Looking for Dicom-145 sample files

Tue Aug 5 04:39:38 EDT 2014

Hi John,

Nice tool, but what's the purpose? We talked amongst ourselves a lot about
writing a univeral convertor, so we'd only need to use a single
vendor-specific viewer anymore, but decided against it, because it becomes
almost impossible to prove that the original data is not tampered with when
audit-time comes around.

Here's an example: You scan slides on a Ventana Roche scanner (which has the
most irregularly shaped tiling pattern that we know of thus far) at 80% lossy
compression. You then convert the irregular tiles to regular tiles to be used
in the dicom format. You then re-compress those tiles at 80% lossy compression
again, most likely introducing other artifacts than were present in the
original tiles... How can you 'prove' (to both your (pharma) client and
regulatory agency) that your new dataset is still 'good enough' for the
pathologist to make an accurate diagnosis? Have you done any intra- and
inter-observer concordance studies already according to CAP-guidelines for
DP?

@Benjamin, I apologize if this is out of scope of the list.

Yves

------ Original Message ------
Received: 10:21 AM CEST, 08/05/2014
From: John Stevenson-Hoare <John.Stevenson-Hoare at ffei.co.uk>
To: "openslide-users at lists.andrew.cmu.edu"
<openslide-users at lists.andrew.cmu.edu>
Subject: Looking for Dicom-145 sample files

Hi,

I have created a utility that provides a capability to convert from many
vendor formats to the DICOM (supplement 145 now embodied in standard) media
file format for VL Whole Slide Microscopy Images.

The utility is for Windows only, and is available as a GUI and command line
program. I have made available both the 32-bit (x86) and 64-bit (x64) variants
at:

*        
https://s3-eu-west-1.amazonaws.com/uk-co-ffei-sierra/Downloads/SierraConverter_Setup_x86.exe

*        
https://s3-eu-west-1.amazonaws.com/uk-co-ffei-sierra/Downloads/SierraConverter_Setup_x64.exe

You may also need to install the Microsoft Visual C++ 2010 runtime libraries
as these are not currently installed with the application.

*         http://www.microsoft.com/en-gb/download/details.aspx?id=8328 (x86)

*         http://www.microsoft.com/en-gb/download/details.aspx?id=13523 (x64)

A user guide for the utility can be downloaded from
https://s3-eu-west-1.amazonaws.com/uk-co-ffei-sierra/Downloads/SierraConverter_UserGuide.pdf.

The utility uses the OpenSlide library, and as it has been used for a viewer
that I also developed (sorry, but I cannot make this available to you) and I
needed that to be able to open the DICOM images that I had converted (and from
other sources), I modified the sources to allow me to do this. In due
diligence I have made available the modified OpenSlide sources. These can be
downloaded from
https://s3-eu-west-1.amazonaws.com/uk-co-ffei-sierra/Downloads/openslide_src.zip.

The sources include a new vendor driver 'nema' chosen as this is the body that
oversees changes to the DICOM standard. There is also a new 'ffei' vendor
driver for a format that we are using internally so this can be ignored.

Please note that the DICOM support in the OpenSlide library only opens the
first image in the file-set. Also if you analyse the resulting file(s) from
the conversion you will see that I have made some assumptions about the image
orientation relative to the DICOM standard. These may not always be correct as
I have no other vendor originated file sets to check.

I believe that the file set written by the converter is valid as I used the
'dciodvfy' utility written by David Clunie (http://www.dclunie.com) to check.

I use the excellent (and free) Rubo DICOM parser to look inside the DICOM
files generated (http://www.rubomedical.com/dicomparser).

Note that you will need an ICC profile in order to use the utility. However
the utility does not check that it is a scanner profile, so you could just use
a monitor profile. Several are available in the
C:\Windows\System32\spool\drivers\color folder on Windows machines. The file
will be populated with whichever you choose, but is unlikely to be
semantically 'correct' as a result if you do not have access to the original
vendor's ICC profile. Vendors such as Aperio embed theirs so you could try
extracting it with a hex editor or such.

John Stevenson-Hoare

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