fedorov at ece.ucsb.edu
Tue Jan 12 12:21:36 EST 2016
You could use libbioimage <https://bitbucket.org/dimin/bioimageconvert>
alongside OpenSlide to achieve full support for OME-TIFF and WSI. In fact
it supports pyramidal and tiled OME-TIFF and OME-BigTIFF that are not
strictly standardised. It also supports other formats not yet available in
OpenSlide, like tiled JPEG-2000 (this will get a lot better with the next
openjpeg library version).
Libbioimage is a complimentary library for OpenSlide since it was designed
to support multi-dimensional and multi-channel fluorescence imagery. In our
system BisQue (management and analysis system) we use openslide for WSI and
libbioimage for OME-TIFF for very large images daily. Finally, I decided to
integrate OpenSlide into libbioimage as one of the decoders and this should
be finished for the next version. I also hope to incorporate OpenSlide
extensions like DICOM-WSI from Mathieu Malaterre and have started writing a
CZI importer supporting fluorescence.
Although I use OME-TIFF as our main interchange format and do like it, we
have encountered a few problems in more than 10 years of use, I'll try to
list those for your consideration.
1) Really large images require BigTIFF packaging and thus become unreadable
by most programs supporting TIFF.
2) Pyramidal-tiled OME-TIFF is not standardised. I prefer sub-directory
based approach (similar to Photoshop's pyramid) myself but implemented
support for other cases I know.
3) Every channel plane is stored in a separate directory making it a bit
slower to read all the channels since one must change directory several
times for every tile.
4) TIFFs with many directories become very slow to read since one must
traverse the whole file until the desired directory is reached. I've worked
with very large 4D OME-TIFFs with hundreds of thousands of directories.
Although libbioimage patched libtiff with a few optimizations for this case
it is still a real problem. The solution to this is unfortunately a
multi-file solution where each 3D block is stored as a separate OME-TIFF
5) OME-TIFF metadata model is quite rigid and designed for a specific use.
It does provide a flat name-value list for extended information but it is
very verbose and too simple to store a large amount of complex information.
Thousands of tags will make that list very slow to parse.
Folks at OME consortium published a paper proposing to use an HDF-5 based
format for lifesciences. Although it sounds like a great idea there's no
standard definition for it yet. Many companies are using HDF5 based formats
for a long time but they are all proprietary, for example Imaris ims5.
On Tue, Jan 12, 2016 at 2:46 AM, Andreas Schmid via openslide-users <
openslide-users at lists.andrew.cmu.edu> wrote:
> Thoughts on OME-TIFF as an OpenSlide Format
> Actually our company saves the WSI images as an zipped deepzoom pyramid
> simular to Martin Weihrauchs Smart Zoom Image approach. Unfortunately this
> format lacks third party support and likely ever will and suffers from the
> detriments of a non-image format (Like viewing it in any other tiff
> supported software when it is not too large).
> We took some research in the past weeks and considering to switch to a
> tiff-based WSI format but we are not strigency interested to do our's own
> thing to be just another one who sheers off from a standardized WSI format.
> So we kept an wary eye on the OME-TIFF format.
> What do you think? Is OME-TIFF a canditate for beeing an openslide format
> How do you think will OME develop in the future?
> openslide-users mailing list
> openslide-users at lists.andrew.cmu.edu
Dmitry Fedorov Levit <dima at dimin.net>
Center for Bio-Image Informatics:
Vision Research Lab, Electrical and Computer Engineering:
University of California, Santa Barbara
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