OMERO-backed data in ImgLib2

[crueden-x]

One of the things ImageJ2 was supposed to improve upon was the agnosticism of image data sources. It must be equally possible to process image data drawn from disk on demand, from arrays in memory, or from an OMERO database over the wire—and neither the user nor the algorithm being used should care about that data source. Fortunately, ImgLib2 was designed with exactly this sort of thing in mind. The ImgLib2 architecture is extremely general, and already supports image data from various sources.

However, ImgLib2 does not yet have a fully general cell/block-based image container that supports mix-and-matched "original" and "modified" data sources. I.e., the "original" source could be pixels from a SCIFIO/Bio-Formats reader (e.g., OMEROReader), with blocks paged in on demand. As soon as a block is touched, though, it is converted to a "modified" block which is paged in and out on disk as needed (using a cache library such as ​Ehcache), with the original data source no longer being used.

Once we have this container, ImageJ2 will support working with OMERO-backed data in a very transparent way, with existing ImageJ2 commands operating on the data in exactly the same manner as data from more a conventional source (i.e., arrays in memory).

[crueden-x]

The ​SCIFIO and ​SCIFIO-OMERO projects now implement this feature. SCIFIO provides a cell-based read/write cache, which supports huge image data. And the SCIFIO-OMERO project provides the linkage with OMERO in both directions. Any remaining and future issues will be tracked on the ​scifio-omero issue tracker.