Tiling

OME Files supports the creation of images which are stored as a series of tiles, using the FormatWriter setTileSizeX() and setTileSizeY() methods. For the TIFF format, these are stored as either tiles or strips.

When chosing a tile size for TIFF data, consider these factors:

• The tile size must be a multiple of 16.
• The tile size should be a multiple of the image size or else storage space will be wasted due to tiles overlapping the right and/or bottom borders of the image.
• A smaller tile size results in more tiles; there is a small storage overhead and a larger processing overhead which makes larger tile sizes more efficient.
• Larger tile sizes do not affect write performance, but may affect read performance if it results in data being read and discarded; consider the read access patterns of the stored data.

For images with a width less than 2048 pixels, the OME Files TIFF writers currently default to writing strips of approximately 2¹⁶ pixels (the strip size varies depending upon the image width). For images with a width of 2048 and larger, tiles are used with a default size of 2¹⁶ pixels (256×256). These satisfy the above requirements for many typical cases. If your needs do not match these defaults, please specify your own. Consider profiling with your own hardware and data for optimal performance.

The figures which follow detail various considerations when chosing an appropriate tile size. In all the figures, the separate panels show images of different sizes, from small (4096×4096) to large (131072×131072). Different pixel types have different storage sizes, with consequent changes in storage size and upon performance. These are shown on the panels as separate lines.

These plots were computed using an R script, based upon empirical testing with a TIFF tiling benchmark.

The size of the TIFF file varies with different tile sizes and pixel types. Tile sizes which overlap the image border use more space, which is most apparent with smaller images where it comprises a greater proportion of the total file size. Lower tile sizes show a small increase in file size due to the storage of the tile offsets and sizes.

As the tile size increases, the total number of tiles decreases. The wastage due to image overlap becomes less apparent as the image size increases.

This plot combines the data from the previous plots with the timings derived from this benchmark result. It is not necessarily representative of the timings which would be observed in reality, where write caching, buffer copies and other confounding effects which are not modelled here may cause additional variation.

The size of the TIFF file varies with different strip sizes and pixel types. Strip sizes which overlap the image border use more space, which is most apparent with smaller images where it comprises a greater proportion of the total file size. Lower strip sizes show a small increase in file size due to the storage of the tile offsets and sizes.

As the strip size increases, the total number of strips decreases. The wastage due to image overlap becomes less apparent as the image size increases.

This plot combines the data from the previous plots with the timings derived from this benchmark result. It is not necessarily representative of the timings which would be observed in reality, where write caching, buffer copies and other confounding effects which are not modelled here may cause additional variation. Unlike the tile benchmark, the strip benchmark showed no observable effect of the strip count upon write time.