The OME Blog Because metadata is worth a thousand pictures

Supporting complex formats - what we will and won't do, and what you can do to help

You may have noticed that a few months ago, we received an email asking us about when we expect to support 3D HISTECH .mrxs files. This sort of request isn’t particularly unusual and the reply gives an insight into one of the key challenges we face.

Just because we don’t have a reader, doesn’t mean we haven’t done any work

3D HISTECH .mrxs is an example of a complex format, the design of which does not make our work any easier. In fact, we can say with some confidence that the 3D HISTECH .mrxs file format is the most complex whole slide imaging file format we have ever encountered. We can say this because although we haven’t delivered a full reader for .mrxs—and there hasn’t been substantial public development—we have spent a great deal of time examining the format and potential solutions, and building test readers. Thanks to the example data the community has generously provided, we have been able to analyse the on-disk layout as well as the compression types, and map out the details of what an implementation would entail.

Unfortunately, the result of all this work has been the conclusion that we simply do not have the resources to prioritize delivering a complete solution for this format. This is not the only format we have reached this conclusion about. For example, support for 3i Slidebook 6 files was only added to Bio-Formats last May when 3i committed to developing the reader themselves. Obviously, we are very grateful for this, but that doesn’t change the fact that we had already spent years working on various versions of this format (our initial single-series Slidebook reader was released back in 2006 and obviously the work to produce it started even further back than that). Nikon ND2 and Zeiss CZI are other examples of formats with a complex design that makes them very difficult for us to support.

We won’t deliver something that doesn’t do the job well enough

One thing to understand about our work, strategy and commitment to supporting all file formats, especially formats used in production-scale facilities that use technology like whole slide imaging, is that we insist on delivering as close to complete support as possible. This is important given the size of community we support, the breadth of applications that use our software, and the need for utility and reliability in the software we deliver to the community.

With 3D HISTECH .mrxs, it is very hard and expensive to meet this goal. To be specific:

  1. The design decisions of 3D HISTECH with respect to image pyramid layout are at odds with what we can reasonably handle within the infrastructure currently in place. Our analysis suggests we will have to re-calculate several of the resolution levels, because of choices 3D HISTECH has made in their tiling strategy. This will create a substantial performance penalty for anyone using Bio-Formats to read this format.
  2. The strategy for storing binary data on disk in 3D HISTECH .mrxs brightfield differs substantially from fluorescence images stored in .mrxs. They are essentially two different file formats, thus doubling the work required.
  3. Based on recent data submissions and information from the community, 3D HISTECH scanners default to JPEG-XR compression when acquiring fluorescence data. Another doubling of work and complexity, as we would need to support both compressed and uncompressed data, in brightfield and fluorescence.

These points are specific to this format but similar issues occur with other proprietary formats. As a team, we are not comfortable with releasing a reader implementation that works on a limited set of file format variants, or requires time consuming and computationally expensive reprocessing and pyramid creation, just because of the implementation choices made by the format designers.

A philosophical point about our funding and resources

The OME Consortium and the wider development community have worked steadily since 2002, funded mostly by grants from non-profit charities and public funders, to build tools for the scientific community.

Building readers for proprietary formats has never been funded, and we don’t think it would ever be funded by any grant funding panel. New readers are created either by diverting our precious resources from other projects, by contributions from the community (most recently by the companies themselves), or by work commissioned by customers of Glencoe Software. We certainly listen to the community and adjust our priorities based on requests, but we can’t do everything with limited resources.

Perhaps we could crowdsource the funding for file formats but that misses the point—the formats we often lack the resources to support are those which are complex, expensive, difficult, proprietary, closed formats, designed to lock their users into a single, proprietary software application. The community’s resources are finite and should be used for things other than reverse engineering this type of format; work that, if subjected to peer review, would be declined as a waste of community resources. Several of those “other things” were discussed at our most recent Annual Users Meeting and represent key technologies that the community needs to achieve its scientific goals.

Over the last few years, we have seen efforts by several commercial imaging companies to support open formats, provide open APIs, and to make it easier for researchers and clinicians to work with the data acquired by their instruments. We have also received specifications and input from several imaging companies, which we have used to improve our own work and output. We applaud this trend; ultimately it means scientists, clinicians, engineers and developers spend less time dealing with data formats and more time doing science, developing new technologies and treating patients.

What you can do

The community has the power to change this situation. You are paying for these proprietary formats. You can condition your purchase, continued payment of support and maintenance fees etc. on:

  • the delivery of a rational, well-designed, efficient, open format
  • use of open compression schemes
  • support for the community’s efforts to deliver open readers for these files

You can of course also commit your own development resources to help solve this problem.