Software tools & Data Management

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Revision as of 14:56, 12 September 2010

Topics

Defining strategy for delivering software tools for data management, data archiving, and data analysis

Members

Daniel Zicha (London Res. Inst., CRUK), Jason Swedlow (Univ. Dundee), Paul Thomas (Univ. East Anglia),

Introduction

After 25 years of development most imaging methodologies are well established and in common use across all biological and biomedical research laboratories. As noted in the accompanying BioImagingUK working group documents, the need for sophisticated imaging tools continues to grow and many new developments are coming online rapidly. This growth has driven the need for computational tools for processing, analysing and managing data. Indeed in our own surveys of BioImagingUK participants, we have found unanimous need for new and more advance imaging tools at all sites in the UK. Thus there is clear evidence that despite significant development and the availability of sophisticated imaging tools both in the commercial and open domain; there is significant un-met need that limits discovery and the development of biological insight. It is these limitations that we address in this working document.

Activities

Questions:

1. Would UK biological research be improved by better integration of image processing and analysis software?

2. If so, would a single, standardized file format be advantageous?

3. If the answer to 2 is yes, what should this format be? OME-TIFF?

4. Seamless analysis of saved data requires development of tools that can be used directly on the saved data without “exporting”. If a standardized file format is chosen, it must be readable by the majority of image analysis programmes. Clearly, different questions will arise depending on the chosen format, but if the OME-TIFF format is chosen, it would be essential to provide the majority of tools that users need embedded in the OME. How can the community increase the development of new software tools for the OME? Alternatively, does it make more sense to promote further developments in ImageJ which is open-source and can already read OME-TIFF? Or, can we carry on without a standardized format and rely upon tools such as Bio-Formats to read the various image formats, either into OMERO or ImageJ?

5. Do UK biological researchers need a repository for images that is freely and publicly available to the global community (akin to the Protein Data Bank)?

6. If so, should this be a single, central repository, or distributed over several (regional?) sites?

7. Should the database system be based on the OMERO server? Or, are there other alternative models?

8. How can the archived data be easily accessed by the community? Do we need new applications, or are there tools already available; e.g., the JCB DataViewer?

9. At a local level, should individual institutes create an archiving system for their imaging data; and if so, what platform should be used?

Polling the Community:

The answers to all these questions must be agreed to by the UK bioimaging community. As a first step to this, we discussed these questions at the 2010 Imaging Facility Managers’ meeting. A summary of the conclusions to the questions above is shown below.

Answers & solutions:

1. The overwhelming verdict of Imaging Facility managers from across the UK is that research productivity would be significantly improved by improving cross-platform compatibility, thus facilitating the processing and analysis of images.

2. Furthermore, the Facility managers believed that better integration could only come about by adopting a single, standardized file format.

3. There are a few candidates for such a file format, but it is is felt by the majority of imaging scientists in the UK that the most mature, and best characterized, candidate is OME-TIFF.

4. The idea of a single file format is tentatively supported by companies developing image-analysis software, as these companies would have to spend less time and money developing algorithms for importing numerous different file formats. Nevertheless, UK imagers think that a stumbling block would be the acceptance of this idea by image-acquisition companies. To address this problem Imagers must demand that their microscope providers include the ability to save (or at least export) to OME-TIFF. With regards to developing software tools to work on OME-TIFF files, funds could be made available for grants specifically-targeted at image-analysis software development (either for the OME, ImageJ, or alternatives). Also, sites could be identified (e.g., Dundee, Imperial, Liverpool, UEA, etc.) that are already developing tools and, at these sites, provide core programming positions. (Also, need to create better integration of these various sites?)

5. Again the UK Facility managers generally supported the development of an on-line, centralized database for published images.

6. Funds could be provided to establish a central archive at a single location; perhaps, based at the Imaging Solution Centre (Harwell), or at the proposed UK Centre for Medical Research & Innovation (St Pancras)? Alternatively, imaging facilities around the UK could be selected to establish smaller, networked databases; funds could be provided to purchase servers of adequate capacity and to provide network accessibility (with matching funds from institutes?). Also, core positions for database/server management could be funded (either at the central archive, or “roving” experts in the case of a distributed archive).

7. There is less consensus across the imaging community about what platform should be used for local archiving (see 9, below); nevertheless, it would seem that for a central store the most mature programme should be adopted. Considering that the JCB DataViewer is based upon the technology employed in OMERO, it would seem that OMERO would provide the best solution.

8. To provide access, a solution based upon the JCB DataViewer, but increasing its functionality, would seem to be the best option.

9. An informal survey of the Facility managers revealed that few had implemented an archiving system for their imaging data. There was much discussion of the use of both OMERO and commercial alternatives (e.g., Imagik). With respect to commercial database systems, it was felt that there could be problems of data retrieval if the company were to collapse, or if users were no longer able to afford the service. It was thought that this was less of a problem with open-source software such as OMERO; nevertheless, there was not a lot of enthusiasm demonstrated for the adoption of OMERO. In the past, some managers had tried OMERO, but had failed to get it to work. Managers who were present users of OMERO argued that it was much improved, and enabled better organisation of large amounts of data and simpler access to archived images. Most managers thought that uptake of OMERO might be greater if it was simpler to install and had more image analysis tools; thus, funding initiatives such as those described in 4 and 6 (above) may increase uptake of OMERO by solving some of these problems. However, perhaps the biggest incentives to uptake of any database system will come if the centralised database (see 5, above) is implemented, and if funders begin to seriously apply their rules regarding data archiving and access.

Resources

• Open Microscopy Environment (OME)
• Facility Managers' meeting