Looking for Dicom-145 sample files

Tue Aug 5 04:20:26 EDT 2014

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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