Problem with opening .tif Files

[SimonTUD]

Hello!

I'm just writing my diploma thesis at the moment and therefor I am analysing recordings of an incident light microscope. The subject is about dropwise condensation of steam.
The microscope shots one picture every second for about 2:30 min (=151 pictures). These package of pictures is saved as a tif.-File.

When I try to open these files with ImageJ there is the following problem. The programm stops loading the pictures and sending me this error message:

ImageJ 1.49b; Java 1.6.0_20 [64-bit]; Windows 7 6.1; 450MB of 3072MB (14%)
 
java.lang.ArrayIndexOutOfBoundsException: 2381860
        at ij.io.ImageReader.packBitsUncompress(ImageReader.java:981)
        at ij.io.ImageReader.uncompress(ImageReader.java:880)
        at ij.io.ImageReader.readCompressedChunkyRGB(ImageReader.java:463)
        at ij.io.ImageReader.readChunkyRGB(ImageReader.java:367)
        at ij.io.ImageReader.readPixels(ImageReader.java:806)
        at ij.io.ImageReader.readPixels(ImageReader.java:857)
        at ij.io.Opener.openTiffStack(Opener.java:699)
        at ij.io.Opener.openTiff2(Opener.java:957)
        at ij.io.Opener.openTiff(Opener.java:780)
        at ij.io.Opener.openImage(Opener.java:268)
        at ij.io.Opener.openImage(Opener.java:334)
        at ij.io.Opener.open(Opener.java:144)
        at ij.io.Opener.openAndAddToRecent(Opener.java:247)
        at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:176)
        at ij.plugin.DragAndDrop.run(DragAndDrop.java:152)
        at java.lang.Thread.run(Thread.java:619)

Or Sometimes just:

ImageJ 1.49b; Java 1.6.0_20 [64-bit]; Windows 7 6.1; 368MB of 3072MB (11%)
 
java.lang.ArrayIndexOutOfBoundsException


So it doesn't load all images but additionally the images that were loaded are damaged. Here is an example:
This is how it should look like:


And this is how the damaged images look like:


Not only that the color changes but there are edges too.
I am not good at Java so I don`t know what the error message is telling me. Maybe someone knows this problem or understands that error and can help me with this issue. It doesn't happen with every image set but with most of them.

Thanks in advance!

Greetings

[Rasband, Wayne (NIH/NIMH) [E]]

On Jun 22, 2014, at 10:25 AM, SimonTUD wrote:

> Hello!
>
> I'm just writing my diploma thesis at the moment and therefor I am analysing
> recordings of an incident light microscope. The subject is about dropwise
> condensation of steam.
> The microscope shots one picture every second for about 2:30 min (=151
> pictures). These package of pictures is saved as a tif.-File.
>
> When I try to open these files with ImageJ there is the following problem.
> The programm stops loading the pictures and sending me this error message:

The latest ImageJ daily build (1.49c20) fixes a couple of bugs related to importing TIFF files or try working around the bug by using File>Import>TIFF Virtual Stack.

-wayne

> ImageJ 1.49b; Java 1.6.0_20 [64-bit]; Windows 7 6.1; 450MB of 3072MB (14%)
>
> java.lang.ArrayIndexOutOfBoundsException: 2381860
> at ij.io.ImageReader.packBitsUncompress(ImageReader.java:981)
> at ij.io.ImageReader.uncompress(ImageReader.java:880)
> at ij.io.ImageReader.readCompressedChunkyRGB(ImageReader.java:463)
> at ij.io.ImageReader.readChunkyRGB(ImageReader.java:367)
> at ij.io.ImageReader.readPixels(ImageReader.java:806)
> at ij.io.ImageReader.readPixels(ImageReader.java:857)
> at ij.io.Opener.openTiffStack(Opener.java:699)
> at ij.io.Opener.openTiff2(Opener.java:957)
> at ij.io.Opener.openTiff(Opener.java:780)
> at ij.io.Opener.openImage(Opener.java:268)
> at ij.io.Opener.openImage(Opener.java:334)
> at ij.io.Opener.open(Opener.java:144)
> at ij.io.Opener.openAndAddToRecent(Opener.java:247)
> at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:176)
> at ij.plugin.DragAndDrop.run(DragAndDrop.java:152)
> at java.lang.Thread.run(Thread.java:619)
>
> Or Sometimes just:
>
> ImageJ 1.49b; Java 1.6.0_20 [64-bit]; Windows 7 6.1; 368MB of 3072MB (11%)
>
> java.lang.ArrayIndexOutOfBoundsException
>
>
> So it doesn't load all images but additionally the images that were loaded
> are damaged. Here is an example:
> This is how it should look like:
> <http://imagej.1557.x6.nabble.com/file/n5008367/Original.jpg>
>
> And this is how the damaged images look like:
> <http://imagej.1557.x6.nabble.com/file/n5008367/Damaged.jpg>
>
> Not only that the color changes but there are edges too.
> I am not good at Java so I don`t know what the error message is telling me.
> Maybe someone knows this problem or understands that error and can help me
> with this issue. It doesn't happen with every image set but with most of
> them.
>
> Thanks in advance!
>
> Greetings
>
>
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Problem-with-opening-tif-Files-tp5008367.html
> Sent from the ImageJ mailing list archive at Nabble.com.

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