LEICA BigTIFF

[Agelos Pappas]

Hi Benjamin,

I used the libxml2 branch of your OpenSlide repo and I was able to parse 
the LEICA file's ImageDescription xml tag. These files seem to have a 
few IFDs with thumbnails and then some other IFDs with the hi res image. 
The xml description doesn't seem to have an explicit property to 
distinct between the thumbnail IFDs and the actual image IFDs. Instead 
it has two image tags, for example:

/<image name="UCLAD_0000006055" 
uuid="urn:uuid:f34abfa8-64ef-4d53-82f5-b966b0c6a688">
<creationDate>2011-10-18T09:20:15.067Z</creationDate>
       <device model="Leica SCN400;Leica SCN" version="1.2.5.8691 
2010/07/15 06:56:41;1.4.0.9708" />
*      <pixels sizeX="1616" sizeY="4668">
         <dimension sizeX="1616" sizeY="4668" r="0" ifd="0" />
         <dimension sizeX="404" sizeY="1167" r="1" ifd="1" />
         <dimension sizeX="101" sizeY="291" r="2" ifd="2" />
       </pixels>
*      <view sizeX="26564529" sizeY="76734666" offsetX="0" offsetY="0" 
spacingZ="0" />
       <scanSettings>
         <objectiveSettings>
           <objective>0.60833</objective>
         </objectiveSettings>
         <illuminationSettings>
<numericalAperture>0.7</numericalAperture>
<illuminationSource>brightfield</illuminationSource>
         </illuminationSettings>
       </scanSettings>
     </image>//
/
and a second one:

/    <image name="UCLAD_0000006059" 
uuid="urn:uuid:18082cde-57fd-4eb8-9e23-5da506cc202c">
<creationDate>2011-10-18T09:23:28.277Z</creationDate>
       <device model="Leica SCN400;Leica SCN" version="1.2.5.8691 
2010/07/15 06:56:41;1.4.0.9708" />
*      <pixels sizeX="22112" sizeY="13696">
         <dimension sizeX="22112" sizeY="13696" r="0" ifd="3" />
         <dimension sizeX="5528" sizeY="3424" r="1" ifd="4" />
         <dimension sizeX="1382" sizeY="856" r="2" ifd="5" />
         <dimension sizeX="346" sizeY="214" r="3" ifd="6" />
       </pixels>
*      <view sizeX="11056000" sizeY="6848000" offsetX="7359742" 
offsetY="27020003" spacingZ="400" />
       <scanSettings>
         <objectiveSettings>
           <objective>20</objective>
         </objectiveSettings>
         <illuminationSettings>
<numericalAperture>0.4</numericalAperture>
<illuminationSource>brightfield</illuminationSource>
         </illuminationSettings>
       </scanSettings>
     </image>
/
I can attach the full xml (there's not much more) if you want, but there 
doesn't seem to be a property that defines which is the thumbnail and 
which is the main image.
Moreover, all the layers are tiled (in the files that I have), so a 
distinction between striped and tiled cannot work either.

My question here is: Would it be safe / acceptable to assume that the 
first tag always refers to the the thumbnail IFDs and the second to the 
main image? In the images that I have seen there are always three tags 
in the description and nothing more. The hierarchy is like this:

scn (root element)
     collection
         barcode
         image
         image

So there is always a barcode and two image tags. In the files that I 
have, image #1 is the thumbnail.

Regards
Agelos

On 3/7/2012 1:46 ??, Benjamin Gilbert wrote:
> On 06/22/2012 04:22 PM, Agelos Pappas wrote:
>> Thank you, I will let you know when I have the leica vendor file ready.
> I have created a wiki page:
>
>       https://github.com/openslide/openslide/wiki/AddingASlideFormat
>
> with some initial documentation that might help you.
>
> Additions and corrections welcome.
>
> --Benjamin Gilbert
> _______________________________________________
> openslide-users mailing list
> openslide-users at lists.andrew.cmu.edu
> https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users
>
>
> -----
> No virus found in this message.
> Checked by AVG - www.avg.com
> Version: 2012.0.2180 / Virus Database: 2437/5105 - Release Date: 07/01/12
>
>


-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://lists.andrew.cmu.edu/pipermail/openslide-users/attachments/20120706/cd67bfe1/attachment.html