AWARE SYSTEMS
TIFF and LibTiff Mail List Archive

Thread

2017.11.10 19:23 "Re: [Tiff] Right way to make a multi-resolution pyramid", by dsudar
2017.11.11 02:38 "Re: [Tiff] Right way to make a multi-resolution pyramid", by Kemp Watson
2017.11.11 21:43 "Re: [Tiff] Right way to make a multi-resolution pyramid", by Damir Sudar
2017.11.11 23:02 "Re: [Tiff] Right way to make a multi-resolution pyramid", by Aaron Boxer
2017.11.11 23:26 "Re: [Tiff] Right way to make a multi-resolution pyramid", by Kemp Watson
2017.11.11 23:44 "Re: [Tiff] Right way to make a multi-resolution pyramid", by Kemp Watson

2017.11.11 23:02 "Re: [Tiff] Right way to make a multi-resolution pyramid", by Aaron Boxer

Don't mean to hijack the thread, but why not lossless JPEG 2000 for digital pathology?

Yes, it is a lot slower, but lately the open source codecs have matured and performance is improving.

Also, storage size would be a lot lower: 2:1 compression, and pyramid is built into the format.

Pathology images are quite large, but JPEG 2000 supports decoding a small sub-region.

Aaron

On Sat, Nov 11, 2017 at 4:43 PM, Damir Sudar <dsudar@lbl.gov> wrote:

Indeed unfortunate that there is no proper and spec-compliant approach and also that Adobe as the owner of the spec hasn't stepped up to define the compliant way. While I agree that TIFF itself has many problems for digital pathology, especially multi-channel digital pathology, in its various improper and incompatible varieties, it IS the most commonly used base file format. E.g. Aperio's (now Leica) SVS format is just a BigTIFF with a .svs extension, Hamamatsu's NDPI is mostly a TIFF with a non-compliant header and some other nastiness, and Philips, Ventana, and others use TIFF (or BigTIFF) with a variety of non-standard header info. There is at least a fair bit of support for such files in e.g. Bio-Formats and OpenSlide so I would like to stick as close as possible to such an approach.

And so to avoid inventing yet another image file format, I'm planning, just as you did, to accept the "wrong way" and use BigTIFF and use all top-level IFDs for the resolution levels. May I ask how you encode how many sub-resolution levels (and thus top-level IFDs) there are in the file? I haven't yet figured out how those other vendor-specific TIFF-formats do it.

For much of our software we rely on work by the Open Microscopy Environment's (www.openmicroscopy.org) and via their forum I'm asking them what their plans for supporting pyramids in their OME-TIFF format. Hopefully that can move the needle towards something more compliant or at least standardized.

Cheers,
- Damir

On 11/10/2017 18:38, Kemp Watson wrote:

As far as I can see, absolutely EVERYONE violates the TIFF standard, or at least it¹s intent, when it come to zoomable images.

Everyone seems to be storing resolution levels in pages (top-level IFDs), as opposed to SubIFDs, when SubIFDs exist to represent alternative views of the SAME image, which is what a resolution level is. Also, most everyone still names their files with a .tif extension, a non-no per the spec. My take, apparently alone.

We¹re attempting to address the standardization of a common subset, 3-channel 8-bit zoomable images, for web viewing, via ZIF (a BigTIFF-derived format, not TIFF), but this won¹t help you with multispectral imagesŠ even for our use case, we¹re stuck with doing it the ³wrong² way as a less-favoured option.

If you¹re dealing with digital pathology slides, TIFF is likely not a practical option, in any case.

W. Kemp Watson

On 2017-11-10, 2:23 PM, "dsudar" <tiff-bounces@lists.maptools.org on behalf of dsudar@lbl.gov> wrote:

I've started looking at this same issue for our large number of channels TIFF images from multiplex immunofluorescent staining of tissue on slides. Has a

> >> consensus been reached how the pyramid of resolution levels should be > >> stored? There seem to be many different and incompatible approaches in

> use
> >> now and I would like to stick to an agreed standard. This appears to be
> >> the
> >> forum that would know.
> >> Thanks,
> >> - Damir
> >>
> >>
> >>
> >> --
> >> Sent from: http://maptools-org.996276.n3.nabble.com/Tiff