Posted by
Olivier Burri on
Sep 12, 2013; 8:00am
URL: http://imagej.273.s1.nabble.com/Image-J-VSI-Reader-tp5004596p5004764.html
Dears Melissa, Crystal and all,
The LOCI Bioformats library works perfectly well with the .VSI files since 2 major releases already. (So over a year now).
It reads and associates the .VSI file with the folder containing the .ETS files perfectly. And it's thanks to this that we were able to build a tool that helps to open the .VSI file sin Fiji for our users.
> > @ Oliver: This forum won't allow me to upload the subfiles, as they
> > seem to be too large.
We can either setup a server where you can upload your files or I will message you with a dropbox link to a public folder
In response to:
> > 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.
If the resulting image looks blurry, I can think of the following. Usually the order of the file series as read from LOCI follows a certain order in our system (Series 1=label, Series 2=First acquisition, Series 3=...) And we've managed to sort of guess the order of the files depending on whether there is a label or not, and other variants.
So blurriness can be that the VSI reader cannot associate the thumbnail preview to the right image series, which means the structure of the file output by your machine is different than that of ours. I can't help you unless I have the full dataset (.vsi file + "_folder_" ).
Seeing as you can open the image using option 2, this means they are not so big that you would need the VSI reader. We had to use it because of slide scans that were over 100'000 pixels in both directions, and thus impossible to open directly.
Again the best would be for you to send me your file and we'll open it / modify the VSI reader to cope with your format.
Best
Oli
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