> 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>
>
>
>
>
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