Add support for DICOM (aka Supp 145) #157

Fri Oct 7 05:02:42 EDT 2016

El 07/10/16 a las 09:01:04, Mathieu Malaterre escribió: 

> On Fri,
Oct 7, 2016 at 8:44 AM, David De Mena García via
> openslide-users
wrote:
> 
>> Hi: On Mon, Oct 03, 2016 at 02:18:14PM +0200, Mathieu
Malaterre via openslide-users wrote: Case 2: A single file contains a
single JPEG stream I did not have any dataset, so I used GDCM to split
the above dataset into individual file. In this case the header is 104K
(x 4824 files). This is nasty mostly because the ICC profile is repeated
in every single file (that may explain why no vendor choose to implement
this option). As I understand the spec, all tiles from a given level,
Z-plane, and wavelength must be stored in a single image object, and
thus in a single file. (I think that's also what David is saying?) Am I
misunderstanding the spec, or is there another reason that there could
be a large number of files? There is no requirement for the the tiles of
a given level to be stored in a single file. Technically I also missed
that, Alvaro did pointed the missing functionality in his original post:
https://lists.andrew.cmu.edu/pipermail/openslide-users/2015-March/001029.html
[1] About Matthieu said I would like to make a comment, because the
Supplement 145 said it clear about the "normal" tiles: DESCRIPTION OF
WSI PROPOSAL (line 287) "The basic mechanism proposed for storing WSI
images for Pathology in DICOM is to store the individual "tiles" of a
single WSI pyramid level as individual frames in a DICOM multi-frame
image object" But the Z-planes and Wavelength could be stored in
separated objects: (line 293) "Where multiple Z-plane images are needed
for the WSI, each plane may be stored separately in an object in the
series, or all the planes at one level may be stored in the same image
object. Similarly, for multispectral imaging each wavelength may be
stored separately, or all in the same object." So, when you talking
about separated objects for one level I suppose or you are talking about
Aperio proposition (that is DICOM image, but not a VL Whole Slide
Microscopy Image SOP) or this case.
> 
> I have no clue what you mean by
'Aperio proposition'. The paragraph
> you quoted is from the original
proposal (Supp) however this is not
> the normative text. Instead you
should be refering to the PS 3.3
> documentation only.
> 
> Which
states:
> 
> [...]
> An entire set of tiles for an acquisition may be
encoded in the frames
> of a single SOP Instance, in multiple SOP
Instances of a single
> concatenation, or in multiple SOP Instances in a
series (with or
> without concatenations). E.g., a single SOP Instance
may contain an
> entire low resolution image as a single tile (single
frame), or a
> single SOP Instance may contain an entire high
resolution, multi-focal
> depth, multi-spectral acquisition (multiple
frames).
> [...]
> 
> ref:
>
http://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_A.32.8.html#para_6f94f2c4-a42f-4d0a-9230-e08ef79837bb
[3]
> 
> -- Mathieu

Hi, Mathieu: 

When you read this paragraphe
alone, without any information, you can have a non correct
interpretation. Of course the supplements are not DICOM normative part,
but help with the interpretation. (because it's the WG that has
published the supplment who propuse the change in the normative) When in
Anex A.32.8 is talking about "multiple SOP Instances in a series" is
about tiles from different levels, not in one level.  

You can see some
presentation about this topic by Harry Salomon
(http://slideplayer.com/slide/5805325/), David Clunie
(http://dicom.nema.org/dicom/minutes/WG-26/2009/2009-09-05/WG-26_2009-09-05_Min.doc),
Marcial Garcia
(https://www.researchgate.net/figure/49762223_fig6_Fig-6-Whole-slide-image-WSI-DICOM-supplement-145-Multi-frame-objects-support-a)
and even myself
(http://www.diagnosticpathology.eu/ojs-2.4.5/index.php/dpath/article/view/175)

Anyway I will ask to the official group about to better clarify the
normative part.  

I means by "Aperio proposition" what Aperio patented
(US 8,086,077 B2) about storage Digital Pathology Images with a "one
Tile - one Instance" approche.  

Best  

-- 
David de Mena
García
Anatomía Patológica
H.U. de Jerez

Links:
------
[1]
https://lists.andrew.cmu.edu/pipermail/openslide-users/2015-March/001029.html
[2]
mailto:openslide-users at lists.andrew.cmu.edu
[3]
http://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_A.32.8.html#para_6f94f2c4-a42f-4d0a-9230-e08ef79837bb
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