> LOCI Bio-Formats Library is baked inside ImageJ / Fiji. From my
> itself - it is not concerned with sub folders with .ets files. (LOCI team,
read .ets files associated with .vsi files. For those who wish to
to have an ImageJ plugin, but is not tied to ImageJ in any way. It can
> will see only low resolution version of the large image. But small images
> 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.
> <
http://www.simagis.com>
http://live.simagis.com>
>
>
> On Wed, Sep 11, 2013 at 2:13 PM, Crystal <
[hidden email]> wrote:
>
> > Hi all,
> >
> > Thank you for the assistance. I'll reply to the last three posts one at a
> > time.
> >
> > @ Oliver: This forum won't allow me to upload the subfiles, as they seem to
> > be too large.
> > @ Curtis & Oliver: I removed the duplicate .jar files and updated Image J,
> > which fixed the problem. I was then able to open the .vsi file.
> > @ Vitali: Yes, I have two subfolders that correspond to each .vsi file. I
> > tried to upload the .ETS files but they are too large. I am acquiring my
> > images and then trying to work with them offline (different lab without
> > access to the original Olympus software). I am familiar with the OlyVIA
> > software but its very basic and I can't do any of my planned analyses. I'm
> > planning to use the Object Counter/Nuclei Counter/OBCOL plugin(s) for my
> > data but needed to figure out how to get the Olympus files into ImageJ. You
> > mention LOCI as a possible reader. Would I need to access this through
> > Plugins --> LOCI --> Bio-Formats Importer or am I essentially doing the
> > same
> > thing by File--> Import--> Bio-Formats? I pretty much have to figure out
> > this situation in the next few weeks but will probably be revisiting this
> > issue for future work so any updates on your software would be welcome.
> >
> >
> > To all:
> > Now that the bugs are fixed, I noticed there are two ways to open the .vsi
> > file and resolution seems dependent on which method I use.
> >
> > Option 1: Action Bar --> Shared Bars --> BIOP VSI Reader --> Open tile file
> > The resultant image looks blurry
> >
> > Option 2: File --> Import --> Bio Formats --> open as hyperstack
> > I decided not to use the "crop on import" feature. I'm imaging blood
> > vessels
> > and each slide has a different size vessel and they are all not mounted in
> > the same place. Not sure how I would handle this problem if the file needs
> > to be cropped but will address that if I need to in the future. This option
> > provided a image that seems to have a close resolution to what I can view
> > using the Olympus software.
> >
> > Today, I tried to crop my section of interest and save as a separate .vsi
> > file. Another option I plan to try is to extract the 10x layer and save
> > that
> > as a .vsi. That way, my import is smaller (no 2x overview, etc.)
> >
> > Thanks again for the help and forgive any silly questions. I was used to
> > working with Metamorph and now have had to teach myself ImageJ.
> >
> > Crystal
> >
> >
> > ----------------------------------------
> >
> > Olivier Burri
> > Reply | Threaded | More star
> > Sep 10, 2013; 8:45am
> > Re: Image J - VSI Reader
> > Olivier Burri
> > 51 posts
> >
> > Dear Crystal,
> >
> > In the error log I read this line:
> > Caused by: loci.formats.MissingLibraryException: The JAI Image I/O Tools
> > are
> > required to read JPEG-2000 files. Please obtain jai_imageio.jar from
> >
> >
http://www.openmicroscopy.org/site/support/bio-formats/developers/java-library.html> >
> > You need to go to that page, download jai_imageio.jar and place it in your
> > Fiji "jars" folder (not "plugins");
> >
> > That should fix the error
> >
> > On a second note, the .VSI file you annexed is only a fraction of your
> > data.
> > Each .vsi file has a folder with the same name. In your case, there should
> > be a "_yay_" folder in the same location as yay.vsi
> >
> > The vsi file contains only the metadata and some thumbnails. The actual
> > full
> > resolution image data is on the above-mentioned folder.
> >
> > Hope this helps!
> >
> > Best
> >
> > Oli
> >
> > Olivier Burri
> > Engineer - Image Processing
> > & Software Development
> > EPFL - SV - PTECH - PTBIOP
> >
> >
> > ----------------------
> > Curtis Rueden
> > Reply | Threaded | More star
> > Sep 10, 2013; 9:48am
> > Re: Image J - VSI Reader
> > Curtis Rueden
> > 735 posts
> >
> > Hi Crystal,
> >
> > > loci.formats.MissingLibraryException: The JAI Image I/O Tools are
> > > required to read JPEG-2000 files
> >
> > Oli is right that the above error message gives a good hint to the problem.
> > However, the file Oli mentioned, jai_imageio.jar, is already supposed to
> > ship with Fiji. The fact that it wasn't being shipped was a bug, which I
> > have now remedied. You should *not* have to download that file manually in
> > order to read .vsi files in ImageJ.
> >
> > In short: I think I fixed it. Can you update your Fiji, try opening your
> > file again, and let us know whether it works?
> >
> > Thanks,
> > Curtis
> > ----------------------
> >
> > Vitali Khvatkov-2
> > Reply | Threaded | More star
> > Sep 11, 2013; 12:25pm
> > Re: Image J - VSI Reader
> > Vitali Khvatkov-2
> > 16 posts
> >
> > In reply to this post by Crystal
> >
> > Crystal,
> >
> > Does your VSI structure have sub-folders with .ETS files in them?
> > If it does, you have large multi-scale image structure and you need
> > specialty software to handle it.
> >
> > Olympus provides free Windows software for viewing those files called
> > OlyVIA, you can download it here:
> >
> >
> >
http://www.olympusamerica.com/seg_section/product.asp?product=1089&p=-1&c=10> >
> > Beyond that, I don't know any third-party software that can handle large
> > complex VSI structures correctly. (if image is small than .vsi file
> > contains actual image pixel array and LOCI can read it )
> >
> > Our engineers spent last 3 months working with Olympus software team out of
> > Germany to implement proper support for large VSI files on our Simagis Live
> > Servers and we are still not quite there yet. I can keep you updated on the
> > progress if you are interested.
> >
> > Regards,
> >
> >
> > *Vitali Khvatkov*
> > Smart Imaging Technologies Co.
> > <
http://www.simagis.com>
http://live.simagis.com> >
> >
> >
> >
> >
> > --
> > View this message in context:
> >
http://imagej.1557.x6.nabble.com/Image-J-VSI-Reader-tp5004596p5004757.html> > Sent from the ImageJ mailing list archive at Nabble.com.
> >
> > --
> > ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> >
>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html