OpenSlide & annotations?

[Yves Sucaet]

This is a tough one from a regulatory point of view as well: good luck 
proving to FDA/EMA that the timestamps on your files differ from what you 
would expect because you added annotations to the native format (and NOT 
because you tampered with the original file contents).

We recommend (and practice accordingly) storing annotations in a separate 
datastore and leaving the original annotations untouched. That would 
somewhat render the effort of reading annotations through OpenSlide moot .

2c,

Yves



From:   Benjamin Gilbert <bgilbert at cs.cmu.edu>
To:     openslide-users at lists.andrew.cmu.edu
Date:   11-03-14 23:28
Subject:        Re: OpenSlide & annotations?
Sent by:        
openslide-users-bounces+sucaet=histogenex.com at lists.andrew.cmu.edu



On 03/11/2014 01:48 PM, Mark Ungrin wrote:
> What additional work would be required for OpenSlide to support
> annotations (ideally in the web browser)?

Depends what you mean.  You can already build your own annotation system 
on top of OpenSlide, where the annotations are stored in a separate 
database indexed by filename or quickhash-1.  OpenSeadragon should 
already have sufficient infrastructure to let you render those 
annotations on top of the slide image.  It should also be possible to 
build UI for *creating* annotations with OpenSeadragon, but that is 
probably not trivial.  I don't know how things stand with other zoomable 
image viewers.

If you're asking about reading existing annotations from the slide file, 
that would take some work.  There is an open issue for this:

     https://github.com/openslide/openslide/issues/118

We would need to add some API, then add annotation data decoders to the 
various format drivers.  We currently don't have any sample slides with 
annotation data, though those may not be difficult to generate (at least 
for vendors that provide publicly-available viewer software).

How important is it that OpenSlide be able to read existing annotations 
from slide files?  OpenSlide will never be able to write annotations 
back to the file (we are a read-only library), so any complete 
annotation system would already have to keep its own annotation database.

--Benjamin Gilbert
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