Extracting bar code label and overview image from MRXS slide

[Benjamin Gilbert]

On 07/30/2014 01:45 PM, Sharma, Ashish wrote:
> Is there a way to strip a WSI file of these associated images? We have
> some that have some private information on the labels and we’d like the
> label to be blank.

For Aperio slides, you can use this script:

     https://gist.github.com/bgilbert/7955715

It may be possible to write such a script for other formats.  Otherwise, 
if you want to keep the slide file in the original format, you will need 
to see whether the scanner vendor's software can delete associated 
images or export a slide file without them.  For example, we have 
de-identified MRXS slides using the "Export" function in the vendor viewer.

You can also use VIPS to convert the slide to a different format, e.g. 
pyramidal tiled TIFF.  This will retile the slide and can consume 
non-trivial CPU time, but the resulting file will omit the associated 
images.

--Benjamin Gilbert