We're Hiring!

Questions about VSI/Olympus format

General user discussion about using and improving the OME Data Model. Please ask new questions at https://forum.image.sc/tags/ome-xml
Please note:
Historical discussions about the OME Data Model. Please look for and ask new questions at https://forum.image.sc/tags/ome-xml

Questions about VSI/Olympus format

Postby brad.polant » Mon Mar 17, 2014 3:19 pm

This is a question about the Olympus format, and in particular how it is handled by the reader.

Normally there is a vsi file next to a similarly named directory like this

and in test sample there is a directory named
and under it will be the file test_sample.est

My question is
If there are additional stack directories , what do they represent?
For example in a sample I user I saw

How is this used?
I see the code that shows how the reader will pull in the file, but what that data represents is a a mystery to me.

Does anyone have any thoughts?
Posts: 9
Joined: Wed Feb 26, 2014 8:13 pm

Re: Questions about VSI/Olympus format

Postby mlinkert » Tue Mar 18, 2014 1:41 am

Each stack directory represents a separate slide that is in some way related to the other slides in the parent directory. The .ets files each contain an entire imaged slide at varying resolution levels - generally the highest imaged resolution, and then 50% reductions down to about a 512x512 thumbnail.

The reader will show one "series" (i.e. 5-dimensional set of images) for each image in the parent .vsi file, and one series for each resolution level in each of the .ets files.

As far as I know, it is up to whoever performs the acquisition to choose which slides end up in a single .vsi dataset, so the way in which .ets files relate to each other from a pathology perspective may vary.
User avatar
Team Member
Posts: 353
Joined: Fri May 29, 2009 2:12 pm
Location: Southwest Wisconsin

Return to User Discussion and Suggestions

Who is online

Users browsing this forum: No registered users and 1 guest