Image5D loading problem

[Adam Rodaway]

Hi all,

Apologies in advance if this is a dumb question - I'm an imager, not a programmer!

I'm trying (for the first time) to open some timelapse stacks using the Image5D plugin - I'd like to
analyse them using Erik Meijering's MTrackJ.

Basically, I can't get the stacks to open with Image5D. I get as far as the dialogue boxes to specify
dimensions, but when I click 'OK' I immediately get an exception message (this one from
attempting to convert a stack using plugins/image5D/stack to image5D):

java.lang.NoSuchMethodError: ij.process.ImageProcessor.getLutUpdateMode()I
        at i5d.Image5D.<init>(Image5D.java:231)
        at i5d.Image5D.<init>(Image5D.java:141)
        at i5d.Image5D.<init>(Image5D.java:122)
        at i5d.Image5D.<init>(Image5D.java:133)
        at Stack_to_Image5D.run(Stack_to_Image5D.java:124)
        at ij.IJ.runUserPlugIn(IJ.java:265)
        at ij.IJ.runPlugIn(IJ.java:120)
        at ij.Executer.runCommand(Executer.java:95)
        at ij.Executer.run(Executer.java:49)
        at java.lang.Thread.run(Thread.java:552)

This doesn't seem to depend on the data type, since it occurs with both 8bit and RGB stacks
(including the test stacks from the plugin page). Nor on  how I try to get the data into Image5D
(open series as Image5D , RGB to Image5D etc. etc, depending on source files). All that changes in
these cases is line 5 of the exception message to, for example "at
Open_Series_As_Image5D.run(Open_Series_As_Image5D.java:32)".

It looks a bit like the problem that David Knecht had back in January 2006...I don't know if this got
solved.

Other info as follows:

I'm running MacOSX (10.3.8) on a powerbook with lots (!) of RAM
ImageJ is latest version (1.38c), recently downloaded. (I didn't try Image5D on my previous
version, 1.34, so I don't know if behaviour has changed)
Java is
java version "1.4.2_09"
Java(TM) 2 Runtime Environment, Standard Edition (build 1.4.2_09-233)
Java HotSpot(TM) Client VM (build 1.4.2-56, mixed mode)

Thanks in advance for any help!
Adam

[Wayne Rasband]

This is a bug in ImageJ 1.38c that is fixed in 1.38d, available at
<http://rsb.info.nih.gov/ij/notes.html>.

-wayne

On Dec 1, 2006, at 11:48 AM, Adam Rodaway wrote:

> Hi all,
>
> Apologies in advance if this is a dumb question - I'm an imager, not a
> programmer!
>
> I'm trying (for the first time) to open some timelapse stacks using
> the Image5D plugin - I'd like to
> analyse them using Erik Meijering's MTrackJ.
>
> Basically, I can't get the stacks to open with Image5D. I get as far
> as the dialogue boxes to specify
> dimensions, but when I click 'OK' I immediately get an exception
> message (this one from
> attempting to convert a stack using plugins/image5D/stack to image5D):
>
> java.lang.NoSuchMethodError:
> ij.process.ImageProcessor.getLutUpdateMode()I
> at i5d.Image5D.<init>(Image5D.java:231)
> at i5d.Image5D.<init>(Image5D.java:141)
> at i5d.Image5D.<init>(Image5D.java:122)
> at i5d.Image5D.<init>(Image5D.java:133)
> at Stack_to_Image5D.run(Stack_to_Image5D.java:124)
> at ij.IJ.runUserPlugIn(IJ.java:265)
> at ij.IJ.runPlugIn(IJ.java:120)
> at ij.Executer.runCommand(Executer.java:95)
> at ij.Executer.run(Executer.java:49)
> at java.lang.Thread.run(Thread.java:552)
>
> This doesn't seem to depend on the data type, since it occurs with
> both 8bit and RGB stacks
> (including the test stacks from the plugin page). Nor on  how I try to
> get the data into Image5D
> (open series as Image5D , RGB to Image5D etc. etc, depending on source
> files). All that changes in
> these cases is line 5 of the exception message to, for example "at
> Open_Series_As_Image5D.run(Open_Series_As_Image5D.java:32)".
>
> It looks a bit like the problem that David Knecht had back in January
> 2006...I don't know if this got
> solved.
>
> Other info as follows:
>
> I'm running MacOSX (10.3.8) on a powerbook with lots (!) of RAM
> ImageJ is latest version (1.38c), recently downloaded. (I didn't try
> Image5D on my previous
> version, 1.34, so I don't know if behaviour has changed)
> Java is
> java version "1.4.2_09"
> Java(TM) 2 Runtime Environment, Standard Edition (build 1.4.2_09-233)
> Java HotSpot(TM) Client VM (build 1.4.2-56, mixed mode)
>
> Thanks in advance for any help!
> Adam
>

[Adam Rodaway]

Thanks Wayne,
I feel proud to have hit the three day window when this was a problem!
cheers,
Adam
On 1 Dec 2006, at 18:20, Wayne Rasband wrote:

> This is a bug in ImageJ 1.38c that is fixed in 1.38d, available at
> <http://rsb.info.nih.gov/ij/notes.html>.
>
> -wayne
>
> On Dec 1, 2006, at 11:48 AM, Adam Rodaway wrote:
>
>> Hi all,
>>
>> Apologies in advance if this is a dumb question - I'm an imager, not
>> a programmer!
>>
>> I'm trying (for the first time) to open some timelapse stacks using
>> the Image5D plugin - I'd like to
>> analyse them using Erik Meijering's MTrackJ.
>>
>> Basically, I can't get the stacks to open with Image5D. I get as far
>> as the dialogue boxes to specify
>> dimensions, but when I click 'OK' I immediately get an exception
>> message (this one from
>> attempting to convert a stack using plugins/image5D/stack to image5D):
>>
>> java.lang.NoSuchMethodError:
>> ij.process.ImageProcessor.getLutUpdateMode()I
>> at i5d.Image5D.<init>(Image5D.java:231)
>> at i5d.Image5D.<init>(Image5D.java:141)
>> at i5d.Image5D.<init>(Image5D.java:122)
>> at i5d.Image5D.<init>(Image5D.java:133)
>> at Stack_to_Image5D.run(Stack_to_Image5D.java:124)
>> at ij.IJ.runUserPlugIn(IJ.java:265)
>> at ij.IJ.runPlugIn(IJ.java:120)
>> at ij.Executer.runCommand(Executer.java:95)
>> at ij.Executer.run(Executer.java:49)
>> at java.lang.Thread.run(Thread.java:552)
>>
>> This doesn't seem to depend on the data type, since it occurs with
>> both 8bit and RGB stacks
>> (including the test stacks from the plugin page). Nor on  how I try
>> to get the data into Image5D
>> (open series as Image5D , RGB to Image5D etc. etc, depending on
>> source files). All that changes in
>> these cases is line 5 of the exception message to, for example "at
>> Open_Series_As_Image5D.run(Open_Series_As_Image5D.java:32)".
>>
>> It looks a bit like the problem that David Knecht had back in January
>> 2006...I don't know if this got
>> solved.
>>
>> Other info as follows:
>>
>> I'm running MacOSX (10.3.8) on a powerbook with lots (!) of RAM
>> ImageJ is latest version (1.38c), recently downloaded. (I didn't try
>> Image5D on my previous
>> version, 1.34, so I don't know if behaviour has changed)
>> Java is
>> java version "1.4.2_09"
>> Java(TM) 2 Runtime Environment, Standard Edition (build 1.4.2_09-233)
>> Java HotSpot(TM) Client VM (build 1.4.2-56, mixed mode)
>>
>> Thanks in advance for any help!
>> Adam
>>
>
>

Dr Adam Rodaway
http://www.kcl.ac.uk/depsta/biomedical/randall/arodaway.html

King's College London
The Randall Centre
3rd Floor North
New Hunt's House
Guy's Campus
London SE1 1UL

tel. office [phone]
tel. lab. [phone]
fax [phone]
tel. mobile [phone]

[Catherine Degnin]

Can two 5-D image stacks be merged?  I have 2-color confocal images  
I'd like to merge and save as 'movies'

Catherine

On Dec 1, 2006, at 10:20 AM, Wayne Rasband wrote:

> This is a bug in ImageJ 1.38c that is fixed in 1.38d, available at  
> <http://rsb.info.nih.gov/ij/notes.html>.
>
> -wayne
>
> On Dec 1, 2006, at 11:48 AM, Adam Rodaway wrote:
>
>> Hi all,
>>
>> Apologies in advance if this is a dumb question - I'm an imager,  
>> not a programmer!
>>
>> I'm trying (for the first time) to open some timelapse stacks  
>> using the Image5D plugin - I'd like to
>> analyse them using Erik Meijering's MTrackJ.
>>
>> Basically, I can't get the stacks to open with Image5D. I get as  
>> far as the dialogue boxes to specify
>> dimensions, but when I click 'OK' I immediately get an exception  
>> message (this one from
>> attempting to convert a stack using plugins/image5D/stack to  
>> image5D):
>>
>> java.lang.NoSuchMethodError:  
>> ij.process.ImageProcessor.getLutUpdateMode()I
>> at i5d.Image5D.<init>(Image5D.java:231)
>> at i5d.Image5D.<init>(Image5D.java:141)
>> at i5d.Image5D.<init>(Image5D.java:122)
>> at i5d.Image5D.<init>(Image5D.java:133)
>> at Stack_to_Image5D.run(Stack_to_Image5D.java:124)
>> at ij.IJ.runUserPlugIn(IJ.java:265)
>> at ij.IJ.runPlugIn(IJ.java:120)
>> at ij.Executer.runCommand(Executer.java:95)
>> at ij.Executer.run(Executer.java:49)
>> at java.lang.Thread.run(Thread.java:552)
>>
>> This doesn't seem to depend on the data type, since it occurs with  
>> both 8bit and RGB stacks
>> (including the test stacks from the plugin page). Nor on  how I  
>> try to get the data into Image5D
>> (open series as Image5D , RGB to Image5D etc. etc, depending on  
>> source files). All that changes in
>> these cases is line 5 of the exception message to, for example "at
>> Open_Series_As_Image5D.run(Open_Series_As_Image5D.java:32)".
>>
>> It looks a bit like the problem that David Knecht had back in  
>> January 2006...I don't know if this got
>> solved.
>>
>> Other info as follows:
>>
>> I'm running MacOSX (10.3.8) on a powerbook with lots (!) of RAM
>> ImageJ is latest version (1.38c), recently downloaded. (I didn't  
>> try Image5D on my previous
>> version, 1.34, so I don't know if behaviour has changed)
>> Java is
>> java version "1.4.2_09"
>> Java(TM) 2 Runtime Environment, Standard Edition (build 1.4.2_09-233)
>> Java HotSpot(TM) Client VM (build 1.4.2-56, mixed mode)
>>
>> Thanks in advance for any help!
>> Adam
>>

[Joachim Walter]

Catherine,

currently there is no plugin to do that. As a workaround you can convert
the Image5Ds to Stacks (Image5D to Stack plugin), then merge them using
the Stack concatenater plugin and then use the "Stack to Image5D plugin"
to make an Image5D.

Joachim



Catherine Degnin schrieb:

> Can two 5-D image stacks be merged?  I have 2-color confocal images
> I'd like to merge and save as 'movies'
>
> Catherine
>
> On Dec 1, 2006, at 10:20 AM, Wayne Rasband wrote:
>
>> This is a bug in ImageJ 1.38c that is fixed in 1.38d, available at
>> <http://rsb.info.nih.gov/ij/notes.html>.
>>
>> -wayne
>>
>> On Dec 1, 2006, at 11:48 AM, Adam Rodaway wrote:
>>
>>> Hi all,
>>>
>>> Apologies in advance if this is a dumb question - I'm an imager, not
>>> a programmer!
>>>
>>> I'm trying (for the first time) to open some timelapse stacks using
>>> the Image5D plugin - I'd like to
>>> analyse them using Erik Meijering's MTrackJ.
>>>
>>> Basically, I can't get the stacks to open with Image5D. I get as far
>>> as the dialogue boxes to specify
>>> dimensions, but when I click 'OK' I immediately get an exception
>>> message (this one from
>>> attempting to convert a stack using plugins/image5D/stack to image5D):
>>>
>>> java.lang.NoSuchMethodError:
>>> ij.process.ImageProcessor.getLutUpdateMode()I
>>>     at i5d.Image5D.<init>(Image5D.java:231)
>>>     at i5d.Image5D.<init>(Image5D.java:141)
>>>     at i5d.Image5D.<init>(Image5D.java:122)
>>>     at i5d.Image5D.<init>(Image5D.java:133)
>>>     at Stack_to_Image5D.run(Stack_to_Image5D.java:124)
>>>     at ij.IJ.runUserPlugIn(IJ.java:265)
>>>     at ij.IJ.runPlugIn(IJ.java:120)
>>>     at ij.Executer.runCommand(Executer.java:95)
>>>     at ij.Executer.run(Executer.java:49)
>>>     at java.lang.Thread.run(Thread.java:552)
>>>
>>> This doesn't seem to depend on the data type, since it occurs with
>>> both 8bit and RGB stacks
>>> (including the test stacks from the plugin page). Nor on  how I try
>>> to get the data into Image5D
>>> (open series as Image5D , RGB to Image5D etc. etc, depending on
>>> source files). All that changes in
>>> these cases is line 5 of the exception message to, for example "at
>>> Open_Series_As_Image5D.run(Open_Series_As_Image5D.java:32)".
>>>
>>> It looks a bit like the problem that David Knecht had back in
>>> January 2006...I don't know if this got
>>> solved.
>>>
>>> Other info as follows:
>>>
>>> I'm running MacOSX (10.3.8) on a powerbook with lots (!) of RAM
>>> ImageJ is latest version (1.38c), recently downloaded. (I didn't try
>>> Image5D on my previous
>>> version, 1.34, so I don't know if behaviour has changed)
>>> Java is
>>> java version "1.4.2_09"
>>> Java(TM) 2 Runtime Environment, Standard Edition (build 1.4.2_09-233)
>>> Java HotSpot(TM) Client VM (build 1.4.2-56, mixed mode)
>>>
>>> Thanks in advance for any help!
>>> Adam
>>>

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