OME at LOCI –
OME-TIFF – Sample data and benchmarks
This page provides some sample data in OME-TIFF format, as well as an
analysis of several file formats and compression techniques. There are also
some artificial sample datasets (i.e., not produced from an acquisition
system) designed for developer testing that illustrate some possible data
organizations, which should be useful if you are interested in implementing
support for OME-TIFF within your software.
All datasets in the following table were
artificially generated
with each plane labeled according to its dimensional position for easy
testing. Each one consists of a single OME-TIFF file containing every
constituent image plane. For an example of an OME-TIFF dataset distributed
across multiple TIFF files, see the tubhiswt biological example in the next
section.
Links to download the tubhiswt datasets have been temporarily removed until
we have time to update these files to support the latest multi-file
OME-TIFF specification, but compression statistics are still listed below.
The following OME-TIFF datasets consist of tubulin histone GFP coexpressing
C. elegans embryos. Many thanks to
Josh Bembenek
for preparing and imaging this sample data.
The datasets were acquired on a multiphoton workstation (2.1 GHz Athlon XP
3200+ with 1GB of RAM) using WiscScan. All
image planes were collected at 512x512 resolution in 8-bit grayscale, with
an integration value of 2. The table below also lists the space
requirements for each dataset with various formats and compression types.
| Dataset |
tubhiswt-2D.zip |
tubhiswt-3D.zip |
tubhiswt-4D.zip |
| Dimensionality |
2D (single plane, 2 channels) |
3D (20 time points, 2 channels) |
4D (10 focal planes, 43 time points, 2 channels) |
| Size (raw pixels only) |
524,288 bytes |
10,485,760 bytes |
225,443,840 bytes |
| Size (OME-XML) |
314,346 bytes |
5,964,603 bytes |
142,498,355 bytes |
| Size (gzipped OME-XML) |
236,708 bytes |
4,511,329 bytes |
107,788,464 bytes |
| Size (zipped OME-XML) |
236,836 bytes |
4,511,457 bytes |
107,788,592 bytes |
| Size (7-zipped OME-XML) |
239,052 bytes |
4,551,263 bytes |
108,708,700 bytes |
| Size (OME-TIFF) |
531,384 bytes |
10,499,384 bytes |
225,874,680 bytes |
| Size (OME-TIFF with LZW) |
273,190 bytes |
4,998,148 bytes |
118,517,497 bytes |
| Size (zipped OME-TIFF) |
235,764 bytes |
4,446,727 bytes |
105,389,599 bytes |
| Size (zipped OME-TIFF with LZW) |
264,875 bytes |
4,937,246 bytes |
116,418,287 bytes |
| Size (7-zipped OME-TIFF) |
209,593 bytes |
3,891,846 bytes |
93,939,055 bytes |
| Size (7-zipped OME-TIFF with LZW) |
264,292 bytes |
4,950,897 bytes |
116,567,097 bytes |
The following table compiles our results with average plane size computed
from the numbers above, and briefly summarizes each format's ability to
efficiently access individual image planes. We have not performed
benchmarks involving individual planar access for each format—mostly
because for many of these formats (especially zip, gzip and 7-zip) it is
quite impractical to attempt efficient access to individual planes.
| Format |
Average plane size |
Efficiency of access to individual planes |
| Raw pixels only |
Worst –
262,144 bytes |
Best –
Pixels can be ripped directly from disk. |
| OME-TIFF |
Worst –
262,645 bytes |
Great –
IFDs identify planar offsets. |
| OME-TIFF+LZW |
Good –
137,238 bytes |
Good – The plane must be
decoded from LZW, but IFDs identify planar offsets. |
OME-TIFF,
zipped |
Great –
122,031 bytes |
Poor – The appropriate
OME-TIFF file must be uncompressed from the archive. |
OME-TIFF+LZW,
zipped |
Good –
134,834 bytes |
Poor – The appropriate
OME-TIFF file must be uncompressed from the archive, and the plane must
be decoded from LZW. |
OME-TIFF,
7-zipped |
Best –
108,692 bytes |
Poor – The appropriate
OME-TIFF file must be uncompressed from the archive. |
OME-TIFF+LZW,
7-zipped |
Good –
135,014 bytes |
Poor – The appropriate
OME-TIFF file must be uncompressed from the archive, and the plane must
be decoded from LZW. |
| OME-XML |
Poor –
164,942 bytes |
Poor – Entire dataset must be
read before offsets are known, then the plane must be decoded from
base64. |
OME-XML,
zipped |
Great –
124,764 bytes |
Worst – Entire dataset must be
uncompressed and read to determine offsets, then the plane must be
decoded from base64. |
OME-XML,
gzipped (omez) |
Great –
124,763 bytes |
Worst – Entire dataset must be
uncompressed and read to determine offsets, then the plane must be
decoded from base64. |
OME-XML,
7-zipped |
Great –
125,830 bytes |
Worst – Entire dataset must be
uncompressed and read to determine offsets, then the plane must be
decoded from base64. |
The performance penalty for accessing individual image planes from
externally compressed formats (zip, gzip, and 7-zip) is high, since the
data must be decompressed. The penalty for accessing them from uncompressed
OME-XML is also high, since the entire file must be parsed to determine the
offset to each image plane.
Accessing them from an uncompressed OME-TIFF file, however, is efficient.
In addition, the TIFF format maintains compatibility with the multitude of
existing software that works with single- and multi-page TIFF files.
As shown in the table above, and the chart to the right, our figures
indicate that the most efficient format for space is OME-TIFF compressed
with the 7-zip utility. Also good are
gzipped OME-XML (omez) and zipped OME-TIFF.
Uncompressed OME-TIFF format, while the least space-efficient, provides its
own advantages: it is highly compatible and provides efficient access to
individual image planes.
OME-TIFF with LZW often performs nearly as well as the externally
compressed formats (zip, gzip and 7-zip), without the performance penalty
of searching through a compressed archive. However, LZW is noticably less
efficient to decode than uncompressed TIFF is, and LZW is an additional
requirement for client software—it may be that some software supports
uncompressed multi-page TIFF, but not LZW. Even more unfortunate, the 7-zip
algorithm appears to perform less well on LZW-compressed OME-TIFFs than on
uncompressed OME-TIFFs.
Lastly, we saw no advantage to zipping or 7-zipping OME-XML. If you want
to distribute an OME-XML file, we recommend gzipped OME-XML (omez) format,
as it is the OME standard.
In conclusion, we highlight the following formats as most useful, depending
on your circumstances:
- Zipped OME-TIFF – Cuts down on file size while retaining
the underlying compatibility of OME-TIFF. Use zipped OME-TIFF for wide
distribution of data to colleagues. Zip is a ubiquitous compression
format, decodable on all major operating systems. The downside is that
it typically does not compress as well as 7-zip does.
- 7-zipped OME-TIFF – Minimizes file size. As the most
space-efficient format, use 7-zipped OME-TIFF for archival purposes,
for transport from one OME database to another, and possibly for online
distribution if space is a major concern and your target audience is
computer-savvy enough to install 7-zip. The only downsides are that
7-zip is less ubiquitous than zip, and compressing a dataset with 7-zip
takes longer than doing so with zip.
- OME-TIFF with LZW – Provides space advantages nearly as
good as the externally compressed formats (zip, gzip, 7-zip) without
sacrificing the accessibility of TIFF, for the most part. The downsides
are that LZW takes somewhat longer to process than uncompressed TIFF,
some software does not support LZW compression, and OME-TIFF with LZW
does not shrink as much as uncompressed OME-TIFF does with external
compression techniques.
- OME-TIFF – Maximizes compatibility. When actively
working with data, storing it in uncompressed OME-TIFF format provides
many options for efficient analysis and visualization. The downside is
that the data takes up more space on disk.
- OME-XML – Provides metadata in a directly human-readable
form. In addition, OME-XML maximizes compatibility with XML software.
The downsides are that very few image software packages support
OME-XML, and accessing individual image planes is inefficient.
Last update: Thursday, April 24, 2008
