Bio-Formats release (2006 Sep 27)

[ctrueden]

Hi,

Today LOCI has released a new version of Bio-Formats. Major changes include:

* PerkinElmer: support for PE UltraView
* Openlab LIFF: support for Openlab v5
* Leica LEI: bugfixes, and support for multiple series
* ZVI, OIB, IPW: more robust handling of these formats (eliminated
custom OLE parsing logic in favor of Apache POI)
* OIB: better metadata parsing (but maybe still not perfect?)
* LSM: fixed a bug preventing import of certain LSMs
* Metamorph STK: fixed a bug resulting in duplicate image planes
* User interface: use of system look & feel for file chooser dialog
when available
* Better notification when JAR libraries are missing

You can download the release from the Bio-Formats web site:
   http://www.loci.wisc.edu/ome/formats.html

Please note that there is one new library required, poi-loci.jar, in
addition to the old dependencies. It goes in the ImageJ plugins folder
just like the others.

To receive future release notifications, sign up for the LOCI software
mailing list by following the instructions on the LOCI software web
site:
   http://www.loci.wisc.edu/software/

And as always, please let me know if you have any issues or questions
about the software.

Cheers,
Curtis

[Knecht, David]

I have so far been unable to run Bioformats on my MacBook Pro (OSX  
10.4.7) and am wondering if anyone else is having the same problem.  
After installation of the files, LOCI shows up in my plugins list,  
but when I choose Biofromats Importer, nothing happens.  On other  
computers in my lab it works fine with the same ImageJ and OSX  
version (1.36b, Java 1.5). Dave

Dr. David Knecht
Department of Molecular and Cell Biology
U-3125
91 N. Eagleville Rd.
University of Connecticut
Storrs, CT 06269
860-486-2200
860-486-4331 (fax)


On Sep 27, 2006, at 1:02 PM, Curtis Rueden wrote:

> Hi,
>
> Today LOCI has released a new version of Bio-Formats. Major changes  
> include:
>
> * PerkinElmer: support for PE UltraView
> * Openlab LIFF: support for Openlab v5
> * Leica LEI: bugfixes, and support for multiple series
> * ZVI, OIB, IPW: more robust handling of these formats (eliminated
> custom OLE parsing logic in favor of Apache POI)
> * OIB: better metadata parsing (but maybe still not perfect?)
> * LSM: fixed a bug preventing import of certain LSMs
> * Metamorph STK: fixed a bug resulting in duplicate image planes
> * User interface: use of system look & feel for file chooser dialog
> when available
> * Better notification when JAR libraries are missing
>
> You can download the release from the Bio-Formats web site:
>   http://www.loci.wisc.edu/ome/formats.html
>
> Please note that there is one new library required, poi-loci.jar, in
> addition to the old dependencies. It goes in the ImageJ plugins folder
> just like the others.
>
> To receive future release notifications, sign up for the LOCI software
> mailing list by following the instructions on the LOCI software web
> site:
>   http://www.loci.wisc.edu/software/
>
> And as always, please let me know if you have any issues or questions
> about the software.
>
> Cheers,
> Curtis

[Philip Ershler]

I have a MacBook Pro running 10.4.7. I just downloaded the update for  
ImageJ (1.37s) and then dropped loci_plugins.jar, bio-formats.jar,  
poi-loci.jar  and ome-java.jar into my ImageJ/plugins folder. When I  
select Bioformats Importer, I get a file open dialog. I currently  
don't have any applicable files on my machine to test the import.

HTH,

Phil

On Sep 27, 2006, at 8:22 PM, David Knecht-charter wrote:

> I have so far been unable to run Bioformats on my MacBook Pro (OSX  
> 10.4.7) and am wondering if anyone else is having the same  
> problem.  After installation of the files, LOCI shows up in my  
> plugins list, but when I choose Biofromats Importer, nothing  
> happens.  On other computers in my lab it works fine with the same  
> ImageJ and OSX version (1.36b, Java 1.5). Dave
>
> Dr. David Knecht
> Department of Molecular and Cell Biology
> U-3125
> 91 N. Eagleville Rd.
> University of Connecticut
> Storrs, CT 06269
> 860-486-2200
> 860-486-4331 (fax)
>
>
> On Sep 27, 2006, at 1:02 PM, Curtis Rueden wrote:
>
>> Hi,
>>
>> Today LOCI has released a new version of Bio-Formats. Major  
>> changes include:
>>
>> * PerkinElmer: support for PE UltraView
>> * Openlab LIFF: support for Openlab v5
>> * Leica LEI: bugfixes, and support for multiple series
>> * ZVI, OIB, IPW: more robust handling of these formats (eliminated
>> custom OLE parsing logic in favor of Apache POI)
>> * OIB: better metadata parsing (but maybe still not perfect?)
>> * LSM: fixed a bug preventing import of certain LSMs
>> * Metamorph STK: fixed a bug resulting in duplicate image planes
>> * User interface: use of system look & feel for file chooser dialog
>> when available
>> * Better notification when JAR libraries are missing
>>
>> You can download the release from the Bio-Formats web site:
>>   http://www.loci.wisc.edu/ome/formats.html
>>
>> Please note that there is one new library required, poi-loci.jar, in
>> addition to the old dependencies. It goes in the ImageJ plugins  
>> folder
>> just like the others.
>>
>> To receive future release notifications, sign up for the LOCI  
>> software
>> mailing list by following the instructions on the LOCI software web
>> site:
>>   http://www.loci.wisc.edu/software/
>>
>> And as always, please let me know if you have any issues or questions
>> about the software.
>>
>> Cheers,
>> Curtis

[ctrueden]

Hi David,

A couple of notes:

1) The correct place for all JARs to be is the ImageJ plugins folder.
You should have loci_plugins.jar, bio-formats.jar, ome-java.jar and
poi-loci.jar in there.

All old copies of the Bio-Formats JARs should be REMOVED from the
/System/Library/Java/Extensions and /Library/Java/Extensions folders.
Previously, the installation instructions indicated that the support
libraries should be placed there, but doing so is actually not
necessary. Actually, older JAR files in those folders will actually
cause problems, so they should be removed.

I sincerely apologize for the confusion with the Extensions folder; I
did not realize ImageJ was cool that it loaded support libraries from
the plugins folder -- but it does. So installation is as simple as
just dropping everything into plugins.

2) I did hear from one person who had trouble running Bio-Formats on
the Mac with Java 1.4. Upgrading to 1.5 fixed her problem. But since
you are already running Java 1.5, this issue is not relevant to you.
(I mention it here in case anyone else on the list has had trouble
with Bio-Formats on the Mac, as one more thing to try.)

-Curtis

On 9/27/06, David Knecht-charter <[hidden email]> wrote:

> I have so far been unable to run Bioformats on my MacBook Pro (OSX
> 10.4.7) and am wondering if anyone else is having the same problem.
> After installation of the files, LOCI shows up in my plugins list,
> but when I choose Biofromats Importer, nothing happens.  On other
> computers in my lab it works fine with the same ImageJ and OSX
> version (1.36b, Java 1.5). Dave
>
> Dr. David Knecht
> Department of Molecular and Cell Biology
> U-3125
> 91 N. Eagleville Rd.
> University of Connecticut
> Storrs, CT 06269
> 860-486-2200
> 860-486-4331 (fax)
>
>
> On Sep 27, 2006, at 1:02 PM, Curtis Rueden wrote:
>
> > Hi,
> >
> > Today LOCI has released a new version of Bio-Formats. Major changes
> > include:
> >
> > * PerkinElmer: support for PE UltraView
> > * Openlab LIFF: support for Openlab v5
> > * Leica LEI: bugfixes, and support for multiple series
> > * ZVI, OIB, IPW: more robust handling of these formats (eliminated
> > custom OLE parsing logic in favor of Apache POI)
> > * OIB: better metadata parsing (but maybe still not perfect?)
> > * LSM: fixed a bug preventing import of certain LSMs
> > * Metamorph STK: fixed a bug resulting in duplicate image planes
> > * User interface: use of system look & feel for file chooser dialog
> > when available
> > * Better notification when JAR libraries are missing
> >
> > You can download the release from the Bio-Formats web site:
> >   http://www.loci.wisc.edu/ome/formats.html
> >
> > Please note that there is one new library required, poi-loci.jar, in
> > addition to the old dependencies. It goes in the ImageJ plugins folder
> > just like the others.
> >
> > To receive future release notifications, sign up for the LOCI software
> > mailing list by following the instructions on the LOCI software web
> > site:
> >   http://www.loci.wisc.edu/software/
> >
> > And as always, please let me know if you have any issues or questions
> > about the software.
> >
> > Cheers,
> > Curtis
>

[dscho]

Hi,

On Thu, 28 Sep 2006, Curtis Rueden wrote:

> 2) I did hear from one person who had trouble running Bio-Formats on
> the Mac with Java 1.4. Upgrading to 1.5 fixed her problem.

BTW for some, upgrading is not an option. I was stuck with OSX 10.2.8, and
because Apple wants to sell new OSXen and computers, I could not upgrade
to Java 1.5!

Ciao,
Dscho

[Albert Cardona]

>> 2) I did hear from one person who had trouble running Bio-Formats on
>> the Mac with Java 1.4. Upgrading to 1.5 fixed her problem.

>BTW for some, upgrading is not an option. I was stuck with OSX 10.2.8, and
>because Apple wants to sell new OSXen and computers, I could not upgrade
>to Java 1.5!

>Ciao,
>Dscho


To avoid the anual Apple tax (aka "new MaxOSX" or "upgrade"), you can run any
flavor of GNU/Linux and/or *BSD on your Apple laptop, for which java 1.5 is
available.

Albert

[dscho]

Hi,

On Fri, 29 Sep 2006, Albert Cardona wrote:

> >> 2) I did hear from one person who had trouble running Bio-Formats on
> >> the Mac with Java 1.4. Upgrading to 1.5 fixed her problem.
>
> >BTW for some, upgrading is not an option. I was stuck with OSX 10.2.8,
> >and because Apple wants to sell new OSXen and computers, I could not
> >upgrade to Java 1.5!
>
> To avoid the anual Apple tax (aka "new MaxOSX" or "upgrade"), you can
> run any flavor of GNU/Linux and/or *BSD on your Apple laptop, for which
> java 1.5 is available.

That is what I did. But not everybody can; if you lack administrator's
privileges, for example.

Ciao,
Dscho

[ctrueden]

Hi,

> BTW for some, upgrading is not an option. I was stuck with OSX 10.2.8, and
> because Apple wants to sell new OSXen and computers, I could not upgrade
> to Java 1.5!

Well, Bio-Formats is supposed to work with Java 1.4. If anyone else
has problems running it with Java 1.4 on the Mac, I would be
interested to hear about it.

Thanks,
Curtis

[Lucas, Falk /BDF HAM]

Hi,

I just started playing with the bio-formats plugin... opening Imaris 5
files ends up in an error message:

Sorry, there was a problem reading data:
Imaris magic number not found.

Is there an workaround???

Thx,
Falk
 

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[ctrueden]

Hi Falk,

> I just started playing with the bio-formats plugin... opening Imaris 5
> files ends up in an error message:
>
> Sorry, there was a problem reading data:
> Imaris magic number not found.
>
> Is there an workaround???

Imaris 5 is a new format, and unfortunately Bio-Formats does not
support it yet. We will work on adding it as soon as we can. In the
meantime, you can try using the Imaris software to save the file to a
different format. Ideally, you could save as Imaris 4 or earlier,
since Bio-Formats supports that. Otherwise, you can try saving as
TIFF, OME-XML or some other compatible format (depending on what
options the software has).

Also, if you are able to provide us with some sample Imaris 5 data, it
would make adding support a lot easier for us. Let me know if you are
interested, and I can send you our FTP server information.

-Curtis