ImageJ

error adding slice after splitting channels

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Cammer, Michael

error adding slice after splitting channels

We are getting an error when we try to add a slice to a stack.

We drag and drop a 2 channel Z series Zeiss 710 generated image onto ImageJ. It opens fine with two color channels and 34 Z slices.
We split the channels. When we try to add a slice, the following exception is thrown:

java.lang.ArrayIndexOutOfBoundsException: 34
at ij.ImageStack.addSlice(ImageStack.java:69)
at ij.ImageStack.addSlice(ImageStack.java:100)
at ij.ImageStack.addSlice(ImageStack.java:108)
at ij.plugin.StackEditor.addSlice(StackEditor.java:52)
at ij.plugin.StackEditor.run(StackEditor.java:24)
at ij.IJ.runPlugIn(IJ.java:156)
at ij.Executer.runCommand(Executer.java:127)
at ij.Executer.run(Executer.java:61)
at ij.IJ.run(IJ.java:249)
at ij.IJ.run(IJ.java:227)
at ij.macro.Functions.doRun(Functions.java:569)
at ij.macro.Functions.doFunction(Functions.java:80)
at ij.macro.Interpreter.doStatement(Interpreter.java:203)
at ij.macro.Interpreter.doIf(Interpreter.java:852)
at ij.macro.Interpreter.doStatement(Interpreter.java:215)
at ij.macro.Interpreter.doIf(Interpreter.java:865)
at ij.macro.Interpreter.doStatement(Interpreter.java:215)
at ij.macro.Interpreter.doBlock(Interpreter.java:518)
at ij.macro.Interpreter.runMacro(Interpreter.java:130)
at ij.macro.MacroRunner.run(MacroRunner.java:139)
at java.lang.Thread.run(Unknown Source)

To try to solve this, we updated from an ImageJ version a few weeks old to the most recent daily build. But the problem persists. We can get around the problem by saving each channel's stack after the split, closing, and opening.
Saving as TIF before splitting, however, causes the same error.

Thank you.
________________________________________________________
Michael Cammer, Assistant Research Scientist
Skirball Institute of Biomolecular Medicine
Lab: (212) 263-3208 Cell: (914) 309-3270

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<PRE>

Rasband, Wayne (NIH/NIMH) [E]

Re: error adding slice after splitting channels

On Aug 1, 2011, at 1:01 PM, Cammer, Michael wrote:

> We are getting an error when we try to add a slice to a stack.
>
> We drag and drop a 2 channel Z series Zeiss 710 generated image onto ImageJ. It opens fine with two color channels and 34 Z slices.
> We split the channels. When we try to add a slice, the following exception is thrown:

This bug is fixed in the ImageJ 1.45m daily build.

-wayne

> java.lang.ArrayIndexOutOfBoundsException: 34
> at ij.ImageStack.addSlice(ImageStack.java:69)
> at ij.ImageStack.addSlice(ImageStack.java:100)
> at ij.ImageStack.addSlice(ImageStack.java:108)
> at ij.plugin.StackEditor.addSlice(StackEditor.java:52)
> at ij.plugin.StackEditor.run(StackEditor.java:24)
> at ij.IJ.runPlugIn(IJ.java:156)
> at ij.Executer.runCommand(Executer.java:127)
> at ij.Executer.run(Executer.java:61)
> at ij.IJ.run(IJ.java:249)
> at ij.IJ.run(IJ.java:227)
> at ij.macro.Functions.doRun(Functions.java:569)
> at ij.macro.Functions.doFunction(Functions.java:80)
> at ij.macro.Interpreter.doStatement(Interpreter.java:203)
> at ij.macro.Interpreter.doIf(Interpreter.java:852)
> at ij.macro.Interpreter.doStatement(Interpreter.java:215)
> at ij.macro.Interpreter.doIf(Interpreter.java:865)
> at ij.macro.Interpreter.doStatement(Interpreter.java:215)
> at ij.macro.Interpreter.doBlock(Interpreter.java:518)
> at ij.macro.Interpreter.runMacro(Interpreter.java:130)
> at ij.macro.MacroRunner.run(MacroRunner.java:139)
> at java.lang.Thread.run(Unknown Source)
>
> To try to solve this, we updated from an ImageJ version a few weeks old to the most recent daily build. But the problem persists. We can get around the problem by saving each channel's stack after the split, closing, and opening.
> Saving as TIF before splitting, however, causes the same error.
>
> Thank you.
> ________________________________________________________
> Michael Cammer, Assistant Research Scientist
> Skirball Institute of Biomolecular Medicine
> Lab: (212) 263-3208 Cell: (914) 309-3270
>
> </PRE>
> <html>
> <body>
> ------------------------------------------------------------<br />
> This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.<br />
> =================================
> </body>
> </html>
> <PRE>