experiment that should be included when sharing and presenting imaging data. So that future researchers can speak the same scientific language, we additionally established ontologies for describing imaging quantities. As science always has the most positive benefit on society when its results are consistent and clearly communicated, thorough documentation of our methodologies has been made through reproducible research reports. As society benefits when scientists collaborate more effectively, we have taken advantage of big data methods (HDF5, PSM) to share imaging data across labs and software modalities. The methods and standards we have established for sharing and processing Systems Microscopy data are now publicly available; this culture of total transparency helps to further increase societal confidence in science. The goal of establishing a prototype database system was to explore various ways of gathering and representing reusable image data. The Cellular Phenotype Database (CPD) is a repository for data derived from high-throughput systems microscopy studies and is available accessible at http://www.ebi.ac.uk/fg/sym.  The valuable experience, the developed standards and technical know-how and elements from this project will be used for establishing a durable infrastructure for future image and related data sharing infrastructure, in particular bioinformatics infrastructure for EuroBioImaging infrastructure. The developed standards are already used for describing and depositing imaging data. As the molecular imaging data are playing increasingly important roles not only in biomedical research, but also in diagnostics, infrastructure for sharing these images that was prototypes in Cellular Phenotype Database (CPD) CPD is expected to have a major impact on biomedical research.

Today, we have the technological and computational tools to comprehensively analyze entire genomes, transcriptomes and proteomes. Yet the detailed description of all aspects of the phenotypes resulting from this molecular basis is still lagging behind. Analyzing these phenotypes in a comprehensive and quantitative way is therefore a prerequisite of understanding the biological processes that are fundamental for live and whose disruption is often the reason for disease. In the frame of Systems Microscopy, we concentrated on two aspects of computational phenotyping. First, we developed new computational workflows in order to comprehensively analyze cell migration from large-scale screening data. Application of these tools has allowed us to infer ontologies of movement types and genes with putative roles in this fundamental process. Importantly, the methods we developed will allow the scientific community to measure many more aspects of cellular movement and to thereby get deeper insights into this fundamental and complex biological process. Second, we focused on building the methodological framework and software tools to computationally phenotype diseased tissues. While the computational analysis of cells in culture is today well established, analyzing phenotypes in cancer tissue remains a very active field of research with many technical aspects that still need to be addressed. On the long run however, we believe that quantitative phenotyping of tissue sections is likely to routinely complement traditional omics techniques used in cancer research today. Indeed, histopathology images provide us with complementary pieces of information regarding spatial distributions and morphologies, which are not at all accessible with molecular techniques dominating the field today. Albeit neglected so far, these aspects turn out to be extremely important. This project therefore contributed to this emerging field that will probably heavily impact future research projects in the field of cancer genomics.

Several frontier technologies to highly important biological questions including cell division and cell migration have been developed within the frame of the Systems Microscopy NoE project. Super-resolution microscopy is a method that allows imaging biological samples at an unprecedented level of detail and spatial resolution. The impact of this method has been recognized by a Nobel Prize in Chemistry in 2014. This is an exciting and fast developing technological frontier, yet, several challenges still remain that limit the applicability of these methods to large scale biological questions. One key limitation is the slow data acquisition speeds and low experimental throughput, which make it challenging to apply these methods to large screens. We have addressed this limitation in the project by taking advantage of new developments in camera technologies that improve acquisition speed and field of view (scientific complementary metal oxide semiconductor, sCMOS cameras) and by implementing automation to streamline the data acquisition process. Based on the results we have obtained in Ricci et al, Cell, 2015, we have filed a patent (Patent n. 14/482,586). In addition, based on the results of the Systems Microscopy project, we were able to consolidate a new European project through the FET-Open scheme, in which we aim to develop a compact, user-friendly super-resolution microscope capable of imaging cellular phenotype at nanoscale spatial resolution with very high throughput, which we name the CellViewer. Overall, the results we achieved here helps consolidate EU’s leading position in key imaging technologies and in the application of these cutting-edge technologies to study the molecular events that ultimately can lead to cancer metastasis. Another highly advanced method which we made use of in this project is the revolutionary gene-editing technology, CRISPR/Cas9, to create reporter cell lines for the development of novel screening approaches to identify cell cycle regulators, both acting in mitosis and in other stages of the cell cycle. We have then adapted the CRISPR/Cas9 methodology to enable screening and identification of genes whose protein products are essential for cell growth and proliferation. We are currently applying this methodology to screen cell lines derived from different tumor types as well as quasi-normal human cells for genes that specifically drive proliferation of defined tumor types, but not of normal cells. In the immediate future, the method will be used to create an atlas of cell-type specific protein essentialities. Such information is expected to greatly aid the development of novel cancer drugs, which are more specific and thus have considerably fewer side-effects than conventional chemotherapeutics. Such improved therapies are expected to both improve the quality of life of cancer patients and at the same time reduce the burden on national health-systems.

  Breast cancer is the most prominent form of cancer for women. Despite the overall good survival rate, still around 30% of breast cancer patients die from metastatic disease. So-called triple negative breast cancer (CTNBC) is the most aggressive form, and cell lines derived from TNBCs are typically highly motile and invasive. In this project we have used a systems microscopy approach in combination with computational approaches to identify candidate genes that could serve as novel future drug targets for the treatment of breast cancer and inhibit the dissemination of cancer cells to distant target organs. For this we have implemented siRNA approaches in combination with high throughput microscopy and automated image analysis and have related our findings to patient material.

The project dedicated an entire work package to leverage the powerful systems microscopy tools developed within the other work packages in specific translational applications, such as exploration and diagnosis of the dependency of cancer on specific targets, or reactivity towards specific drugs. To this end we have established translational laboratory and data analysis strategies, involving fresh tissue samples directly from operations as well as in silico analytics that were applied in personalized medicine and drug discovery projects. The multidisciplinary methods and tools established can also be applied in other diseases than cancer, and we foresee that there is a growing interest towards these strategies and knowhow. For example, drug sensitivity and resistance testing could be expanded to other diseases by creation of living biobank models of the disease as well as disease-specific drug libraries. The image-based tools have led to a new-implemented research project “Next-generation image analysis solutions – towards image-based diagnostics” with Finnish Innovation agency and six partners, including SMEs in area of drug testing/therapeutics, University Hospital Laboratories, and Diagnostics Company. Many of the partners from Systems Microscopy consortium operate actively in new networks related to similar approaches, including international ESFRI infrastructure, such as EU-Openscreen, EATRIS, EuroBioImaging and European Cell-Based Assays Interest group. This will help to expand the impact of the translational application and outcome of systems microscopy and the Systems Microscopy NoE in general towards the European academic and industrial communities by applying the methods established in the project.

The approaches that were established within the System Microscopy project have also allowed establishing systems microscopy approaches in other related fields. Thus, our experiences in RNAi screening using imaging-based technologies have also been applied to the understanding of adaptive stress response signaling. Moreover we have applied these approaches in compound screening settings. Thus, our approaches established in Systems Microscopy have now contributed to a broader field beyond tumor cell proliferation, migration and metastasis. The further development of our technology platforms in the context of both settings has created further opportunities to strengthen the general application of system microscopy technologies. Leiden University is now the coordinator of the EU-Bioimaging High Throughput Microscopy Dutch Flagship Node, a facility that is operated jointly with the Netherlands Cancer Institute and the Utrecht Medical Center. Moreover, the technologies described above have resulted in successful joint applications for the ERC Advanced granting (prof. Foekens) and more recently within the Horizon2020 program (EU-ToxRisk project; Leiden University is coordinator). This would not have been possible without the further maturation of the systems microscopy technologies within Systems Microscopy project.

Systems Microscopy NoE consortium included IDEA Bio-Medical, an SME who contributed its expertise in imaging software development.  IDEA Bio-Medical developed the WiScan® - high content screening systems, and the image analysis software family, WiSoft®. WiSoft is based on standard and formats for files and parameters as defined in the Systems Microscopy consortium. During the work on the Systems Microscopy tasks, WiSoft was developed into a family of software featuring Athena and Minerva. Athena is application-based software for analysis of image-based data using set of pre-defined applications.  Minerva includes modular scripting capability, large variety of statistical tools and post analysis evaluation options. WiSoft can be used for analysis of a large variety of applications. It provides a solution for rapid quantification of large datasets. The flexibility of this software tool provides potential solutions for different users in the academy as well as in pharmaceutical companies. IDEA Bio-Medical continuously interacts with scientists in the academy and in the pharmaceutical industry and introduce adaptations to WiScan and WiSoft, based on input from these researchers. The WiSoft software include features that were specifically adapted for the requirements of the Systems Biology consortium users, including tools to analyze time lapse experiments, sub-population definition for cytometric studies and applications to detect and quantify sub-cellular features.  IDEA Bio-Medical has installations at customer sites in Europe, USA and Israel. IDEA Bio-Medical devoted significant effort to disseminating its technology in trade shows and scientific meetings and via news-release, as well as via training and delivering courses to the Systems Microscopy community and to a large variety of scientists.

The work performed within the frame of the Systems Microscopy NoE project provides tremendous benefits to society by increasing our knowledge of how living cells and tissues function and interact. The studies we have conducted will ultimately lead to advances in healthcare and technological innovation that will directly impact people’s lives. In addition, the newly developed technologies can be used not only in academic research, but as well in industrial research and thus create demand for more instruments which stimulates the economy. Moreover, the generation of data about dynamic protein networks in cells will be important for drug development applications, to better prioritize drug targets whose function is not redundant inside the disease relevant protein network and will therefore have a higher chance of impacting disease progression. Future joint academic and industrial collaborations should therefore undertake significant efforts to map out disease relevant dynamic cellular protein networks comprehensively and make this data and the tools to mine them available to increase the competitiveness of European pharma industry.

Contacts to decision-makers have been made in various occasions to ensure that Systems Microscopy approaches are notified and supported in the future science policies. As translation of science – such as personalized medicine- is of interest of lay people, we have organized public lectures and panels to discuss on these issues, as well as given interviews in TV and newspapers. The impact on training has been achieved by implementing the knowledge gained in the project in teaching personalized medicine, high throughput technologies, image analysis, and translational omics technologies, to students at the masters and PhD levels. The full impact of this Systems Microscopy NoE will continue to reveal itself in the future years.

2. Dissemination activities

Given the overall aim of our research to enable systems microscopy and to shape and promote this area of research, we followed a dissemination plan we set up at the beginning of the project with the goal of reaching out to the systems biology, cell biology, microscopy, biostatistics and bioinformatics research community but also to decision makers and the public.

Next-generation systems biology requires methods that can capture data and build models in four dimensions, three-dimensional space and time, and needs to address dynamic events in single living cells. The overall scientific goals the Systems Microscopy NoE consortium aimed at shaping and promoting a technological platform that can meet these demands in a durable fashion.

Thus, dissemination of the project results within as well as outside this network was a critical and integral part of the project. In addition, we envisioned that our translational and technological R&D results as well as our newly developed methodologies will be of high interest for industry.  

Dissemination of our research was carried out through two axes, horizontal dissemination within the project and to external members of the scientific community, and vertical dissemination covering all levels, from governments and local decision makers to industry and to the general public.

Our main methods to disseminate the project are listed below:

Publications

The Systems Microscopy NoE project has generated a high number of scientific articles (87 articles) in well-recognized peer-review journals (for a complete list, see Dissemination section in the Participant Portal). An overview of our accomplishments during the five years can be seen in Figure 1.

Figure 1. Publication trend during the course of the Systems Microscopy NoE project 2011-2015

We have an average of 22% for publications which appeared in journals with an IF (Impact Factor) above 10, Nature, Cell, Nature Medicine, Lancet, Oncology, only to mention a few of them. Importantly, many of these publications were collaborative publications between 2 or 3 Systems Microscopy NoE partners, thus attesting to the interdisciplinary and collaborative spirit within the project. In addition to these original research articles, a significant number of review articles in high-ranked journals were published by members of the consortium. Members of the consortium also wrote technical reports on general methodologies for mathematical modeling of cell migration and cell division, technical reports on methodologies for statistical methods for multi-dimensional imaged-based data and data integration, technical reports on machine learning methods for defining phenotypic similarity measures and technical report with portable systems microscopy format specifications as well as tutorial document with case studies demonstrating best practice for statistical data analysis of systems microscopy experiments.

Project website

The project website (www.systemsmicroscopy.eu) was set-up at the start of the project and comprises several domains including a public access domain and a password protected domain (access provided to the project partners, project officer). During the course of the Systems Microscopy NoE project, the webpage was updated continuously sharing with both the general public and research community the highlights of our research, and when appropriate availability of PDF files for download.

Several software developed by members of our consortium are available to the research community via our webpage for example: we created a Knowledge base of gene oriented data relevant to mitosis and cell migration named “Micycle” that is fully available to the research community via our website, the CellCognition image analysis platform, EBImage for image analysis, R/Bioconductor software for data analysis just to mention a few. In addition, our prototype database for Systems Microscopy data Cell Phenotype Data base is available to the research community as a prototype for a long term systems microscopy public data base. A population–level modelling software package http://www.bioconductor.org/packages/devel/bioc/html/mitoODE.html as well as the software matching functional gene modules and phenotypic categories www.micycle.uma.es developed by our consortium members is also available to the research community.

Conferences, seminars and workshops

Systems Microscopy NoE partners have attended a significant number of international meetings and conferences all around the world, as invited speaker thus promoting the worked performed within the Systems Microscopy project (for a complete list, see Dissemination section in the Participant Portal).

Moreover, the Systems Microscopy NoE arranged three open symposia on systems microscopy:

  • The first symposia “Mini-symposium on Systems Microscopy” took place in Malaga, Spain, 21th of February, 2011. The symposium was attended by 73 external participants (in addition to the 41 participants connected with the NoE).
  • Conference on “Systems-Level View of Cytoskeletal Function: Multi-scale approaches for understanding cell architecture and dynamics”, took place in Stockholm, 27-31th of October, 2014. This conference was attended by more than 200 participants, several of invites speakers were members of our consortium.
  • One day mini-symposium on “Resolving single cell heterogeneity – Systems microscopy meets single cell omics”, took place in Stockholm, 25th of September 2015. More than 130 researchers attended the symposium and several of the invited speakers were members of our consortium.

In addition, several members of our consortium organized user meetings or were co-organizers in other conferences and mini-symposia:

  • CellCognition user meeting (EMBL Heidelberg, 6.-8. 11.2013) to disseminate current software developments and strategies for improved biological assays within the consortium.
  • Workshop on image analysis How to analyze microscopic images? (20th of May, 2015, Helsinki Finland.
  • Workshop on “Metadata standards and data formats for high-throughput imaging”, 02 - 03. February 2015, EMBL Heidelberg.
  • Building Bridges Spring 2014: (19-20 of May. Helsinki, Finland): Building Bridges – Bio-Imaging in Clinical and Translational Research is a symposium arranged to bridge experts in the field of biomedical imaging with those in translational and clinical research.
  • Building Bridges Autumn 2014:  Personalized Health and Genomics in Clinical and Translational Research The Building Bridges symposia series is arranged to bridge clinical and basic/translational research and provide examples of how teams of investigators are working together to advance personalized medicine approaches.
  • Congress of the International Society for Advancement of Cytometry (CYTO 2015; Glasgow), 26 – 30 of June, Scientific Tutorial: "CellCognition: Image Analysis of Live Cell Imaging Data". Partner 9 lab participated as workshop tutor.

Contacts with media, general public and decision makers

A number of TV interviews, journal interviews and press releases took place during these 5 years. At the coordination site in Sweden, Stockholm, two press releases were issued, one by the press department at Karolinska Institutet at the beginning of the project, 2011, to mark the launch of the project and later on in 2011 in connection with project kick-off. In addition, two sets of brochures enclosing information about the Systems Microscopy NoE, its objectives and members involved in the project were put together and disseminated during the course of the project. These brochures were distributed among the partners whom further distributed the information about Systems Microscopy NoE consortium during meetings and conferences.

  • The www.systemsmicroscopy.eu has a section especially aimed towards non-expert visitor whom would like to get an understanding about Systems Microscopy and the scope of the project. The section was updated with movies presenting two complex biological processes investigated through our research, cell migration and cell division. In addition, the main results and conclusions of the work performed during the lifetime of the project were also disseminated to the public via our homepage (under project development section). The intention was to present in an easily understandable way the tremendous advances we are doing in this cutting-edge project each year.
  • Prof. Bob van de Water (Partner 6) was interviewed for television broadcasting by the Dutch National Television for the television show “Labyrinth”. The broadcasting took place on Wednesday 24th October 2012 (http://www.wetenschap24.nl/programmas/labyrint/labyrint-tv/2012/oktober/Het-Vrouwenhart.html).
  • Furthermore the Cell Observatory imaging facility is demonstrated to the general public through the student’s association Aesculapius at Leiden University:   (http://www.science.leidenuniv.nl/index.php/opening_cell_observatory).
  • ”Ett finsktillverkat mikroskop i fickstorlek, byggt av mobiltelefondelar: Kvanthopp”, Johan Lundin, Partner 4  as  Invited Speaker for, Svenska YLE, Finland (Television program) in 23.01.2014.
  • Prof. Staffan Strömblad (Partner 1) gave a talk to high school students (Popular science, at “Research Friday”, in Stockholm, Sept 27, 2013) and presented the science behind the Systems Microscopy project.
  • Prof. Staffan Strömblad (Partner 1) was hosting high school students from Wärmdö Gymnasium, Stockholm and gave popular science research presentation, demonstration of super-resolution microscopy (16th of Oct, 2014).
  • Prof. Staffan Strömblad (Partner 1) gave a popular science presentation before the university administrators at Karolinska Institutet, Department of biosciences and nutrition (25th of February, 2014).
  • Olli Kallioniemi (Partner 4) “Suomen lääkintäoikeuden ja –etiikan seura,  Ihmisen koko genomin testauksen hyödyntäminen sairausriskin arvioinnissa  - Talk at the Finnish Association for Medical Law and Ethics) Helsinki, Finland,  6th of March, .2014.
  • IDEA Bio-Medical (Partner 8) disseminated articles written by users of WiSoft software to large number of partners, customers and prospects across the globe.  The company also demonstrated WiSoft and associated capabilities to medical universities, primarily in the United States, and through its partners to universities in China, the Czech Republic, France and the United Kingdom. IDEA Bio-Medical presented its products, including WiSoft, in trade shows and exhibits.

 

Dissemination of our work to decision makers including national and international funding bodies was also set as a priority with the aim of sharing our successful results but also to promote funding for the area of systems microscopy in general but also for long-term network durability. Below you can find some of our efforts to ensure visibility towards the decision makers:

  • Prof. Olli Kallioniemi (Partner 4) has given an expert talk to Finnish parliament regarding the patient samples and bio-banking and organized several visits for members Finnish Parliament, rector and vice-rectors of University of Helsinki open day visit for journalists, as well as a visit for summer school students to the High-throughput Biomedicine Unit.
  • Following the release of the Horizon 2020 proposal on Nov 30th, 2011, the Systems Microscopy NoE consortium arranged a workshop in Brussels (23rd of April, 2013) with the aim of exchanging information between the scientists and the decision makers on views and policies regarding the, at that time,  upcoming Horizon 2020 program. The meeting gathered 23 participants representing EC officials (Bernard Mulligan and Philippe Jehenson), coordinators of several FP7 projects (Staffan Strömblad, Jussi Taipale, Rolf Lewensohn, Marc Kirschner), industry representative (Maria Flocco, Pfizer), national representatives for Sweden (Sandra Olivera) and The Netherlands (Sandra de Wild Chardonnens), Grants office Karolinska Institutet (Björn Kull) as well as several partners of the Systems Microscopy consortium.

 

 

 

Dissemination to the industry

A good dialogue with technical experts in industry is a prerequisite for the successful use, and for the continuous development, of modern microscopy techniques. The laboratories of the network performing microscopy regularly communicate areas for improvement to the producers of microscopes and optic components (Nikon, Leica, Andor, Zeiss and others). Industry representatives were invited to the research facilities to discuss ways forward.  Companies producing software for image analysis also belong to an industrial niche with which discussions for improved performance are reoccurring events. Below you can find a few examples around our efforts to create and conduct successful dialogues with the industry:

- IDEA-Bio Medical (Partner 8): presented its products and specifically WiSoft, to researchers in European drug companies and in 4 industrial companies in USA Demos and sales to pharmaceutical companies.

- University of Leiden (Partner 6): actively involved in the automation of the Nikon confocal microscopes. Nikon receives training on the application of the high content imaging platform, and Nikon costumers receive

- Karolinska Intitutet (Partner 1): Launch of collaboration with Nikon Europe in the form of a new Nikon Center of Excellence linked to the Live Cell Imaging microscopy facility at Karolinska Institutet directed by Staffan Strömblad.

- FIMM-UH (Partner 4): Through collaborations with companies, we have successfully presented Systems Microscopy NoE approaches and exploited the market and cooperation networks with industry, including microscope companies such as PerkinElmer (visiting FIMM-UH in August 2015) and Molecular Devices (2 teleconferences in August, microscopic demo and potential collaboration planned for 2016). For example, Prof. Olli Kallioniemi participated, as an invited speaker, to seminar “Science and business in dialogue”, organized by the rector of the University of Helsinki. Partner 4 also presented the Systems Microscopy project in a poster, which won a poster prize at Nordic Trial Alliance, 2015, Helsinki, Finland. This meeting, as well as ChemBio Finnish Fair, where three talks by FIMM researchers about Systems Medicine/Imaging-approaches enabled us to meet with and present our results to the Big Pharma and other industrial representatives. Within our TEKES FiDiPro Fellow Project of Dr. Peter Horvath (Next generation image analysis solutions – towards image-based diagnostics; a complementary project to Systems Microscopy), in which we develop further image analysis tools for future diagnostics, we have been closely collaborating with partner companies, including Quva Oy, Pharmatest Services, Oncos Therapeutics/Thargovax, Salwe Ltd. (Orion Diagnostica), Labcyte, and Helsinki University Hospital Laboratories.

Altogether, our dissemination strategy that we set up at the beginning of the project allowed us to continuously share our results, developments and achievements with the research community and public.

The final results obtained during this project generated data and models that further our systems-level understanding of cell division and migration, both of which are crucially involved in the development and progression of cancer, and thus relevant to human health. We developed novel testing systems for drug sensitivities and gene dependencies in primary cultures of cancer patients, expected to help guide future cancer diagnosis and therapy choices in personalized medicine. Furthermore, we development new imaging technologies and screening platforms as well as new computational methods,  statistics and bioinformatic tools for multi-dimensional image analysis. Moreover, we trained a new generation researchers within the field of systems microscopy whom will further develop the field of systems microscopy beyond the life time of the project.

Seventh Framework Programme

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