[ome-devel] TIFF pyramid support in Bio-Formats - reference files for review

[Damir Sudar]

Hi Roger,

On 3/27/2018 14:45, Roger Leigh wrote:
>
> Did this upload correctly?  I can't see any recent uploads to the QA
> system.  I'll certainly take a look when I can find it!
Lately the Flash uploader appears to be less and less compatible with 
recent web browsers. I'm now trying again. And yes, it completed this 
time: QA # 20589.
>
> In theory, all "C" files should work with all tools with or without
> support for SUBIFDs.  As you say, readers which don't handle SUBIFDS
> should simply ignore them.
Indeed, that's exactly what I'm seeing.
>
> I had noticed the odd behaviour of Leica-Fluorescence-1, but I haven't
> yet dug into why this is happening in detail.  It's likely to be
> something odd in the OME-XML, maybe because the shell script isn't doing
> the conversion quite right.  Since it's only for the OME-XML, and not
> the plain TIFF (I think), this is likely bad OME-XML metadata.
Indeed, that was my observation as well. Would it indeed make sense to 
set as a ground rule (at least for now) that a new-style 
pyramid-OME-TIFF should pass without errors through xmlvalid, showinf, 
and any other current BF tools, readers, etc.?
>
>>>> - also, all these examples carry some of those ancillary images 
>>>> such as
>>>> slide labels, overview images, etc. While the scripts handled those
>>>> correctly as far as I can see, a reader would have to be pretty 
>>>> smart to
>>>> figure out which of the contents of such an output file is the actual
>>>> image and which are those ancillary images.
>>>
>>> Absolutely.  We will need to do something about these as a followup
>>> task, to add the metadata to identify these as labels, overviews, etc.
>>>
>> In the file I uploaded the mocked up label and macro/overview images are
>> stored as top-level IFDs and in the OME-XML coded as separate series.
>> Would this be an appropriate way to store such ancillary images? If so,
>> then we could codify where in the file they should be (at the end?),
>> standardize what name they should have to identify them, and anything 
>> else?
>
> I think they would need to be separate top-level images.  What's needed
> is some extra metadata to tie the images together.  There are several
> possibilities for this, including
>
> - annotations to specify the image is from a particular slide and what
> type of image it is (label, overview, full size image)
Yes, agreed!
> - regions of interest on the overview pointing to the full size image
> for the region
That's a great idea. I like that a lot. Such ROi info should be optional 
but really good to have it.
> - (harder) slide-specific data modelling to parallel the
> screen-plate-well (SPW) support; this could cater for specific metadata
> for digital pathology, arrays of separate cores in wax blocks etc (I
> forget the name)
Yes, that was indeed one of the challenges I had been looking at in the 
context of: 
https://www.openmicroscopy.org/community/viewtopic.php?f=13&t=8374
Those are Tissue Micro Arrays (TMA).
>
> In some ways the metadata for "slides" is very similar to "plates", with
> sections being equivalent to wells with multiple fields of view in each.
>  I wonder if we can't reuse or repurpose some of the logic.
>
Hmmm, very interesting and needs some contemplating. Typically such 
layouts (e.g. in the case of TMAs) are not as rigidly defined as wells 
in plates but they indeed do tend to have some kind of grid pattern. I 
like the concept. Let me upload a CZI file for a (what I typically see) 
TMA slide where each core was acquired as a separate scene (as defined 
in the Zeiss ZEN software and
I had been thinking a bit different direction, namely simply treating 
any multiple regions on a single slide as multiple scenes or "Series" 
similar to that CZI file. That approach does not encode the grid pattern 
but would be very flexible and the per-Series Plane information field 
could hold the XY location of each scene.

Cheers,
- Damir

>
> Regards,
> Roger
>
> The University of Dundee is a registered Scottish Charity, No: SC015096

-- 
Damir Sudar - Affiliate Scientist
Lawrence Berkeley Natl Laboratory / MBIB
One Cyclotron Road, MS 977, Berkeley, CA 94720, USA
T: 510/486-5346 - F: 510/486-5586 - E: DSudar at lbl.gov
http://biosciences.lbl.gov/profiles/damir-sudar-2/

Visiting Scientist, Oregon Health & Science University