troubles opening lif flies with Image J and Fiji

[Laura Lucia Prieto Godino]

Dear List,

I am having troubles importing lif files with both Image J and Fiji.  
The problems are:

Image J: In order to open lif files I need to go to plug ins-LOCI-bio  
formats importer. which is a pain to do for every file, ideall i would  
like to open them directly or to drag them to the tool bar and get  
them open, but when I do that it says that the format is not suported.  
I used to be able to do so until I upgraded to the latest version of  
Image J

Fiji: I can open the lif files by dragging them directly to the tool  
bar, but the default function is to open them pseudocolor (it is  
suppose to be gray scale) and I need them in gray scale (white and  
black), and there is no option to open them in gray sclae. Also the  
function mege channels to RGB does not work properly.

Before someone says it, yes, I have the latest version of both.

Thanks for all you help and support!

Lucia


  Lucia Prieto Godino
PhD student.
Department of Zoology,
Downing street
University of Cambridge.
UK
http://www.neuroscience.cam.ac.uk/directory/profile.php?lauralucia

[dscho]

Hi Lucia,

On Fri, 27 Aug 2010, Laura Lucia Prieto Godino wrote:

> Fiji: I can open the lif files by dragging them directly to the tool
> bar, but the default function is to open them pseudocolor (it is suppose
> to be gray scale) and I need them in gray scale (white and black), and
> there is no option to open them in gray sclae. Also the function mege
> channels to RGB does not work properly.

You can undo the pseudocolor by choosing Image>Lookup Tables>Grays.

If you have a multi-channel image (i.e. if your image window has a slider
labeled with 'C'), you can go to Image>Hyperstacks>Channels Tool... and
select "Grayscale" instead of "Composite".

Ciao,
Johannes

[Melissa Linkert-2]

Hi Lucia,

> Image J: In order to open lif files I need to go to plug
> ins-LOCI-bio formats importer. which is a pain to do for every file,
> ideall i would like to open them directly or to drag them to the
> tool bar and get them open, but when I do that it says that the
> format is not suported.

One option is to select "Plugins > LOCI > LOCI Plugins Shortcut Window"
when you start ImageJ or Fiji.  You can then drag and drop files onto the
resulting "LOCI Plugins Shortcut Window", or click the "Bio-Formats
Importer" button, which has the same behavior as selecting "Plugins >
LOCI > Bio-Formats Importer".

Regards,
-Melissa

On Fri, Aug 27, 2010 at 10:08:32AM +0100, Laura Lucia Prieto Godino wrote:

> Dear List,
>
> I am having troubles importing lif files with both Image J and Fiji.
> The problems are:
>
> Image J: In order to open lif files I need to go to plug
> ins-LOCI-bio formats importer. which is a pain to do for every file,
> ideall i would like to open them directly or to drag them to the
> tool bar and get them open, but when I do that it says that the
> format is not suported. I used to be able to do so until I upgraded
> to the latest version of Image J
>
> Fiji: I can open the lif files by dragging them directly to the tool
> bar, but the default function is to open them pseudocolor (it is
> suppose to be gray scale) and I need them in gray scale (white and
> black), and there is no option to open them in gray sclae. Also the
> function mege channels to RGB does not work properly.
>
> Before someone says it, yes, I have the latest version of both.
>
> Thanks for all you help and support!
>
> Lucia
>
>
>  Lucia Prieto Godino
> PhD student.
> Department of Zoology,
> Downing street
> University of Cambridge.
> UK
> http://www.neuroscience.cam.ac.uk/directory/profile.php?lauralucia

[ctrueden]

Hi Lucia,

Image J: In order to open lif files I need to go to plug ins-LOCI-bio
> formats importer. which is a pain to do for every file, ideall i would like
> to open them directly or to drag them to the tool bar and get them open, but
> when I do that it says that the format is not suported. I used to be able to
> do so until I upgraded to the latest version of Image J
>

With the latest daily build of ImageJ (1.44g3), I am able to open LIF files
using File>Open successfully.

I also downloaded the ImageJ 1.43 bundle fresh from the ImageJ web site,
dropped the latest loci_tools.jar trunk build into the plugins folder, and
it also worked from there. So the same thing might solve your problem as
well.

Fiji: I can open the lif files by dragging them directly to the tool bar,
> but the default function is to open them pseudocolor (it is suppose to be
> gray scale) and I need them in gray scale (white and black), and there is no
> option to open them in gray sclae.


You can control the colorization by changing the "Color mode" setting in the
main dialog box—try using "Grayscale." If you choose "Default," the behavior
with LIFs is to use the embedded color tables present in the LIF metadata.

Also the function mege channels to RGB does not work properly.
>

The "merge channels to RGB" option no longer exists. It has been replaced
with the "Color mode" setting. Are you using the latest version of
Bio-Formats?

-Curtis

On Fri, Aug 27, 2010 at 4:08 AM, Laura Lucia Prieto Godino
<[hidden email]>wrote:

> Dear List,
>
> I am having troubles importing lif files with both Image J and Fiji. The
> problems are:
>
> Image J: In order to open lif files I need to go to plug ins-LOCI-bio
> formats importer. which is a pain to do for every file, ideall i would like
> to open them directly or to drag them to the tool bar and get them open, but
> when I do that it says that the format is not suported. I used to be able to
> do so until I upgraded to the latest version of Image J
>
> Fiji: I can open the lif files by dragging them directly to the tool bar,
> but the default function is to open them pseudocolor (it is suppose to be
> gray scale) and I need them in gray scale (white and black), and there is no
> option to open them in gray sclae. Also the function mege channels to RGB
> does not work properly.
>
> Before someone says it, yes, I have the latest version of both.
>
> Thanks for all you help and support!
>
> Lucia
>
>
>  Lucia Prieto Godino
> PhD student.
> Department of Zoology,
> Downing street
> University of Cambridge.
> UK
> http://www.neuroscience.cam.ac.uk/directory/profile.php?lauralucia
>

[dscho]

Hi Lucia,

On Fri, 27 Aug 2010, Laura Lucia Prieto Godino wrote:

> Thanks, it works! but...is there a way of opening the images directly in
> gray in stead of having to go to Image>Lookup Tables>Grays, for every
> stack?that would make life easier!

Have you tried to update Bio-Formats and then chose the Color mode
"Grayscale"?

Ciao,
Johannes

[md574]

Dear List,

I have very similar problem in opening lif files with the latest version of Fiji. We have recently bought a new Leica microscope with a recent version of their LASAF software, since then I could not ope a single lif file coming from that microscope. I have tried all the solutions listed before, but still I get this message

loci.formats.FormatException: Invalid Memory Block: found magic bytes 0, expected 112
        at loci.formats.in.LIFReader.initFile(LIFReader.java:401)
        at loci.formats.FormatReader.setId(FormatReader.java:1238)
        at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:482)
        at loci.plugins.in.ImportProcess.execute(ImportProcess.java:146)
        at loci.plugins.in.Importer.showDialogs(Importer.java:141)
        at loci.plugins.in.Importer.run(Importer.java:79)
        at loci.plugins.LociImporter.run(LociImporter.java:81)
        at ij.IJ.runUserPlugIn(IJ.java:202)
        at ij.IJ.runPlugIn(IJ.java:166)
        at ij.IJ.runPlugIn(IJ.java:155)
        at loci.plugins.shortcut.ShortcutPanel$1.run(ShortcutPanel.java:192)

Any idea? I might just be idiot, but could not solve the problem.
Thank you very much for your help.

[Lachlan Whitehead]

We had the same problem when we got the upgraded software for one of our leica systems.
We've been told that Leica is aware of the problem and is expecting a fix 'soon'.
I think the bioformats developers are also aware but I'm not sure how that's progressing, at the moment I'm telling our users to export to TIF in the leica software until the issue is resolved.

----- Original Message -----
From: "md574" <[hidden email]>
To: [hidden email]
Sent: Sunday, 21 September, 2014 8:43:32 PM
Subject: Re: troubles opening lif flies with Image J and Fiji

Dear List,

I have very similar problem in opening lif files with the latest version of
Fiji. We have recently bought a new Leica microscope with a recent version
of their LASAF software, since then I could not ope a single lif file coming
from that microscope. I have tried all the solutions listed before, but
still I get this message

loci.formats.FormatException: Invalid Memory Block: found magic bytes 0,
expected 112
        at loci.formats.in.LIFReader.initFile(LIFReader.java:401)
        at loci.formats.FormatReader.setId(FormatReader.java:1238)
        at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:482)
        at loci.plugins.in.ImportProcess.execute(ImportProcess.java:146)
        at loci.plugins.in.Importer.showDialogs(Importer.java:141)
        at loci.plugins.in.Importer.run(Importer.java:79)
        at loci.plugins.LociImporter.run(LociImporter.java:81)
        at ij.IJ.runUserPlugIn(IJ.java:202)
        at ij.IJ.runPlugIn(IJ.java:166)
        at ij.IJ.runPlugIn(IJ.java:155)
        at loci.plugins.shortcut.ShortcutPanel$1.run(ShortcutPanel.java:192)

Any idea? I might just be idiot, but could not solve the problem.
Thank you very much for your help.





--
View this message in context: http://imagej.1557.x6.nabble.com/troubles-opening-lif-flies-with-Image-J-and-Fiji-tp3687147p5009701.html
Sent from the ImageJ mailing list archive at Nabble.com.

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

______________________________________________________________________
The information in this email is confidential and intended solely for the addressee.
You must not disclose, forward, print or use it without the permission of the sender.
______________________________________________________________________

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Melissa Linkert-2]

Hi,

>> I have very similar problem in opening lif files with the latest version of
>> Fiji. We have recently bought a new Leica microscope with a recent version
>> of their LASAF software, since then I could not ope a single lif file coming
>> from that microscope. I have tried all the solutions listed before, but
>> still I get this message
>>
>> loci.formats.FormatException: Invalid Memory Block: found magic bytes 0,
>> expected 112
>> at loci.formats.in.LIFReader.initFile(LIFReader.java:401)
>
> I think the bioformats developers are also aware but I'm not sure how that's progressing, at the moment I'm telling our users to export to TIF in the leica software until the issue is resolved.

The Bio-Formats developers are indeed aware of this problem, as noted
on the OME issue tracking system:

http://trac.openmicroscopy.org.uk/ome/ticket/12144

We expect to have this fixed no later than the 5.1.0 release of
Bio-Formats later this year; if anyone wishes to be notified of updates
to that ticket, please let me know.

Regards,
-Melissa

On Mon, Sep 22, 2014 at 12:24:19PM +1000, Lachlan Whitehead wrote:

> We had the same problem when we got the upgraded software for one of our leica systems.
> We've been told that Leica is aware of the problem and is expecting a fix 'soon'.
> I think the bioformats developers are also aware but I'm not sure how that's progressing, at the moment I'm telling our users to export to TIF in the leica software until the issue is resolved.
>
> ----- Original Message -----
> From: "md574" <[hidden email]>
> To: [hidden email]
> Sent: Sunday, 21 September, 2014 8:43:32 PM
> Subject: Re: troubles opening lif flies with Image J and Fiji
>
> Dear List,
>
> I have very similar problem in opening lif files with the latest version of
> Fiji. We have recently bought a new Leica microscope with a recent version
> of their LASAF software, since then I could not ope a single lif file coming
> from that microscope. I have tried all the solutions listed before, but
> still I get this message
>
> loci.formats.FormatException: Invalid Memory Block: found magic bytes 0,
> expected 112
> at loci.formats.in.LIFReader.initFile(LIFReader.java:401)
> at loci.formats.FormatReader.setId(FormatReader.java:1238)
> at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:482)
> at loci.plugins.in.ImportProcess.execute(ImportProcess.java:146)
> at loci.plugins.in.Importer.showDialogs(Importer.java:141)
> at loci.plugins.in.Importer.run(Importer.java:79)
> at loci.plugins.LociImporter.run(LociImporter.java:81)
> at ij.IJ.runUserPlugIn(IJ.java:202)
> at ij.IJ.runPlugIn(IJ.java:166)
> at ij.IJ.runPlugIn(IJ.java:155)
> at loci.plugins.shortcut.ShortcutPanel$1.run(ShortcutPanel.java:192)
>
> Any idea? I might just be idiot, but could not solve the problem.
> Thank you very much for your help.
>
>
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/troubles-opening-lif-flies-with-Image-J-and-Fiji-tp3687147p5009701.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> ______________________________________________________________________
> The information in this email is confidential and intended solely for the addressee.
> You must not disclose, forward, print or use it without the permission of the sender.
> ______________________________________________________________________
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html