JAVA error messages

[Mark Adelman (Work)]

Can someone give me some guidance regarding JAVA error messages I am  
getting?  An example is included at the end of this message.  Am  
learning to do some wide-field image deconvolution work.  My platform  
is a MacBook (2.13 GHz Intel Core 2 Duo, 4 GB MHz DDR2 SDRAM, OS  
10.5.8).  It is up-to-date on all Mac software updates (including the  
JAVA that Mac provides).  I am running ImageJ 1.45d (under Micro-
Manager 1.3).  My knowledge of JAVA, programming, etc. is quite  
limited.  Have been using an old confocal microscopy (MRC600) data set  
as a test sample.  Have gotten some pretty nice results using the  
plugins by Bob Dougherty (in the Deconvolution folder) to generate a  
PSF and to do Iterative 3D deconvolutions, first of the confocal set  
and then of some actual wide field data sets.  I was also able to run  
a number of the plugins in the DeconvolutionLab folder.  When I tried  
Parallel Iterative Deconvolutions a number of one line JAVA error  
messages (about thrown threads, exceptions, etc....) showed up.  I  
moved on to Parallel Spectral Deconvolutions and, no matter what I  
tried, got long error messages (see example below) and the program  
locked.  Can someone suggest how to figure out what I'm doing wrong?  
Have looked at the Wiki page and done a number of Google searches, to  
no avail.  Am just starting to read on JAVA and other programming  
issues, but am a LONG way from being able to resolve this without some  
guidance from people more knowledgeable than me.  Thanks in advance  
for any help!

Mark Adelman

>
> java.lang.NoSuchMethodError:  
> cern.colt.matrix.tfloat.FloatMatrix3D.size()J
> at  
> edu
> .emory
> .mathcs
> .restoretools.spectral.FloatCommon3D.assignPixelsToMatrix(Unknown  
> Source)
> at  
> edu
> .emory
> .mathcs
> .restoretools
> .spectral.AbstractFloatSpectralDeconvolver3D.<init>(Unknown Source)
> at  
> edu
> .emory
> .mathcs
> .restoretools.spectral.tik.FloatReflexiveTikhonov3D.<init>(Unknown  
> Source)
> at  
> edu
> .emory.mathcs.restoretools.spectral.ParallelSpectralDeconvolution3D
> $MainPanel$DeconvolveButtonActionListener$1.run(Unknown Source)
> at java.lang.Thread.run(Thread.java:655)
>

[Piotr Wendykier-2]

Mark,

I'm the author of Parallel Spectral/Iterative Deconvolution plugins.
There is something wrong with the configuration of your Micro-Manager 1.3.
You can try to search for parallelcolt*.jar in the plugins directory.
There should be only one file that matches this pattern.

I hope this helps,

Piotr


On Mon, Apr 4, 2011 at 9:47 AM, Mark Adelman (Work)
<[hidden email]> wrote:

> Can someone give me some guidance regarding JAVA error messages I am
> getting?  An example is included at the end of this message.  Am learning to
> do some wide-field image deconvolution work.  My platform is a MacBook (2.13
> GHz Intel Core 2 Duo, 4 GB MHz DDR2 SDRAM, OS 10.5.8).  It is up-to-date on
> all Mac software updates (including the JAVA that Mac provides).  I am
> running ImageJ 1.45d (under Micro-Manager 1.3).  My knowledge of JAVA,
> programming, etc. is quite limited.  Have been using an old confocal
> microscopy (MRC600) data set as a test sample.  Have gotten some pretty nice
> results using the plugins by Bob Dougherty (in the Deconvolution folder) to
> generate a PSF and to do Iterative 3D deconvolutions, first of the confocal
> set and then of some actual wide field data sets.  I was also able to run a
> number of the plugins in the DeconvolutionLab folder.  When I tried Parallel
> Iterative Deconvolutions a number of one line JAVA error messages (about
> thrown threads, exceptions, etc....) showed up.  I moved on to Parallel
> Spectral Deconvolutions and, no matter what I tried, got long error messages
> (see example below) and the program locked.  Can someone suggest how to
> figure out what I'm doing wrong?  Have looked at the Wiki page and done a
> number of Google searches, to no avail.  Am just starting to read on JAVA
> and other programming issues, but am a LONG way from being able to resolve
> this without some guidance from people more knowledgeable than me.  Thanks
> in advance for any help!
>
> Mark Adelman
>
>>
>> java.lang.NoSuchMethodError: cern.colt.matrix.tfloat.FloatMatrix3D.size()J
>>        at
>> edu.emory.mathcs.restoretools.spectral.FloatCommon3D.assignPixelsToMatrix(Unknown
>> Source)
>>        at
>> edu.emory.mathcs.restoretools.spectral.AbstractFloatSpectralDeconvolver3D.<init>(Unknown
>> Source)
>>        at
>> edu.emory.mathcs.restoretools.spectral.tik.FloatReflexiveTikhonov3D.<init>(Unknown
>> Source)
>>        at
>> edu.emory.mathcs.restoretools.spectral.ParallelSpectralDeconvolution3D$MainPanel$DeconvolveButtonActionListener$1.run(Unknown
>> Source)
>>        at java.lang.Thread.run(Thread.java:655)
>>
>

[Mark Adelman (Work)]

Piotr -

There is no such file in the the main MM directory, nor in the  
mmplugins folder, nor in the plugins folder (this is the one with  
ImageJ plugins).  But the folder for ParallelSpectralDecovolution  
(within plugins) has "parallelcolt-0.9.jar" and the folder for  
ParallelIterativeDecovolution (within plugins) has  
"parallelcolt-0.7.2.jar".  Should I remove one (or both) of these?  
Move one (or both)?  If so, which should I move/remove?

Thanks!

Mark

>> From: Piotr Wendykier <[hidden email]>
>> Date: April 4, 2011 11:05:39 AM EDT
>> To: ImageJ Interest Group <[hidden email]>
>> Cc: "Mark Adelman (Work)" <[hidden email]>
>> Subject: Re: JAVA error messages
>>
>> Mark,
>>
>> I'm the author of Parallel Spectral/Iterative Deconvolution plugins.
>> There is something wrong with the configuration of your Micro-
>> Manager 1.3.
>> You can try to search for parallelcolt*.jar in the plugins directory.
>> There should be only one file that matches this pattern.
>>
>> I hope this helps,
>>
>> Piotr
>>
>>
>> On Mon, Apr 4, 2011 at 9:47 AM, Mark Adelman (Work)
>> <[hidden email]> wrote:
>>> Can someone give me some guidance regarding JAVA error messages I am
>>> getting?  An example is included at the end of this message.  Am  
>>> learning to
>>> do some wide-field image deconvolution work.  My platform is a  
>>> MacBook (2.13
>>> GHz Intel Core 2 Duo, 4 GB MHz DDR2 SDRAM, OS 10.5.8).  It is up-
>>> to-date on
>>> all Mac software updates (including the JAVA that Mac provides).  
>>> I am
>>> running ImageJ 1.45d (under Micro-Manager 1.3).  My knowledge of  
>>> JAVA,
>>> programming, etc. is quite limited.  Have been using an old confocal
>>> microscopy (MRC600) data set as a test sample.  Have gotten some  
>>> pretty nice
>>> results using the plugins by Bob Dougherty (in the Deconvolution  
>>> folder) to
>>> generate a PSF and to do Iterative 3D deconvolutions, first of the  
>>> confocal
>>> set and then of some actual wide field data sets.  I was also able  
>>> to run a
>>> number of the plugins in the DeconvolutionLab folder.  When I  
>>> tried Parallel
>>> Iterative Deconvolutions a number of one line JAVA error messages  
>>> (about
>>> thrown threads, exceptions, etc....) showed up.  I moved on to  
>>> Parallel
>>> Spectral Deconvolutions and, no matter what I tried, got long  
>>> error messages
>>> (see example below) and the program locked.  Can someone suggest  
>>> how to
>>> figure out what I'm doing wrong?  Have looked at the Wiki page and  
>>> done a
>>> number of Google searches, to no avail.  Am just starting to read  
>>> on JAVA
>>> and other programming issues, but am a LONG way from being able to  
>>> resolve
>>> this without some guidance from people more knowledgeable than  
>>> me.  Thanks
>>> in advance for any help!
>>>
>>> Mark Adelman
>>>
>>>>
>>>> java.lang.NoSuchMethodError:  
>>>> cern.colt.matrix.tfloat.FloatMatrix3D.size()J
>>>>        at
>>>> edu
>>>> .emory
>>>> .mathcs
>>>> .restoretools.spectral.FloatCommon3D.assignPixelsToMatrix(Unknown
>>>> Source)
>>>>        at
>>>> edu
>>>> .emory
>>>> .mathcs
>>>> .restoretools
>>>> .spectral.AbstractFloatSpectralDeconvolver3D.<init>(Unknown
>>>> Source)
>>>>        at
>>>> edu
>>>> .emory
>>>> .mathcs
>>>> .restoretools.spectral.tik.FloatReflexiveTikhonov3D.<init>(Unknown
>>>> Source)
>>>>        at
>>>> edu
>>>> .emory
>>>> .mathcs.restoretools.spectral.ParallelSpectralDeconvolution3D
>>>> $MainPanel$DeconvolveButtonActionListener$1.run(Unknown
>>>> Source)
>>>>        at java.lang.Thread.run(Thread.java:655)
>>>>
>>>
>

[Piotr Wendykier-2]

I would remove parallelcolt-0.9.jar from
ParallelSpectralDeconvolution, remove ParallelIterativeDeconvolution
directory and then install the latest version of
ParallelIterativeDeconvolution that comes with parallelcolt-0.9.jar.

Piotr

On Mon, Apr 4, 2011 at 12:11 PM, Mark Adelman (Work)
<[hidden email]> wrote:

> Piotr -
> There is no such file in the the main MM directory, nor in the mmplugins
> folder, nor in the plugins folder (this is the one with ImageJ plugins).
>  But the folder for ParallelSpectralDecovolution (within plugins) has
> "parallelcolt-0.9.jar" and the folder for ParallelIterativeDecovolution
> (within plugins) has "parallelcolt-0.7.2.jar".  Should I remove one (or
> both) of these?  Move one (or both)?  If so, which should I move/remove?
> Thanks!
> Mark
>
> From: Piotr Wendykier <[hidden email]>
> Date: April 4, 2011 11:05:39 AM EDT
> To: ImageJ Interest Group <[hidden email]>
> Cc: "Mark Adelman (Work)" <[hidden email]>
> Subject: Re: JAVA error messages
> Mark,
> I'm the author of Parallel Spectral/Iterative Deconvolution plugins.
> There is something wrong with the configuration of your Micro-Manager 1.3.
> You can try to search for parallelcolt*.jar in the plugins directory.
> There should be only one file that matches this pattern.
> I hope this helps,
> Piotr
>
> On Mon, Apr 4, 2011 at 9:47 AM, Mark Adelman (Work)
> <[hidden email]> wrote:
>
> Can someone give me some guidance regarding JAVA error messages I am
> getting?  An example is included at the end of this message.  Am learning to
> do some wide-field image deconvolution work.  My platform is a MacBook (2.13
> GHz Intel Core 2 Duo, 4 GB MHz DDR2 SDRAM, OS 10.5.8).  It is up-to-date on
> all Mac software updates (including the JAVA that Mac provides).  I am
> running ImageJ 1.45d (under Micro-Manager 1.3).  My knowledge of JAVA,
> programming, etc. is quite limited.  Have been using an old confocal
> microscopy (MRC600) data set as a test sample.  Have gotten some pretty nice
> results using the plugins by Bob Dougherty (in the Deconvolution folder) to
> generate a PSF and to do Iterative 3D deconvolutions, first of the confocal
> set and then of some actual wide field data sets.  I was also able to run a
> number of the plugins in the DeconvolutionLab folder.  When I tried Parallel
> Iterative Deconvolutions a number of one line JAVA error messages (about
> thrown threads, exceptions, etc....) showed up.  I moved on to Parallel
> Spectral Deconvolutions and, no matter what I tried, got long error messages
> (see example below) and the program locked.  Can someone suggest how to
> figure out what I'm doing wrong?  Have looked at the Wiki page and done a
> number of Google searches, to no avail.  Am just starting to read on JAVA
> and other programming issues, but am a LONG way from being able to resolve
> this without some guidance from people more knowledgeable than me.  Thanks
> in advance for any help!
> Mark Adelman
>
> java.lang.NoSuchMethodError: cern.colt.matrix.tfloat.FloatMatrix3D.size()J
>        at
> edu.emory.mathcs.restoretools.spectral.FloatCommon3D.assignPixelsToMatrix(Unknown
> Source)
>        at
> edu.emory.mathcs.restoretools.spectral.AbstractFloatSpectralDeconvolver3D.<init>(Unknown
> Source)
>        at
> edu.emory.mathcs.restoretools.spectral.tik.FloatReflexiveTikhonov3D.<init>(Unknown
> Source)
>        at
> edu.emory.mathcs.restoretools.spectral.ParallelSpectralDeconvolution3D$MainPanel$DeconvolveButtonActionListener$1.run(Unknown
> Source)
>        at java.lang.Thread.run(Thread.java:655)
>
>
>
>

[Mark Adelman (Work)]

That did it!  No error messages and all the algorithms ran.  I'll now  
be able to explore each in some detail with a variety of data sets.  
Thank you very much!

Mark

On Apr 4, 2011, at 1:47 PM, Piotr Wendykier wrote:

> I would remove parallelcolt-0.9.jar from
> ParallelSpectralDeconvolution, remove ParallelIterativeDeconvolution
> directory and then install the latest version of
> ParallelIterativeDeconvolution that comes with parallelcolt-0.9.jar.
>
> Piotr
>
> On Mon, Apr 4, 2011 at 12:11 PM, Mark Adelman (Work)
> <[hidden email]> wrote:
>> Piotr -
>> There is no such file in the the main MM directory, nor in the  
>> mmplugins
>> folder, nor in the plugins folder (this is the one with ImageJ  
>> plugins).
>>  But the folder for ParallelSpectralDecovolution (within plugins) has
>> "parallelcolt-0.9.jar" and the folder for  
>> ParallelIterativeDecovolution
>> (within plugins) has "parallelcolt-0.7.2.jar".  Should I remove  
>> one (or
>> both) of these?  Move one (or both)?  If so, which should I move/
>> remove?
>> Thanks!
>> Mark
>>
>> From: Piotr Wendykier <[hidden email]>
>> Date: April 4, 2011 11:05:39 AM EDT
>> To: ImageJ Interest Group <[hidden email]>
>> Cc: "Mark Adelman (Work)" <[hidden email]>
>> Subject: Re: JAVA error messages
>> Mark,
>> I'm the author of Parallel Spectral/Iterative Deconvolution plugins.
>> There is something wrong with the configuration of your Micro-
>> Manager 1.3.
>> You can try to search for parallelcolt*.jar in the plugins directory.
>> There should be only one file that matches this pattern.
>> I hope this helps,
>> Piotr
>>
>> On Mon, Apr 4, 2011 at 9:47 AM, Mark Adelman (Work)
>> <[hidden email]> wrote:
>>
>> Can someone give me some guidance regarding JAVA error messages I am
>> getting?  An example is included at the end of this message.  Am  
>> learning to
>> do some wide-field image deconvolution work.  My platform is a  
>> MacBook (2.13
>> GHz Intel Core 2 Duo, 4 GB MHz DDR2 SDRAM, OS 10.5.8).  It is up-
>> to-date on
>> all Mac software updates (including the JAVA that Mac provides).  
>> I am
>> running ImageJ 1.45d (under Micro-Manager 1.3).  My knowledge of  
>> JAVA,
>> programming, etc. is quite limited.  Have been using an old confocal
>> microscopy (MRC600) data set as a test sample.  Have gotten some  
>> pretty nice
>> results using the plugins by Bob Dougherty (in the Deconvolution  
>> folder) to
>> generate a PSF and to do Iterative 3D deconvolutions, first of the  
>> confocal
>> set and then of some actual wide field data sets.  I was also able  
>> to run a
>> number of the plugins in the DeconvolutionLab folder.  When I  
>> tried Parallel
>> Iterative Deconvolutions a number of one line JAVA error messages  
>> (about
>> thrown threads, exceptions, etc....) showed up.  I moved on to  
>> Parallel
>> Spectral Deconvolutions and, no matter what I tried, got long  
>> error messages
>> (see example below) and the program locked.  Can someone suggest  
>> how to
>> figure out what I'm doing wrong?  Have looked at the Wiki page and  
>> done a
>> number of Google searches, to no avail.  Am just starting to read  
>> on JAVA
>> and other programming issues, but am a LONG way from being able to  
>> resolve
>> this without some guidance from people more knowledgeable than  
>> me.  Thanks
>> in advance for any help!
>> Mark Adelman
>>
>> java.lang.NoSuchMethodError:  
>> cern.colt.matrix.tfloat.FloatMatrix3D.size()J
>>        at
>> edu.emory.mathcs.restoretools.spectral.FloatCommon3D.assignPixelsToMa
>> trix(Unknown
>> Source)
>>        at
>> edu.emory.mathcs.restoretools.spectral.AbstractFloatSpectralDeconvolv
>> er3D.<init>(Unknown
>> Source)
>>        at
>> edu.emory.mathcs.restoretools.spectral.tik.FloatReflexiveTikhonov3D.<
>> init>(Unknown
>> Source)
>>        at
>> edu.emory.mathcs.restoretools.spectral.ParallelSpectralDeconvolution3
>> D$MainPanel$DeconvolveButtonActionListener$1.run(Unknown
>> Source)
>>        at java.lang.Thread.run(Thread.java:655)
>>
>>
>>
>>

[Mark Adelman (Work)]

I am trying to expand the range of deconvolution tools available to me  
(ideally under ImageJ) for use with wide field fluorescence microscopy  
Z-series.  It has been suggested to me that I try to compile Clarity (http://cismm.cs.unc.edu/resources/software-manuals/clarity-deconvolution-library/ 
) for use on my MacBook.  Am a total rookie when it comes to  
programming, compiling source code, etc.  Have tried to follow the  
instructions for compiling Clarity using CMake, but I keep getting  
hung up with error messages, etc.  Has anyone compiled Clarity for use  
on the Mac?  Could someone point me to some instructions that will be  
intelligible to a beginner like me?  I've done a lot of web browsing  
but none of the pages I've found seem to be pitched 'low enough' for  
me.  Thanks in advance for any help.

Mark Adelman

[ctrueden]

Hi Mark,

It looks like there are some issues with the Clarity CMake configuration on
Mac OS X.

I gave it a try and got pretty far, but ultimately couldn't get it to build,
either. Best would be to write to the authors of Clarity for further
assistance.

For what it's worth, here is what I did:

1) Compiling Clarity requires the fftw v3 library, which you can install
using MacPorts:
  * Install MacPorts from http://www.macports.org/
  * From Terminal, execute: sudo port install fftw-3

2) After downloading and unpacking the source archive, go to Terminal and
run:
  * cd Clarity-1.0
  * mkdir build
  * cd build
  * ccmake ..

3) On the CMake configuration screen, press C to configure. It should
automatically locate your fftw installation as:
  * FFTW_INCLUDE_DIR   /opt/local/include
  * FFTW_LIBRARY   /opt/local/lib/libfftw3.dylib

If CMake didn't find it, make sure you followed step #1 above correctly.

4) Because Mac OS X builds with gcc, you'll need to follow step 9 of the
Clarity build directions:
  * Press T to toggle advanced mode
  * Navigate down to CMAKE_EXE_LINKER_FLAGS
  * Press Enter to edit the field
  * Type: -lpthread -lgomp

5) Press C to configure again. Then press G to generate the Makefile. Press
E to ignore the warning (it's a notification to the Clarity developers that
their CMakeLists.txt file is not 100% correct).

6) Before you can build, you have to edit one of the source files to correct
a problem:
  * nano ../src/ImagePadSpatialShift.cxx

In the editor, change "#include <malloc.h>" to "#include <malloc/malloc.h>"
Save and quit with Ctrl+O, Enter, Ctrl+X

7) Now you can try building:
  * make

My build gets to 77%, then has a linker error attempting to link
libClarity.dylib to fftw3. My advice, as I said above, is to write an email
to the Clarity developers and see if they can be of further assistance.

-Curtis

On Mon, May 2, 2011 at 12:22 PM, Mark Adelman (Work) <
[hidden email]> wrote:

> I am trying to expand the range of deconvolution tools available to me
> (ideally under ImageJ) for use with wide field fluorescence microscopy
> Z-series.  It has been suggested to me that I try to compile Clarity (
> http://cismm.cs.unc.edu/resources/software-manuals/clarity-deconvolution-library/)
> for use on my MacBook.  Am a total rookie when it comes to programming,
> compiling source code, etc.  Have tried to follow the instructions for
> compiling Clarity using CMake, but I keep getting hung up with error
> messages, etc.  Has anyone compiled Clarity for use on the Mac?  Could
> someone point me to some instructions that will be intelligible to a
> beginner like me?  I've done a lot of web browsing but none of the pages
> I've found seem to be pitched 'low enough' for me.  Thanks in advance for
> any help.
>
> Mark Adelman
>

[Daniel James White]

Hi Mark,

On May 3, 2011, at 6:00 AM, IMAGEJ automatic digest system wrote:

>
> Date:    Mon, 2 May 2011 13:22:05 -0400
> From:    "Mark Adelman (Work)" <[hidden email]>
> Subject: Compiling Clarity for a Mac
>
> I am trying to expand the range of deconvolution tools available to me  
> (ideally under ImageJ) for use with wide field fluorescence microscopy  
> Z-series.  It has been suggested to me that I try to compile Clarity (http://cismm.cs.unc.edu/resources/software-manuals/clarity-deconvolution-library/ 
> ) for use on my MacBook.  

No need to build it I think, and even if you did, I don tthink it has aGUI, so you would not really be able to use it.

Instead, get Image Surfer
http://imagesurfer.cs.unc.edu/
which clarity is incorporated into

but its windows only as far as i can see...


> Am a total rookie when it comes to  
> programming, compiling source code, etc.  Have tried to follow the  
> instructions for compiling Clarity using CMake, but I keep getting  
> hung up with error messages, etc.  Has anyone compiled Clarity for use  
> on the Mac?

you would need to write your own GUI for it.

>  Could someone point me to some instructions that will be  
> intelligible to a beginner like me?  I've done a lot of web browsing  
> but none of the pages I've found seem to be pitched 'low enough' for  
> me.  Thanks in advance for any help.

I think you are probably not on a track that will pay off here.

DeconvolutionLab imageJ plugin from BIG at epfl in Laussanne should do everything that you need.

cheers

Dan

>
> Mark Adelman

Dr. Daniel James White BSc. (Hons.) PhD
Senior Microscopist / Image Visualisation, Processing and Analysis
Light Microscopy and Image Processing Facilities
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 DRESDEN
Germany

[phone] (German Mobile)
[phone] (Work phone at MPI-CBG)
[phone] (Fax MPI-CBG LMF)

http://www.bioimagexd.net  BioImageXD
http://pacific.mpi-cbg.de                Fiji -  is just ImageJ (Batteries Included)
http://www.chalkie.org.uk                Dan's Homepages
https://ifn.mpi-cbg.de  Dresden Imaging Facility Network
dan (at) chalkie.org.uk
( white (at) mpi-cbg.de )

[Daniel James White]

Hi Mark

I played a bit with image surfer... but not much,

if you manage to build clarity on osx, thats great.

but then i dont know how you will use it.... unless the imageJ plugin johannes mentioned does exist:

http://micro-manager.3463995.n2.nabble.com/Re-3D-deconvolution-plugins-Clarity-td6232579.html

the problem is that its using JNI for platform dependent interface between java and the calrity library.
the supplied plugin is already compiled... but maybe for windows...?  so that would also need to be re compiled for mac osx,
and that might be tricky if it was not set up for that already....

you might need to talk directly to the author of that plugin (possible ccd here)
Chris Nicolai at buffalo
[hidden email]

and ask if its going to work without changing the source code.


is there something that DeconvolutionLab plugin can not do that you need?

D



On May 3, 2011, at 1:33 PM, Mark Adelman (Work) wrote:

> Thanks Dan.  I'll check on it.  BTW:  Did you forward my post (on ImageJ listserv) to him, or are you also interested in Clarity?  If the latter, let me know and I'll summarize my quest for you.  Mark
> On May 3, 2011, at 4:58 AM, Daniel James White wrote:
>
>> FYI....
>>
>> D
>>
>>
>>
>> Begin forwarded message:
>>
>>> From: Johannes Schindelin <[hidden email]>
>>> Date: May 3, 2011 10:00:54 AM GMT+02:00
>>> To: Daniel James White <[hidden email]>
>>> Subject: Re: Compiling Clarity for a Mac
>>>
>>> Hi Dan,
>>>
>>> I heard that there is an ImageJ plugin using Clarity, although I cannot
>>> find it ATM. I _think_ I read about it on the Micro-Manager mailing list,
>>> you might find it there.
>>>
>>> Gotta run,
>>> Dscho
>>>
>>>
>>
>> Dr. Daniel James White BSc. (Hons.) PhD
>> Senior Microscopist / Image Visualisation, Processing and Analysis
>> Light Microscopy and Image Processing Facilities
>> Max Planck Institute of Molecular Cell Biology and Genetics
>> Pfotenhauerstrasse 108
>> 01307 DRESDEN
>> Germany
>>
>> [phone] (German Mobile)
>> [phone] (Work phone at MPI-CBG)
>> [phone] (Fax MPI-CBG LMF)
>>
>> http://www.bioimagexd.net  BioImageXD
>> http://pacific.mpi-cbg.de                Fiji -  is just ImageJ (Batteries Included)
>> http://www.chalkie.org.uk                Dan's Homepages
>> https://ifn.mpi-cbg.de  Dresden Imaging Facility Network
>> dan (at) chalkie.org.uk
>> ( white (at) mpi-cbg.de )
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>

Dr. Daniel James White BSc. (Hons.) PhD
Senior Microscopist / Image Visualisation, Processing and Analysis
Light Microscopy and Image Processing Facilities
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 DRESDEN
Germany

[phone] (German Mobile)
[phone] (Work phone at MPI-CBG)
[phone] (Fax MPI-CBG LMF)

http://www.bioimagexd.net  BioImageXD
http://pacific.mpi-cbg.de                Fiji -  is just ImageJ (Batteries Included)
http://www.chalkie.org.uk                Dan's Homepages
https://ifn.mpi-cbg.de  Dresden Imaging Facility Network
dan (at) chalkie.org.uk
( white (at) mpi-cbg.de )