Posted by
Aryeh Weiss on
Sep 22, 2015; 12:47pm
URL: http://imagej.273.s1.nabble.com/problem-using-BIOP-vsi-reader-tp5014387p5014399.html
Hi Oli and thank you for your quick reply.
On 9/22/15 3:33 PM, Burri Olivier wrote:
> Hi All,
>
>>> 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->> 0000619d7dcd
> Thanks I got the file and modified the way the VSI reader searches for series in the file structure to include the current case.
> If interested, we were using the fact that our "real" series contained the magnification used during acquisition (10x, 4x, etc...) and we used that to find them.
>
> The image you provided did not have this string and thus caused the issue. Now we are using the fact that intermediate sizes contain a # character, while keeping previous functionality.
>
> You can download the latest VSI reader through our update site.
I updated and indeed it now finds hte series. However, when I select
"small" thumbnails and tryto continue, it pops up a window
that says "Macro error", and the Log window shas the following:
java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at
loci.plugins.macro.MacroFunctions.handleExtension(MacroFunctions.java:82)
at ij.macro.ExtensionDescriptor.dispatch(ExtensionDescriptor.java:288)
at ij.macro.Functions.doExt(Functions.java:4445)
at ij.macro.Functions.getStringFunction(Functions.java:274)
and a lot more....
>>> 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.
> Aah the beauty of the Mac, can't copy things from the Macro Recorder either... Thanks for trying.
>
>> One 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).
> Check the latest actionBar version, at least on our PCs this element does not appear anymore since a little while...
I use the update site, so I should have the latest version.
> Hope it will work for you now.
>
> All the best
>
> Oli
>
Many thanks.
--aryeh
--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel
Ph: 972-3-5317638
FAX: 972-3-7384051
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