Re: IMAGEJ Digest - 14 Feb 2009 to 15 Feb 2009 (#2009-45)

[Jeff Hardin]

Hi Dave,

Works for me, using either the built-in File menu command or my QT  
Stack Writer plugin, under QT 7.6, QTJ 7.6, ImageJ 1.42h, which seems  
to be what you've got. I'm running on an Intel Mac.

Did you use a non-standard codec for compression?

Cheers,

Jeff
----------------------------------------------
Jeff Hardin
Professor and Chair, Department of Zoology
Director, Biology Core Curriculum
University of Wisconsin
1117 W. Johnson St.
Madison, WI 53706
voice: [phone]
fax: [phone]
email: [hidden email]



On Feb 15, 2009, at 11:00 PM, IMAGEJ automatic digest system wrote:

> From:    David Knecht ATT <[hidden email]>
> Subject: Quicktime error
>
> I have once again lost the ability to save stacks as movies from
> ImageJ.  I am running version 1.42h with OSX (latest).  Here is the
> error I get:
>
> quicktime.std.StdQTException[QTJava:7.6.0g],-47=fBsyErr,QT.vers:
> 7608000
> at quicktime.std.StdQTException.checkError(StdQTException.java:38)
> at quicktime.std.movies.Movie.createMovieFile(Movie.java:115)
> at QuickTime_Writer.writeMovie(QuickTime_Writer.java:117)
> at QuickTime_Writer.run(QuickTime_Writer.java:94)
> at ij.IJ.runUserPlugIn(IJ.java:176)
> at ij.IJ.runPlugIn(IJ.java:142)
> at ij.Executer.runCommand(Executer.java:119)
> at ij.Executer.run(Executer.java:58)
> at java.lang.Thread.run(Thread.java:613)
>
> Anyone know what is wrong?  Thanks- Dave

[Knecht, David]

I have tried several of the built in codecs with the same result.  
Also, in answer to Wayne's query, I am not running 64bit.  This  
problem has come and gone over time and versions.  Are there any old  
plugins or .jar files that could interfere with it working?  Dave

On Feb 17, 2009, at 9:51 AM, Jeff Hardin wrote:

> Hi Dave,
>
> Works for me, using either the built-in File menu command or my QT  
> Stack Writer plugin, under QT 7.6, QTJ 7.6, ImageJ 1.42h, which  
> seems to be what you've got. I'm running on an Intel Mac.
>
> Did you use a non-standard codec for compression?
>
> Cheers,
>
> Jeff
> ----------------------------------------------
> Jeff Hardin
> Professor and Chair, Department of Zoology
> Director, Biology Core Curriculum
> University of Wisconsin
> 1117 W. Johnson St.
> Madison, WI 53706
> voice: [phone]
> fax: [phone]
> email: [hidden email]
>
>
>
> On Feb 15, 2009, at 11:00 PM, IMAGEJ automatic digest system wrote:
>
>> From:    David Knecht ATT <[hidden email]>
>> Subject: Quicktime error
>>
>> I have once again lost the ability to save stacks as movies from
>> ImageJ.  I am running version 1.42h with OSX (latest).  Here is the
>> error I get:
>>
>> quicktime.std.StdQTException[QTJava:7.6.0g],-47=fBsyErr,QT.vers:
>> 7608000
>> at quicktime.std.StdQTException.checkError(StdQTException.java:38)
>> at quicktime.std.movies.Movie.createMovieFile(Movie.java:115)
>> at QuickTime_Writer.writeMovie(QuickTime_Writer.java:117)
>> at QuickTime_Writer.run(QuickTime_Writer.java:94)
>> at ij.IJ.runUserPlugIn(IJ.java:176)
>> at ij.IJ.runPlugIn(IJ.java:142)
>> at ij.Executer.runCommand(Executer.java:119)
>> at ij.Executer.run(Executer.java:58)
>> at java.lang.Thread.run(Thread.java:613)
>>
>> Anyone know what is wrong?  Thanks- Dave

Dr. David Knecht
Department of Molecular and Cell Biology
Co-head Flow Cytometry and Confocal Microscopy Facility
U-3125
91 N. Eagleville Rd.
University of Connecticut
Storrs, CT 06269
860-486-2200
860-486-4331 (fax)

[dpoburko]

Hi all,
 
  I'm not really sure who to address this to, but I need to lament the
replacement of Stacks>Remove Slices with Stacks>Reduce Size in the
upcoming release of IJ 1.42i. I'm hoping someone will hear my plea to
bring Remove Slices back. or at least add the ability to chose a first
and last slice in Reduce Size. It seems like the new tool losses
functionality without really offering much more functionality than the
previous Reduce Size. Hopefully I'm not the only one out there who used
Remove Slices frequently.

Best Regards,
Damon

Damon Poburko, PhD
Postdoctoral Research Fellow
Stanford University School of Medicine
Dept. of Molecular & Cellular Physiology
279 Campus Dr., Beckman B103, Stanford, CA 94305
Ph: 650 725 7564, fax: [phone]

[ctrueden]

Hi Dave,

How do the Bio-Formats Importer and Exporter plugins work with your
Quicktime data?

-Curtis

On Tue, Feb 17, 2009 at 9:31 AM, David Knecht <[hidden email]>wrote:

> I have tried several of the built in codecs with the same result.  Also, in
> answer to Wayne's query, I am not running 64bit.  This problem has come and
> gone over time and versions.  Are there any old plugins or .jar files that
> could interfere with it working?  Dave
>
> On Feb 17, 2009, at 9:51 AM, Jeff Hardin wrote:
>
>  Hi Dave,
>>
>> Works for me, using either the built-in File menu command or my QT Stack
>> Writer plugin, under QT 7.6, QTJ 7.6, ImageJ 1.42h, which seems to be what
>> you've got. I'm running on an Intel Mac.
>>
>> Did you use a non-standard codec for compression?
>>
>> Cheers,
>>
>> Jeff
>> ----------------------------------------------
>> Jeff Hardin
>> Professor and Chair, Department of Zoology
>> Director, Biology Core Curriculum
>> University of Wisconsin
>> 1117 W. Johnson St.
>> Madison, WI 53706
>> voice: [phone]
>> fax: [phone]
>> email: [hidden email]
>>
>>
>>
>> On Feb 15, 2009, at 11:00 PM, IMAGEJ automatic digest system wrote:
>>
>>  From:    David Knecht ATT <[hidden email]>
>>> Subject: Quicktime error
>>>
>>> I have once again lost the ability to save stacks as movies from
>>> ImageJ.  I am running version 1.42h with OSX (latest).  Here is the
>>> error I get:
>>>
>>> quicktime.std.StdQTException[QTJava:7.6.0g],-47=fBsyErr,QT.vers:7608000
>>>        at quicktime.std.StdQTException.checkError(StdQTException.java:38)
>>>        at quicktime.std.movies.Movie.createMovieFile(Movie.java:115)
>>>        at QuickTime_Writer.writeMovie(QuickTime_Writer.java:117)
>>>        at QuickTime_Writer.run(QuickTime_Writer.java:94)
>>>        at ij.IJ.runUserPlugIn(IJ.java:176)
>>>        at ij.IJ.runPlugIn(IJ.java:142)
>>>        at ij.Executer.runCommand(Executer.java:119)
>>>        at ij.Executer.run(Executer.java:58)
>>>        at java.lang.Thread.run(Thread.java:613)
>>>
>>> Anyone know what is wrong?  Thanks- Dave
>>>
>>
> Dr. David Knecht
> Department of Molecular and Cell Biology
> Co-head Flow Cytometry and Confocal Microscopy Facility
> U-3125
> 91 N. Eagleville Rd.
> University of Connecticut
> Storrs, CT 06269
> 860-486-2200
> 860-486-4331 (fax)
>

[Glen MacDonald-2]

Hello,
A colleague is recording the swimming motions of zebrafish larvae in  
response to water flow, using  a macro lens on a CCD camera.  We need  
to determine the angle of orientation relative to the x-axis. The  
larvae are thresholded in a timelapse stack and Analyze Particles  
provides the information, with parameters set for exclude edges,  
minimum size and circularity below .26 (the larvae resemble small  
nails at this magnification with a tapered body and a bulge at the  
head).

Analyze Particles correctly identifies about 25 larvae in each frame  
of the timelapse.  But, 3-5 larvae are not measured in each frame.  
The display of the best fit ellipses and numbering the thresholded  
larvae by result line identifies the missed larvae.  Individual  
measurement of the missed larvae indicates they meet all criteria for  
particle analysis.  In some instances, a larva may not have changed  
position for several frames, yet will have been measured in some  
frames, but not in others.


Thanks,
Glen



Glen MacDonald
Core for Communication Research
Virginia Merrill Bloedel Hearing Research Center
Box 357923
University of Washington
Seattle, WA 98195-7923  USA
[phone]
[hidden email]

******************************************************************************
The box said "Requires WindowsXP or better", so I bought a Macintosh.
******************************************************************************

[Gabriel Landini]

On Wednesday 18 February 2009, Glen MacDonald wrote:
> Analyze Particles correctly identifies about 25 larvae in each frame
> of the timelapse.
> But, 3-5 larvae are not measured in each frame.

Unless you post pictures with examples and code, knowing what is going on will
be just guesswork.

> The display of the best fit ellipses and numbering the thresholded
> larvae by result line identifies the missed larvae.  Individual
> measurement of the missed larvae indicates they meet all criteria for
> particle analysis.  In some instances, a larva may not have changed
> position for several frames, yet will have been measured in some
> frames, but not in others.

There is a tendency to using only the built in threshold for object
segmentation. While it works for many instances, it is by no means the optimal
nor the most appropriate method for all possible cases. Perhaps you colleague
should try other segmentation algorithms.

G.

[Knecht, David]

Thanks for the help.  I was doing another set of data today, and the  
quicktime save is working fine.  I have not changed anything I know  
of, so I have no idea what is different, but will update you if it  
stops again.  Perhaps a restart somewhere along the line cleaned  
things up?  Dave

On Feb 17, 2009, at 4:02 PM, Curtis Rueden wrote:

> Hi Dave,
>
> How do the Bio-Formats Importer and Exporter plugins work with your
> Quicktime data?
>
> -Curtis
>
> On Tue, Feb 17, 2009 at 9:31 AM, David Knecht  
> <[hidden email]>wrote:
>
>> I have tried several of the built in codecs with the same result.  
>> Also, in
>> answer to Wayne's query, I am not running 64bit.  This problem has  
>> come and
>> gone over time and versions.  Are there any old plugins or .jar  
>> files that
>> could interfere with it working?  Dave
>>
>> On Feb 17, 2009, at 9:51 AM, Jeff Hardin wrote:
>>
>> Hi Dave,
>>>
>>> Works for me, using either the built-in File menu command or my QT  
>>> Stack
>>> Writer plugin, under QT 7.6, QTJ 7.6, ImageJ 1.42h, which seems to  
>>> be what
>>> you've got. I'm running on an Intel Mac.
>>>
>>> Did you use a non-standard codec for compression?
>>>
>>> Cheers,
>>>
>>> Jeff
>>> ----------------------------------------------
>>> Jeff Hardin
>>> Professor and Chair, Department of Zoology
>>> Director, Biology Core Curriculum
>>> University of Wisconsin
>>> 1117 W. Johnson St.
>>> Madison, WI 53706
>>> voice: [phone]
>>> fax: [phone]
>>> email: [hidden email]
>>>
>>>
>>>
>>> On Feb 15, 2009, at 11:00 PM, IMAGEJ automatic digest system wrote:
>>>
>>> From:    David Knecht ATT <[hidden email]>
>>>> Subject: Quicktime error
>>>>
>>>> I have once again lost the ability to save stacks as movies from
>>>> ImageJ.  I am running version 1.42h with OSX (latest).  Here is the
>>>> error I get:
>>>>
>>>> quicktime.std.StdQTException[QTJava:7.6.0g],-47=fBsyErr,QT.vers:
>>>> 7608000
>>>>       at  
>>>> quicktime.std.StdQTException.checkError(StdQTException.java:38)
>>>>       at quicktime.std.movies.Movie.createMovieFile(Movie.java:115)
>>>>       at QuickTime_Writer.writeMovie(QuickTime_Writer.java:117)
>>>>       at QuickTime_Writer.run(QuickTime_Writer.java:94)
>>>>       at ij.IJ.runUserPlugIn(IJ.java:176)
>>>>       at ij.IJ.runPlugIn(IJ.java:142)
>>>>       at ij.Executer.runCommand(Executer.java:119)
>>>>       at ij.Executer.run(Executer.java:58)
>>>>       at java.lang.Thread.run(Thread.java:613)
>>>>
>>>> Anyone know what is wrong?  Thanks- Dave
>>>>
>>>
>> Dr. David Knecht
>> Department of Molecular and Cell Biology
>> Co-head Flow Cytometry and Confocal Microscopy Facility
>> U-3125
>> 91 N. Eagleville Rd.
>> University of Connecticut
>> Storrs, CT 06269
>> 860-486-2200
>> 860-486-4331 (fax)
>>

Dr. David Knecht
Department of Molecular and Cell Biology
Co-head Flow Cytometry and Confocal Microscopy Facility
U-3125
91 N. Eagleville Rd.
University of Connecticut
Storrs, CT 06269
860-486-2200
860-486-4331 (fax)

[ctrueden]

Hi Dave,

Hi Curtis- Not sure what you mean. The files are tif and I am trying export
> as .mov.  I didn't think you could do anything like that with LOCI.  Dave
>

There is a Bio-Formats Exporter plugin that allows you to save your TIFF
files as QuickTime movies. Just name the file with a ".mov" extension, and
it will prompt you for which codec to use.

Bio-Formats includes its own "native" QuickTime writer, and also a QT writer
that uses QuickTime for Java (which is what the normal ImageJ stuff uses).
You can control which one is used in the LOCI Plugins Configuration dialog
-- choose "QuickTime" from the list on the Formats tab, and check the
"Legacy" box to use QTJava instead of native or vice versa. If one mode
doesn't work, try the other mode, and let us know how it goes.

HTH,
Curtis

On Tue, Feb 17, 2009 at 5:30 PM, David Knecht <[hidden email]>wrote:

> Hi Curtis- Not sure what you mean. The files are tif and I am trying export
> as .mov.  I didn't think you could do anything like that with LOCI.  Dave
>
> On Feb 17, 2009, at 4:02 PM, Curtis Rueden wrote:
>
> Hi Dave,
>
> How do the Bio-Formats Importer and Exporter plugins work with your
> Quicktime data?
>
> -Curtis
>
> On Tue, Feb 17, 2009 at 9:31 AM, David Knecht <[hidden email]
> >wrote:
>
> I have tried several of the built in codecs with the same result.  Also, in
>
> answer to Wayne's query, I am not running 64bit.  This problem has come and
>
> gone over time and versions.  Are there any old plugins or .jar files that
>
> could interfere with it working?  Dave
>
>
> On Feb 17, 2009, at 9:51 AM, Jeff Hardin wrote:
>
>
> Hi Dave,
>
>
> Works for me, using either the built-in File menu command or my QT Stack
>
> Writer plugin, under QT 7.6, QTJ 7.6, ImageJ 1.42h, which seems to be what
>
> you've got. I'm running on an Intel Mac.
>
>
> Did you use a non-standard codec for compression?
>
>
> Cheers,
>
>
> Jeff
>
> ----------------------------------------------
>
> Jeff Hardin
>
> Professor and Chair, Department of Zoology
>
> Director, Biology Core Curriculum
>
> University of Wisconsin
>
> 1117 W. Johnson St.
>
> Madison, WI 53706
>
> voice: [phone]
>
> fax: [phone]
>
> email: [hidden email]
>
>
>
>
> On Feb 15, 2009, at 11:00 PM, IMAGEJ automatic digest system wrote:
>
>
> From:    David Knecht ATT <[hidden email]>
>
> Subject: Quicktime error
>
>
> I have once again lost the ability to save stacks as movies from
>
> ImageJ.  I am running version 1.42h with OSX (latest).  Here is the
>
> error I get:
>
>
> quicktime.std.StdQTException[QTJava:7.6.0g],-47=fBsyErr,QT.vers:7608000
>
>       at quicktime.std.StdQTException.checkError(StdQTException.java:38)
>
>       at quicktime.std.movies.Movie.createMovieFile(Movie.java:115)
>
>       at QuickTime_Writer.writeMovie(QuickTime_Writer.java:117)
>
>       at QuickTime_Writer.run(QuickTime_Writer.java:94)
>
>       at ij.IJ.runUserPlugIn(IJ.java:176)
>
>       at ij.IJ.runPlugIn(IJ.java:142)
>
>       at ij.Executer.runCommand(Executer.java:119)
>
>       at ij.Executer.run(Executer.java:58)
>
>       at java.lang.Thread.run(Thread.java:613)
>
>
> Anyone know what is wrong?  Thanks- Dave
>
>
>
> Dr. David Knecht
>
> Department of Molecular and Cell Biology
>
> Co-head Flow Cytometry and Confocal Microscopy Facility
>
> U-3125
>
> 91 N. Eagleville Rd.
>
> University of Connecticut
>
> Storrs, CT 06269
>
> 860-486-2200
>
> 860-486-4331 (fax)
>
>
>
> Dr. David Knecht
> Department of Molecular and Cell Biology
> Co-head Flow Cytometry and Confocal Microscopy Facility
> U-3125
> 91 N. Eagleville Rd.
> University of Connecticut
> Storrs, CT 06269
> 860-486-2200
> 860-486-4331 (fax)
>
>
>

[Glen MacDonald-2]

Gabriel,
thresholding was not the issue. The fish were thresholded, but some  
were not selected by the particle analyzer.
Wayne looked at the stack and macro, and found that increasing the  
circularity setting from .2 to .6 resulted in all being selected.  
This also selected intersecting profiles of 2 or more, which is why I  
was using a stringent value.
However, measurements of individual fish that had been missed did not  
demonstrate circularity or area as the problems, and analysis on  
single planes from the stack did not miss any fish.
today, I repeated the particle analysis with same parameters for  
thresholding and particle analysis.   it all works with no missed  
objects.
In the end, we are checking our macro set for errant variables.

Regards,
Glen


On Feb 18, 2009, at 12:56 AM, Gabriel Landini wrote:

> On Wednesday 18 February 2009, Glen MacDonald wrote:
>> Analyze Particles correctly identifies about 25 larvae in each frame
>> of the timelapse.
>> But, 3-5 larvae are not measured in each frame.
>
> Unless you post pictures with examples and code, knowing what is  
> going on will
> be just guesswork.
>
>> The display of the best fit ellipses and numbering the thresholded
>> larvae by result line identifies the missed larvae.  Individual
>> measurement of the missed larvae indicates they meet all criteria for
>> particle analysis.  In some instances, a larva may not have changed
>> position for several frames, yet will have been measured in some
>> frames, but not in others.
>
> There is a tendency to using only the built in threshold for object
> segmentation. While it works for many instances, it is by no means  
> the optimal
> nor the most appropriate method for all possible cases. Perhaps you  
> colleague
> should try other segmentation algorithms.
>
> G.