new Bio-Formats

[ctrueden]

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

[Bill Mohler]

Curtis-

Thanks!  Any chance metamorph tif & stk files are supported, for extraction of metadata?

Bill


-----Original Message-----

From:  Curtis Rueden <[hidden email]>
Subj:  new Bio-Formats
Date:  Thu Aug 24, 2006 8:03 pm
Size:  835 bytes
To:  [hidden email]

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


Bill Mohler
Dept of Genetics & Dev Bio
UConn Health Center
p: 860-679-1833
m: 860-985-2719

[Nas-5]

Dear all,

I would like to get a list of the values for each
pixel inside a ROI. how could I do that. I just know
about the list that you can get through
Analyze-->distribustion bye setting bins which is not
what I'm looking for.

Thanks for your help,
Nas

__________________________________________________
Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection around
http://mail.yahoo.com 

[ctrueden]

Hi Bill,

Bio-Formats does support Metamorph STK, as well as many other flavors of
TIFF, so hopefully it will do what you want. I just added a little option to
the Bio-Formats Importer that pops up the parsed metadata in its own window.
If all you want is to browse textual and numerical metadata within your
files, it might be sufficient for your needs.

If you give it a try, let me know how it works for you. If you find it
lacking, I would welcome suggestions and/or sample data to help us improve
things.

Thanks,
Curtis

On 8/25/06, Bill Mohler <[hidden email]> wrote:

>
> Curtis-
>
> Thanks!  Any chance metamorph tif & stk files are supported, for
> extraction of metadata?
>
> Bill
>
>
> -----Original Message-----
>
> From:  Curtis Rueden <[hidden email]>
> Subj:  new Bio-Formats
> Date:  Thu Aug 24, 2006 8:03 pm
> Size:  835 bytes
> To:  [hidden email]
>
> 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
>
>
> Bill Mohler
> Dept of Genetics & Dev Bio
> UConn Health Center
> p: 860-679-1833
> m: 860-985-2719
>

[ctrueden]

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
>

[Knecht, David]

I installed the files where indicated and when I run ImageJ, the Loci  
plug-ins are there.  However, nothing happens when I choose them.  I  
presume a dialog box should come up?  (ImageJ 1.37j, Java 1.5 MacOSX)

Unrelated, but when I start ImageJ I get a message:  "Unrecognized  
Command: Common Toolbar".  I can't figure out where this is coming  
from.  Any ideas?

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 Aug 25, 2006, at 2:42 PM, Curtis Rueden wrote:

> 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
>>

[ctrueden]

Hi David,

Sorry to hear of your troubles. Did you put both bio-formats.jar and
ome-java.jar in /System/Library/Java/Extensions?

On Monday, I will perform some tests on a Mac in our lab, and let you know
what I find.

As for the Common Toolbar error, I have not heard of it. You could try
downloading and installing a fresh version of ImageJ.

-Curtis

On 8/25/06, David Knecht-charter <[hidden email]> wrote:

>
> I installed the files where indicated and when I run ImageJ, the Loci
> plug-ins are there.  However, nothing happens when I choose them.  I
> presume a dialog box should come up?  (ImageJ 1.37j, Java 1.5 MacOSX)
>
> Unrelated, but when I start ImageJ I get a message:  "Unrecognized
> Command: Common Toolbar".  I can't figure out where this is coming
> from.  Any ideas?
>
> 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 Aug 25, 2006, at 2:42 PM, Curtis Rueden wrote:
>
> > 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
> >>
>

[Wayne Rasband]

> I installed the files where indicated and when I run ImageJ, the  
> Loci plug-ins are there.  However, nothing happens when I choose  
> them.  I presume a dialog box should come up?  (ImageJ 1.37j, Java  
> 1.5 MacOSX)
>
> Unrelated, but when I start ImageJ I get a message:  "Unrecognized  
> Command: Common Toolbar".  I can't figure out where this is coming  
> from.  Any ideas?

Look for run("Common Toolbar") in ImageJ/macros/StartupMacros.txt and  
remove it. The Common_Toolbar plugin is part of the WCIF collection  
of plugins at <http://www.uhnresearch.ca/facilities/wcif/imagej/>.

-wayne

[William O'Connell]

Hi Nas,
For questions like this, the searchable ImageJ archives are useful:
https://list.nih.gov/archives/imagej.html

Here's the answer wayne gave a few days ago for a related question:
<snip>
Get the ROI's mask and only process pixels that correspond to non-zero
pixels in the mask. Here is an example:

public void run(ImageProcessor ip) {
    byte[] pixels = (byte[])ip.getPixels();
    int width = ip.getWidth();
    Rectangle r = ip.getRoi();
    ImageProcessor mask = ip.getMask();
    for (int y=r.y; y<(r.y+r.height); y++) {
       for (int x=r.x; x<(r.x+r.width); x++) {
          if (mask==null || mask.getPixel(x-r.x,y-r.y)!=0) {
            ...DO What YOU WISH TO DO
          }    
       }
    }
}
<snap>


Notice that the example assumes the data is 8-bit. For 16-bit data use 'short', for 32-bit data use 'float', for RGB use 'int'.
Here's another way, slower,  but perhaps more transparent.
<snip>
    byte[] pixels = (byte[])ip.getPixels();
    int width = ip.getWidth();

      Roi roi = Imp.getRoi();
      Rectangle rect = roi.getBounds();
      rx = rect.x; ry = rect.y; w = rect.width; h = rect.height;
        for(int y=ry; y<ry+h; y++) {
           for(int x=rx; x<rx+w; x++) {
                if(roi.contains(x, y)) {
                    byte pixVal = pixels[y*width + x];
                 ...DO What YOU WISH TO DO WITH pixVal
                }            
           }
        }      
<snap>
 -------------- Original message ----------------------
From: Nas <[hidden email]>

> Dear all,
>
> I would like to get a list of the values for each
> pixel inside a ROI. how could I do that. I just know
> about the list that you can get through
> Analyze-->distribustion bye setting bins which is not
> what I'm looking for.
>
> Thanks for your help,
> Nas
>
> __________________________________________________
> Do You Yahoo!?
> Tired of spam?  Yahoo! Mail has the best spam protection around
> http://mail.yahoo.com 

[leo durosemont]

Nas,
The previous answer will work from a plugin. You can also do this easily with a simple macro. In the example below, a mask is created from the active selection, and dumped into an array (m). Then the mask is closed, and the positions and values of pixels that are not empty in the mask array are printed.

Leo.

// list pixels values inside a selection
run("Blobs (25K)");
w=getWidth();h=getHeight();
makePolygon(110,24,73,41,95,52,116,38);
getSelectionBounds(xmin, ymin, selwidth, selheight);
run("Create Mask");
m=newArray(w*h);
for(x=0;x<w;x++){
       for(y=0;y<h;y++){
               m[y*w+x]=getPixel(x,y);
       }
}
close(); //close mask
for(x=xmin;(x<=xmin+selwidth);x++){
       for(y=ymin;(y<=ymin+selheight);y++){
               if (m[y*w+x]!=0) print (x,y,getPixel(x,y));
       }
}

Nas <[hidden email]> wrote: Dear all,

I would like to get a list of the values for each
pixel inside a ROI. how could I do that. I just know
about the list that you can get through
Analyze-->distribustion bye setting bins which is not
what I'm looking for.

Thanks for your help,
Nas

__________________________________________________
Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection around
http://mail.yahoo.com 


 
---------------------------------
Do you Yahoo!?
 Everyone is raving about the  all-new Yahoo! Mail.

[Jean-Christophe Ame]

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
Parc d'innovation, Boulevard Sébastien Brant
BP 10413
67412 ILLKIRCH CEDEX
France

tel.: [phone]
Fax.: [phone]

http://parplink.u-strasbg.fr
http://idg.u-strasbg.fr/

« Science sans conscience n'est que ruine de l'âme ...» (François  
Rabelais, 1483-1553)

[ctrueden]

Hi Jean-Christophe,

We would be glad to improve the Openlab support, if we can obtain some
sample data. Do you have any we could use? I will email you privately with
an FTP server you can use to upload some, if you are willing.

Thanks,
Curtis

On 8/30/06, Jean-Christophe AME <[hidden email]> wrote:

>
> 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
> Parc d'innovation, Boulevard Sébastien Brant
> BP 10413
> 67412 ILLKIRCH CEDEX
> France
>
> tel.: [phone]
> Fax.: [phone]
>
> http://parplink.u-strasbg.fr
> http://idg.u-strasbg.fr/
>
> « Science sans conscience n'est que ruine de l'âme ...» (François
> Rabelais, 1483-1553)
>

[Jean-Christophe Ame]

Hi Curtis,
No problem I can send you anything you would like.  keep in touch.
Thanks.

Jean-Christophe

Le 30 août 06 à 18:14, Curtis Rueden a écrit :

> Hi Jean-Christophe,
>
> We would be glad to improve the Openlab support, if we can obtain some
> sample data. Do you have any we could use? I will email you  
> privately with
> an FTP server you can use to upload some, if you are willing.
>
> Thanks,
> Curtis
>
> On 8/30/06, Jean-Christophe AME <[hidden email]> wrote:
>>
>> 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
>> Parc d'innovation, Boulevard Sébastien Brant
>> BP 10413
>> 67412 ILLKIRCH CEDEX
>> France
>>
>> tel.: [phone]
>> Fax.: [phone]
>>
>> http://parplink.u-strasbg.fr
>> http://idg.u-strasbg.fr/
>>
>> « Science sans conscience n'est que ruine de l'âme ...» (François
>> Rabelais, 1483-1553)
>>

________________________
Jean-Christophe Amé, PhD
Département Intégrité du Génome, UMR 7175-LC1 du CNRS
École Supérieure de Biotechnologie de Strasbourg
Pôle API
Parc d'innovation, Boulevard Sébastien Brant
BP 10413
67412 ILLKIRCH CEDEX
France

tel.: [phone]
Fax.: [phone]

http://parplink.u-strasbg.fr
http://idg.u-strasbg.fr/

« Science sans conscience n'est que ruine de l'âme ...» (François  
Rabelais, 1483-1553)