Development of freely available software tools from the perspective of a multi user core facility

Within the last ten to fifteen years the landscape of research infrastructures has changed remarkably, especially in the field of life science. In order to perform state-of-the-art research nowadays, it is necessary to have access to a variety of different high-end technologies. Individual researchers or even research groups can hardly master all of these rapidly advancing technologies. “Post-docs” are typically employed on non-permanent contracts or even individual fellowships and do have -understandablymore interest in advancing their own career than establishing long-term research infrastructures. Therefore it turned out to be useful to bundle these technologies in so called core facilities or platforms. The clear benefit of these platforms was the presence of well trained staff scientists able to accumulate and redistribute knowledge and experience to other scientists and projects as well as to push the emerging technologies to their limits. It is not surprising that more and more institutes have invested substantially in the recent years to establish so-called multi-user core facilities. As a positive side-effect, equipment could be used more efficiently and the purchase of unnecessary instruments could be avoided. Nevertheless, supporting scientists and helping them to answer challenging questions was the main driving force for the establishment of these facilities. In the field of light microscopy, this required the parallel development and implementation of image processing and analysis capabilities as well as instrumentation for the acquisitions. Only by accumulating expertise in both fields could high-level support be guaranteed. Even so, there had always been interactions between groups in the field of signal/image processing and biologists or life scientists who were in need of customized solutions in order to process or analyze images coming from image based instrumentation. Without any doubt this helped to decipher a variety of challenging biological problems, but often led to the development of extremely customized processing pipelines which were of very limited generic use. Development and maintenance of user friendly, easily usable software packages with a state-of-the-art generic user interfaces (GUI) is time consuming. Therefore this is seldom in the interest of research groups with a high level expertise in developing new image processing algorithms. This results that access to powerful and new algorithms is somewhat hindered for biologists. Thus the utility of these algorithms could be massively increased if the gap between developers and potential end-users was reduced. Once established, microscopy core-facilities are well positioned to at least partially close this gap. As facilitating access to instruments and analysis infrastructure is the main goal, they have the possibility to invest in assembling and maintaining easily accessible software solutions. However, in most of the cases they do neither have the expertise nor the means to develop powerful algorithms therefore making use of already available algorithms is often a very promising approach which has been exploited by the BioImaging & Optics platform (BIOP) in the last years. Recently, the increasing degree of automation added another layer of complexity. Single data-sets of a microscopy experiment can easily reach several Gigabytes (GB) nowadays. Combined with automated loading robots, motorized stages, spectral detectors or high-speed cameras, Terabytes of data can be produced within a single day by these instruments. Slide-scanners, which are becoming more and more popular even outside clinical routine laboratories, might serve as one prominent example. Although the processing power of computers is continuously increasing, the display and analysis of large datasets still remains a challenge and is becoming a bottle-neck for obtaining results. Automated image analysis pipe-lines are highly desirable as they are a key requirement in order to make image-based technologies more quantitative and reproducible. Multi-user facilities in particular are often confronted with the fact that the existing software solutions typically included with the instrument/microscope are limited in functionality and often are not compatible with customized analysis algorithms. Even if commercial solutions exist, is it often cumbersome to share them with the entire user community of a platform, either because shared licenses are not available or because they are simply too expensive. Therefore freely available software tools are essential especially in the field of light microscopy. If the developed software tools are provided with the source code (open source) they guarantee transparent, platform independent and portable analysis strategies which can be easily repeated by the research community. Microscopy: advances in scientific research and education (A. Mendez-Vilas, Ed.) __________________________________________________________________