Re: new Bio-Formats

Posted by Jean-Christophe Ame on
URL: http://imagej.273.s1.nabble.com/new-Bio-Formats-tp3701686p3701688.html

Hi Curtis,

Bio-Formats is really good addtion to imageJ. Opening Improvision  
Openlab .liff files seems to work quite well as long as there were  
created with openlab 4. With the new version 5, they changed the file  
format as it is now compressed. Is-it possible for you to add this  
feature to Bio-Formats.

Thank a lot for your help.
Jean-Christophe



Le 25 août 06 à 20:42, Curtis Rueden a écrit :

> Hi again,
>
> Some additional notes about the Bio-Formats release:
>
> First, if you tried out Bio-Formats yesterday or early this morning, I
> failed to mention that there is an additional support library  
> required (
> ome-java.jar) that goes into ImageJ/jre/lib/ext (or
> /System/Library/Java/Extensions on Mac OS X) along with bio-
> formats.jar. You
> can download this library from the Bio-Formats web site (and I have  
> updated
> the instructions accordingly). Apologies for my mistake.
>
> Second, I have updated loci_plugins.jar to include a simple  
> metadata viewer
> with the Bio-Formats Importer plugin. Just make sure "Show associated
> metadata" is checked, and the metadata parsed from your file(s)  
> will appear
> in a table in its own window.
>
> Lastly, I should mention that Bio-Formats only works with Java 1.4  
> or later,
> so if you are running the Windows version of ImageJ bundled with  
> Java 1.3,
> you'll need to upgrade to the Java 5.0 version if you want to use
> Bio-Formats.
>
> -Curtis
>
> On 8/24/06, Curtis Rueden <[hidden email]> wrote:
>>
>> Hi,
>>
>> Today LOCI has released a new version of the Bio-Formats plugin for
>> reading and writing common microscopy formats with ImageJ.  
>> Significant
>> improvements have been made to Leica LIF and Olympus FV1000 OIB  
>> support, as
>> well as many other bugfixes.
>>
>> You can download the release from the Bio-Formats website:
>>     http://www.loci.wisc.edu/ome/formats.html
>>
>> Please note that the library has been split into two files: bio-
>> formats.jar
>> (the core library) and loci_plugins.jar (the ImageJ plugins). Just  
>> put bio
>> -formats.jar in your extensions folder (ImageJ\jre\lib\ext on  
>> Windows,
>> /System/Library/Java/Extensions on Mac OS X), and put  
>> loci_plugins.jar in
>> the ImageJ plugins folder.
>>
>> As always, please let me know if you have problems reading data in  
>> any
>> supported format, or would like support added for additional formats.
>>
>> Cheers,
>> Curtis
>>


________________________
Jean-Christophe Amé, PhD
Département Intégrité du Génome, UMR 7175-LC1 du CNRS
École Supérieure de Biotechnologie de Strasbourg
Pôle API
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