New open image format

[Adam Goode]

Have a look at this discussion:
http://stackoverflow.com/questions/1905359/self-describing-file-format-for-gigapixel-images

On Wed, Jun 26, 2013 at 11:56 PM, Benjamin Gilbert <bgilbert at cs.cmu.edu> wrote:
> On 06/26/2013 08:39 AM, Dr. M. Weihrauch wrote:
>> Now I would like to define an image format for his company that would be
>> completely open for openslide.
>>
>> 4. Is there already a free, open, well-documented format that we could
>> tap into?
>
> There is DICOM supplement 145:
>
>      ftp://medical.nema.org/medical/dicom/final/sup145_ft.pdf
>
> 145 is reasonable in itself, but it's essentially a patch to an enormous
> set of specifications containing a large number of options.  As such,
> it'd be a pain to implement, plus there's no guarantee that your
> software would interoperate with other DICOM WSI software (depending on
> the options that you and they supported).  But it's the only open
> specification that tries to anticipate WSI-specific issues.
>
> I'm told that adoption of DICOM 145 has been slow to nonexistent.
> Perhaps others on the list can fill in more details.
>
> AFAICT, the only plausible alternative is to create Yet Another TIFF
> Variant.  Leica SCN does this reasonably well: it uses standard TIFF
> structures and metadata tags where possible, plus a custom XML document
> (contained in a TIFF ImageDescription field) for metadata that doesn't
> fit into standard TIFF tags.
>
> To reduce file size, you may not want to store pixel data for blank
> parts of the image.  However, TIFF doesn't anticipate sparse images.  It
> may be possible to hack around this via a slight abuse of the TIFF
> standard, but that's not ideal.  DICOM does support sparse images.
>
> I recommend reading DICOM 145, the TIFF 6 specification, and TIFF
> supplement 2.
>
>> What is the format inside?   JPEG?  JPEG2000?
>
> If you need more than 8 bits per channel, JPEG is a poor choice.  It
> technically has a 12-bit mode, and some medical imaging formats use it,
> but open-source support for 12-bit JPEG is abysmal.
>
> Conversely, I'm not aware of a standardized way to use JP2K tiles in TIFF.
>
>  From the image-compression perspective, I'm completely unqualified to
> answer this.
>
>> 2. Is it necessary to pretile the 256x256 tiles and how are they
>> accessed "from the outside"?
>
> You do need to store tiles into the slide file.  Otherwise the viewer
> software would need to read an entire row in order to display a small
> piece of it.  TIFF supports tiled images, so no problem there.
>
> One caution about tiling.  Scanner hardware often produces tiles which
> are overlapping and misaligned; these then need to be rendered into the
> correct location by software.  Different vendors do this at different times:
>
> - Some formats (e.g. Aperio SVS) align everything before writing the
> file, so the on-disk tiles are in a regular grid.
>
> - Some formats (e.g. Trestle, Ventana BIF) write out the unaligned tiles
> and expect the viewer to do the alignment.  This has the advantage that
> the original scanner data is still available if the alignment algorithms
> improve later, but of course it's harder to read.  TIFF and DICOM both
> require a regular tile grid, so vendors who do this with TIFF have to
> abuse the format.  Also, you still have to do the alignment calculations
> while writing out the file, in order to produce the downsampled levels.
>   (Unless you're MIRAX, but that was a disaster.)
>
>> 3. If there is a complete image pyramid inside - comparable to the
>> deepzoom-directory structure, do we need an extra thumbnail?
>
> It's probably not *strictly* necessary, but it'd be nice.  It allows the
> writer to decide what should be shown in the thumbnail, rather than
> forcing each reader to make its own thumbnailing decisions.  (For
> example, how should a reader thumbnail a fluorescence image that
> includes an RGB overview?)
>
> --Benjamin Gilbert
>
> _______________________________________________
> openslide-users mailing list
> openslide-users at lists.andrew.cmu.edu
> https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users