Grey’s Anatomy

Platform

Chair of the consortium: Jorma Isola, IBT (former IMT) Members: Johan Lundin, FIMM

Development and restructuring of technology services

Tissue biobanking technology patform has progressed according to the study plan in developing new im- proved virtual microscopy based methods, which will have a central role in cancer specimen biobanking. New improved virtual microscopy techniques have been developed and have been introduced also to the customers, such as LabQuality Inc., and to the organiz- ers of the European Congress of Pathology (to be held in Helsinki in August 2011). The virtual microscopy technologies produced have been increasingly vis- ible in many educational programmes and the virtual slides are used in all Finnish medical faculties in cell biology, microscopic anatomy and pathology teaching. The image analysis part has grown considerably during the first year of the consortium. Three types of image analysis software have been published (Immu- noRatio, ImmunoMembrane, and IHCJ). Of these, Im- munoRatio has gained popularity among pathologists as a ready-to-use web application, which can be used with any microscope camera without software down- load and installation. Since summer 2010, over 10,000 images have been analyzed using our freely available ImmunoRatio web application.

Our current efforts focus on new high-throughput virtual slide scanner technologies and implementa- tion of new virtual slide image server-viewing tech- nologies, which are aimed to solve the obstacles of the currently used systems. As part of the project, we are testing new efficient server hardware, which enables storage of >100,000 virtual slides. The need for storage space for imaging applications is huge and requires strong computer science skills. The new cloud com- puting systems have been used to solve the problem of serving simultaneously thousands of clients.

In addition to the virtual microscopy technologies, progress has also been made in developing and test- ing user-friendly tissue sample storage systems based on the new molecular tissue fixative approach. These technologies developed are tested in close collabora- tion with the FinTIB biobank organisation (Tampere University Hospital Tissue Biobank project).

User statistics

The virtual microscopy internet webpages of the plat- form are world-famous. For example, during a recent 30 day period the Webmicroscope website has been accessed 29513 times (with 153,790 page views in to- tal).

Recently opened ImmunoRatio image analysis website has been used to analyze 9,900 images of im- munostains (the figure excludes our own use). Our freely available JVS software has been downloaded ap- proximately 6000 times.

Virtual microscopy services for teaching purposes are in use in all Finnish medical faculties. The virtual slides produced by the Tissue Biobanking technology platform are used in all Finnish medical faculties for teaching of cell biology, microscopic anatomy and pa- thology.

Impact of Biocenter Finland Funding

Owing to the financial support from BF, we have been able to provide virtual microscopy services to the academic teaching organizations free of charge. This has been the only possibility for the teachers to utilise virtual slides, because funds allocated to basic teaching are minimal and do not allow investments to incorporate new teaching technologies. Moreover, fees for our services to LabQuality Inc., and Pathology departments in Helsinki and Tampere have been kept low. This has helped us to increase the visibility of our virtual microscopy services. The image analysis plat- forms (ImmunoRatio and ImmunoMembrane) were

designed to be free web applications, applying the same concept as the famous Finnish software projects Linux, MySQL etc.

During the intra-department phase (year one of the project), a bottleneck has been processing capacity for computer vision analysis of the huge amount of image data (up to 300GB in a single image). From year two on, a new high-capacity server is available, and as the ultimate solution a joint project with CSC Finland has been initiated (February 2011) for outsourcing labori- ous computing tasks on the upcoming, scalable CSC cloud computing service.

Participation in European networking activities

As the main focus of the Tissue Biobanking Technology Platform, as the name indicates, has been on development of analysis technologies of biobanked samples, its role in the ESFRI project BBMRI has been peripheral. However, participation of Finnish biocenters in BBMRI has been very strong, particularly through the participation of BF GWM Network. Currently FIMM and THL (National In- stitute for Health and Welfare) are playing a central role in setting-up the Finnish national BBMRI.fi node.

Future perspectives

The main goal of the technology platform is to support incorporation of virtual microscopy in medical tis- sue biobanking projects, which are about to start when the legislation issues are hopefully solved during 2011. Thus, the platform has plans to provide know-how for best histological characterization of biobanked samples. The systems will be developed further to enable seam- less integration of virtual microscopy information to biobank sample and clinical databases.

Technology transfer

During the year 2010, we have hosted a national train- ing course of meeting to teach pathologists to use the ImmunoRatio image analysis tools. More than 40 Finn- ish pathologists attended the course. The projects have also been highlighted in an international conference of virtual microscopy.

The idea of technology transfer is best fulfilled in our software development. The software developed dur- ing the past years (JVSview, JVSserv, JVSdicom, Immu- noRatio, ImmunoMembrane, LargeMontage, IHC-J, FISH-J) are all freely available for non-commercial use and represents valuable technology transfer for an in- creasingly large user community.

PlATFORM