Posted by
Crystal on
Sep 11, 2013; 10:09pm
URL: http://imagej.273.s1.nabble.com/Image-J-VSI-Reader-tp5004596p5004761.html
Thank you Curtis, this helps.
Vitali,
Thank you for explaining the process in such detail. That is exactly what I'm running across and thought the loss of resolution was somehow related to import into ImageJ/ export from Olympus.
I will definitely wait to hear back from you and could wait the two weeks until it's completed.
Re:
> As results if you try to open large VSI structure with LOCI library, you
> will see only low resolution version of the large image. But small images
> like single camera frames will show fine.
I'm working with a tiled image of cross-sectionally sliced blood vessels and am trying to identify colocalized small puncta, so maintaining the resolution would be preferred. Not sure how many frames the tile ends up being on this machine but when I was using a confocal, the final image was anywhere from ~ 5x3 to 8x6 tiles in size, just to give you an idea.
Re:
> .vsi file itself contains some, but not all image data. More precisely, it
> contains low resolution levels of image pyramid, up to certain pixel size,
> the high resolution levels are stored in additional .ets files in sub
> folders.
Do you know what pixel size it maintains? I think at 10x, its ~600nm/pixel.
Lastly, will this improved reader be incorporated into the current VSI Reader or do you plan to create a separate plugin?
Best,
Crystal
-----------------
Vitali Khvatkov-2
Reply | Threaded | More star
Sep 11, 2013; 5:38pm
Re: Image J - VSI Reader
Vitali Khvatkov-2
17 posts
In reply to this post by Crystal
Crystal,
Olympus VSI format is very special.
.vsi file itself contains some, but not all image data. More precisely, it
contains low resolution levels of image pyramid, up to certain pixel size,
the high resolution levels are stored in additional .ets files in sub
folders.
But, if image is small enough, like a single frame from camera, it will fit
inside just .vsi file and you will not see additional sub folders with .ets
files.
LOCI Bio-Formats Library is baked inside ImageJ / Fiji. From my
understanding of LOCI source code, LOCI Library handles just .vsi file
itself - it is not concerned with sub folders with .ets files. (LOCI team,
feel free to correct)
As results if you try to open large VSI structure with LOCI library, you
will see only low resolution version of the large image. But small images
like single camera frames will show fine.
We hope to finish full support for VSI digital slides on Simagis Live
servers within next 10 days, there you will be able to run image analysis
applications including ImageJ macros on full-size VSI images. I will keep
you posted.
Regards,
*Vitali Khvatkov*
Smart Imaging Technologies Co.
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http://www.simagis.com>
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