Posted by
Olivier Burri on
Sep 13, 2013; 10:40am
URL: http://imagej.273.s1.nabble.com/Image-J-VSI-Reader-tp5004596p5004771.html
Dear Crystal,
> Would it help if I first extracted the layer of interest and
> saved it as a separate .vsi file.
> That way there is no confusion between the 2x overview
> scan and 10x scan of interest?
> On another note, I was thinking about "cropping" the
> section of interest from the 10x scan and saving that as a separate file anyway.
The idea of the VSI reader is to try and locate these relationships by using the least tampered-with files. Ideally I'd like to complete acquisition as it came out of the system. You can provide me with both if you'd like.
What size are the files?
Best
Oli
Olivier Burri
Engineer - Image Processing
& Software Development
EPFL - SV - PTECH - PTBIOP
-----Original Message-----
From: ImageJ Interest Group [mailto:
[hidden email]] On Behalf Of Crystal
Sent: vendredi 13 septembre 2013 00:59
To:
[hidden email]
Subject: Re: Image J - VSI Reader
Dear Oli,
>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
Either option works for me.
> 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.
Would it help if I first extracted the layer of interest and saved it as a separate .vsi file. That way there is no confusion between the 2x overview scan and 10x scan of interest? On another note, I was thinking about "cropping" the section of interest from the 10x scan and saving that as a separate file anyway.
> 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_" ).
Extracting and saving the isolated 10x scan should result in a corresponding subfolder, which may solve this problem (?)
>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.
The "yay" scan I'm referencing was for simplicity, as it's only a partial scan of a vessel. The real images I'll be working with should be much larger.
>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.
Let me know the easiest way for me to send you the file(s).
Best,
Crystal
--
View this message in context:
http://imagej.1557.x6.nabble.com/Image-J-VSI-Reader-tp5004596p5004770.htmlSent 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