Reading headers with Fiji/ImageJ

[Xavier Heiligenstein]

Dear Fiji/ImageJ users,

I face an issue opening tif files (taken with iTEM) with ImageJ or Fiji.
It never extracts the pixel size correctly. Hence I have to enter it
manually afterwards for proper image analysis.
If I open the same files with Icy or Olympus Soft Imaging viewer it
works correctly. Meaning that the headers are embedded correctly in the
tif headers.

Would anyone have a suggestion for me ?
In advance, thank you for your help.

Best regards.

Xavier

--
Xavier Heiligenstein, PhD


Computer Configuration:

Intel Core i7-2860QM CPU @ 2.50Ghz
RAM: 16,0 GB
NVIDIA Quadro 2000M / Intel HD Graphics Family
Windows 7-64bits, SP1



Institut Curie,
France

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

[ctrueden]

Hi Xavier,

> I face an issue opening tif files (taken with iTEM) with ImageJ or
> Fiji. It never extracts the pixel size correctly. Hence I have to
> enter it manually afterwards for proper image analysis.

Did you try opening your TIFF using File > Import > Bio-Formats?

Regards,
Curtis


On Thu, Mar 14, 2013 at 12:26 PM, Xavier Heiligenstein <
[hidden email]> wrote:

> Dear Fiji/ImageJ users,
>
> I face an issue opening tif files (taken with iTEM) with ImageJ or Fiji.
> It never extracts the pixel size correctly. Hence I have to enter it
> manually afterwards for proper image analysis.
> If I open the same files with Icy or Olympus Soft Imaging viewer it works
> correctly. Meaning that the headers are embedded correctly in the tif
> headers.
>
> Would anyone have a suggestion for me ?
> In advance, thank you for your help.
>
> Best regards.
>
> Xavier
>
> --
> Xavier Heiligenstein, PhD
>
>
> Computer Configuration:
>
> Intel Core i7-2860QM CPU @ 2.50Ghz
> RAM: 16,0 GB
> NVIDIA Quadro 2000M / Intel HD Graphics Family
> Windows 7-64bits, SP1
>
>
>
> Institut Curie,
> France
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html>
>

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

[Glen MacDonald-2]

Dear Xavier,
Open the file through the LOCI plugin.  It will read the scale.  Note, however, that resaving the iTEM tiff with some applications may lose the spatial calibration.  You will want to test before saving your files with Fiji
Glen MacDonald
        Core for Communication Research
Virginia Merrill Bloedel Hearing Research Center
        Cellular Morphology Core
Center on Human Development and Disability
Box 357923
University of Washington
Seattle, WA 98195-7923  USA
[phone]
[hidden email]
[hidden email]





On Mar 14, 2013, at 10:26 AM, Xavier Heiligenstein <[hidden email]> wrote:

> Dear Fiji/ImageJ users,
>
> I face an issue opening tif files (taken with iTEM) with ImageJ or Fiji. It never extracts the pixel size correctly. Hence I have to enter it manually afterwards for proper image analysis.
> If I open the same files with Icy or Olympus Soft Imaging viewer it works correctly. Meaning that the headers are embedded correctly in the tif headers.
>
> Would anyone have a suggestion for me ?
> In advance, thank you for your help.
>
> Best regards.
>
> Xavier
>
> --
> Xavier Heiligenstein, PhD
>
>
> Computer Configuration:
>
> Intel Core i7-2860QM CPU @ 2.50Ghz
> RAM: 16,0 GB
> NVIDIA Quadro 2000M / Intel HD Graphics Family
> Windows 7-64bits, SP1
>
>
>
> Institut Curie,
> France
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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

[Krs5]

Dear List,

I seem to have problems opening files using LOCI. Not sure when this problem started, if it was an update from today or earlier.

If I for example drop a file on FIJI (tried OIF and LIF files) I get the error:

--------------------------------------------
Fiji/ImageJ 1.47m; Java 1.6.0_20 [32-bit]; Windows XP 5.1; 10MB of 1084MB (<1%)
 
java.lang.IllegalAccessError: tried to access method loci.formats.ImageReader.getDefaultReaderClasses()Lloci/formats/ClassList; from class loci.plugins.util.LociPrefs
 at loci.plugins.util.LociPrefs.makeImageReader(LociPrefs.java:73)
 at loci.plugins.in.ImportProcess.createBaseReader(ImportProcess.java:594)
 at loci.plugins.in.ImportProcess.initializeReader(ImportProcess.java:472)
 at loci.plugins.in.ImportProcess.execute(ImportProcess.java:142)
 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:193)
 at ij.IJ.runPlugIn(IJ.java:160)
 at ij.IJ.runPlugIn(IJ.java:149)
 at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:405)
 at HandleExtraFileTypes.run(HandleExtraFileTypes.java:57)
 at ij.IJ.runUserPlugIn(IJ.java:193)
 at ij.IJ.runPlugIn(IJ.java:160)
 at ij.IJ.runPlugIn(IJ.java:149)
 at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:434)
 at ij.io.Opener.openImage(Opener.java:306)
 at ij.io.Opener.openImage(Opener.java:329)
 at ij.io.Opener.open(Opener.java:142)
 at ij.io.Opener.openAndAddToRecent(Opener.java:242)
 at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:176)
 at ij.plugin.DragAndDrop.run(DragAndDrop.java:152)
 at java.lang.Thread.run(Thread.java:619)
--------------------------------------------------------------------

When I use in a macro:

run("Bio-Formats Importer", "open="+path);

this line is ignored and I get the error: "There are no images open" when the macro has to make manipulations to the image.

Any suggestions?

Best wishes

Kees

Dr Ir K.R. Straatman
Senior Experimental Officer
Centre for Core Biotechnology Services
University of Leicester, UK
http://www.le.ac.uk/biochem/microscopy/home.html
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[Melissa Linkert-2]

Hi Kees,

> I seem to have problems opening files using LOCI. Not sure when this problem started, if it was an update from today or earlier.
>
> If I for example drop a file on FIJI (tried OIF and LIF files) I get the error:
>
> --------------------------------------------
> Fiji/ImageJ 1.47m; Java 1.6.0_20 [32-bit]; Windows XP 5.1; 10MB of 1084MB (<1%)
>  
> java.lang.IllegalAccessError: tried to access method loci.formats.ImageReader.getDefaultReaderClasses()Lloci/formats/ClassList; from class loci.plugins.util.LociPrefs
>  at loci.plugins.util.LociPrefs.makeImageReader(LociPrefs.java:73)
>  at loci.plugins.in.ImportProcess.createBaseReader(ImportProcess.java:594)
>  at loci.plugins.in.ImportProcess.initializeReader(ImportProcess.java:472)
>  at loci.plugins.in.ImportProcess.execute(ImportProcess.java:142)
>  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:193)
>  at ij.IJ.runPlugIn(IJ.java:160)
>  at ij.IJ.runPlugIn(IJ.java:149)
>  at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:405)
>  at HandleExtraFileTypes.run(HandleExtraFileTypes.java:57)
>  at ij.IJ.runUserPlugIn(IJ.java:193)
>  at ij.IJ.runPlugIn(IJ.java:160)
>  at ij.IJ.runPlugIn(IJ.java:149)
>  at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:434)
>  at ij.io.Opener.openImage(Opener.java:306)
>  at ij.io.Opener.openImage(Opener.java:329)
>  at ij.io.Opener.open(Opener.java:142)
>  at ij.io.Opener.openAndAddToRecent(Opener.java:242)
>  at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:176)
>  at ij.plugin.DragAndDrop.run(DragAndDrop.java:152)
>  at java.lang.Thread.run(Thread.java:619)
> --------------------------------------------------------------------

That looks like you somehow have multiple conflicting versions of Bio-Formats
installed in Fiji.  Does "Help > Update Fiji" show that you have locally
modified files?  If so, does removing those files solve the problem?

Regards,
-Melissa

On Fri, Mar 15, 2013 at 04:51:52PM +0000, Straatman, Kees R. (Dr.) wrote:

> Dear List,
>
> I seem to have problems opening files using LOCI. Not sure when this problem started, if it was an update from today or earlier.
>
> If I for example drop a file on FIJI (tried OIF and LIF files) I get the error:
>
> --------------------------------------------
> Fiji/ImageJ 1.47m; Java 1.6.0_20 [32-bit]; Windows XP 5.1; 10MB of 1084MB (<1%)
>  
> java.lang.IllegalAccessError: tried to access method loci.formats.ImageReader.getDefaultReaderClasses()Lloci/formats/ClassList; from class loci.plugins.util.LociPrefs
>  at loci.plugins.util.LociPrefs.makeImageReader(LociPrefs.java:73)
>  at loci.plugins.in.ImportProcess.createBaseReader(ImportProcess.java:594)
>  at loci.plugins.in.ImportProcess.initializeReader(ImportProcess.java:472)
>  at loci.plugins.in.ImportProcess.execute(ImportProcess.java:142)
>  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:193)
>  at ij.IJ.runPlugIn(IJ.java:160)
>  at ij.IJ.runPlugIn(IJ.java:149)
>  at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:405)
>  at HandleExtraFileTypes.run(HandleExtraFileTypes.java:57)
>  at ij.IJ.runUserPlugIn(IJ.java:193)
>  at ij.IJ.runPlugIn(IJ.java:160)
>  at ij.IJ.runPlugIn(IJ.java:149)
>  at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:434)
>  at ij.io.Opener.openImage(Opener.java:306)
>  at ij.io.Opener.openImage(Opener.java:329)
>  at ij.io.Opener.open(Opener.java:142)
>  at ij.io.Opener.openAndAddToRecent(Opener.java:242)
>  at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:176)
>  at ij.plugin.DragAndDrop.run(DragAndDrop.java:152)
>  at java.lang.Thread.run(Thread.java:619)
> --------------------------------------------------------------------
>
> When I use in a macro:
>
> run("Bio-Formats Importer", "open="+path);
>
> this line is ignored and I get the error: "There are no images open" when the macro has to make manipulations to the image.
>
> Any suggestions?
>
> Best wishes
>
> Kees
>
> Dr Ir K.R. Straatman
> Senior Experimental Officer
> Centre for Core Biotechnology Services
> University of Leicester, UK
> http://www.le.ac.uk/biochem/microscopy/home.html
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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