Posted by
Aryeh Weiss on
Sep 22, 2015; 9:43am
URL: http://imagej.273.s1.nabble.com/problem-using-BIOP-vsi-reader-tp5014387p5014397.html
Hi Romain
Thank you for your reply.
On 9/22/15 10:13 AM, Romain Guiet wrote:
> Hi Aryeh,
>
> thank you for your report.
>
> Can you check a couple of thing.
> 1. Do you have the lastest LOCI Bio-formats installed? or the bio-formats update site activated ?
I have the bio-formats update site selected
> 2. If you try, can you open your image (or a downscale version of it) using Bio-formats importer ?
When I open it with the importer, I get a 512x300 x 6 image, which
appears to be thumbnails of the full images. The image is not attached
to this version of the reply, so that it will go through the listserver.
> 3. Can you send us the informations you get from the windows Bio-formats Plugins Configuration -> Log
I can generate the log, but I cannot figure out how to copy what is in
the window. There are no menu items to do that, and highlight followed
by cmd-C does not work.
> Can you provide us with a link to download your file so we can check that everything is fine with it ?
This should work
https://filesender.huji.ac.il/filesender/?vid=37f1710c-1db5-3bc9-4a6e-0000619d7dcdOne other thing -- the action bar plugin causes Fiji (maybe also ImageJ
-- I dont know) to produce a grayed out help drop-down list.
This also happened in the past, so I have to dig up the bug report (or
file a new one).
Thank you for your help.
--aryeh
> Cheers,
>
> Romain
>
>
>
>
> ---------------------------------------------------------------
> Dr. Romain Guiet
> Bioimaging and Optics Platform (PT-BIOP)
> Ecole Polytechnique Fédérale de Lausanne (EPFL)
> Faculty of Life Sciences
> Station 19, AI 0140
> CH-1015 Lausanne
>
> Phone: [+4121 69] 39629
>
http://biop.epfl.ch/> ---------------------------------------------------------------
>
> ________________________________________
> De : ImageJ Interest Group [
[hidden email]] de la part de Aryeh Weiss [
[hidden email]]
> Envoyé : lundi 21 septembre 2015 15:40
> À :
[hidden email]
> Objet : problem using BIOP vsi reader
>
> I am trying to help a colleague open his VSI files using ImageJ.
> The file he sent me has a two parts:
> Process_2297.vsi, which si 651kB in size.
> _Process_2297_/stack1/frame_t_0_ets , which a 19.93GB in size.
>
> When I run BIOP VSI reader, it comes up fine. I press "Select VSI" and
> get the following two windows:
>
> 1. VSI Reader
> This window contains data the macro needs. Please don't close it
> Series ID :
> /Users/amw1/Desktop/projects/itamarSimonCombing/shwarts/Process_2297.vsi
> Image Folder : /Users/amw1/Desktop/projects/itamarSimonCombing/shwarts/
> totSeries : 1
> Has Label : No
> Has Overview : No
> Has Macro Image : No
> Has Mask : No
> Number Of Series : 0
> Mode : Basic
>
> 2. Log
> Relative Path, adding Path to Fiji
> Full path to BIOPLib
> :/Applications/local/fiji/Fiji.app/plugins/BIOP/BIOPLib.ijm
> Empty Library. Adding BIOPLib Library.
>
> I do not get the "Pick series" window which I found in the tutorial ppt
> presentation, in
>
http://biop.epfl.ch/downloads/VSIreader_tutov2.pdf>
> I have not been able to figure out how to display an image oy part of an
> image.
> I assume that I am missing something obvious, and any help in finding it
> will be much appreciated.
>
> --aryeh
>
> --
> Aryeh Weiss
> Faculty of Engineering
> Bar Ilan University
> Ramat Gan 52900 Israel
>
> Ph: 972-3-5317638
> FAX: 972-3-7384051
>
>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>
--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel
Ph: 972-3-5317638
FAX: 972-3-7384051
--
ImageJ mailing list:
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