SPIM multi view deconvolution via GPU

[Douglas Richardson]

Hello all,


Sorry to bother everyone as I know you're busy with ImageJ 2.0 questions,
but here's a hopefully small issue I've been having:



I recently just installed a processing station with an NVIDIA Titan Black
GPU. I'm trying to run the "SPIM multi-view deconvolution" algorithm on the
it but am having some problems.

Whenever I try to run deconvolution on the GPU I receive the following
error:



ChannelPattern:

Channels: (0)

ChannelsToRegister:

ChannelsRegister: (0)

ChannelsToFuse:

ChannelsFuse: (0)

Z-stretching = 4.824561403508772

channel 0 takes it from channel 0

Cannot find CUDA JNA library: java.lang.UnsatisfiedLinkError: Unable to
load library 'Convolution3D_fftCUDAlib': The specified module could not be
found.



I’ve downloaded the CUDA_code_conv3d files from the Nature Methods website
and placed all of the files from the ‘precompiled’ folder into the
‘Fiji.app’ folder or the ‘Fiji.app\plugins’ but I get the same error no
matter which location the files are in.



Any ideas as to what I’m doing wrong?  I'm still running v1.49b on a
Windows 7 64bit machine.



Thanks for the help!



-Doug

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Stephan Preibisch]

Hi Doug,

which version of CUDA do you have installed on your machine?

Cheers,
Stephan

On Jun 9, 2014, at 11:30 , Douglas Richardson <[hidden email]> wrote:

> Hello all,
>
>
> Sorry to bother everyone as I know you're busy with ImageJ 2.0 questions,
> but here's a hopefully small issue I've been having:
>
>
>
> I recently just installed a processing station with an NVIDIA Titan Black
> GPU. I'm trying to run the "SPIM multi-view deconvolution" algorithm on the
> it but am having some problems.
>
> Whenever I try to run deconvolution on the GPU I receive the following
> error:
>
>
>
> ChannelPattern:
>
> Channels: (0)
>
> ChannelsToRegister:
>
> ChannelsRegister: (0)
>
> ChannelsToFuse:
>
> ChannelsFuse: (0)
>
> Z-stretching = 4.824561403508772
>
> channel 0 takes it from channel 0
>
> Cannot find CUDA JNA library: java.lang.UnsatisfiedLinkError: Unable to
> load library 'Convolution3D_fftCUDAlib': The specified module could not be
> found.
>
>
>
> I’ve downloaded the CUDA_code_conv3d files from the Nature Methods website
> and placed all of the files from the ‘precompiled’ folder into the
> ‘Fiji.app’ folder or the ‘Fiji.app\plugins’ but I get the same error no
> matter which location the files are in.
>
>
>
> Any ideas as to what I’m doing wrong?  I'm still running v1.49b on a
> Windows 7 64bit machine.
>
>
>
> Thanks for the help!
>
>
>
> -Doug
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Douglas Richardson]

Hi Stephan,

6.0.1

-Doug


On Mon, Jun 9, 2014 at 11:37 AM, Stephan Preibisch <[hidden email]>
wrote:

> Hi Doug,
>
> which version of CUDA do you have installed on your machine?
>
> Cheers,
> Stephan
>
> On Jun 9, 2014, at 11:30 , Douglas Richardson <[hidden email]>
> wrote:
>
> > Hello all,
> >
> >
> > Sorry to bother everyone as I know you're busy with ImageJ 2.0 questions,
> > but here's a hopefully small issue I've been having:
> >
> >
> >
> > I recently just installed a processing station with an NVIDIA Titan Black
> > GPU. I'm trying to run the "SPIM multi-view deconvolution" algorithm on
> the
> > it but am having some problems.
> >
> > Whenever I try to run deconvolution on the GPU I receive the following
> > error:
> >
> >
> >
> > ChannelPattern:
> >
> > Channels: (0)
> >
> > ChannelsToRegister:
> >
> > ChannelsRegister: (0)
> >
> > ChannelsToFuse:
> >
> > ChannelsFuse: (0)
> >
> > Z-stretching = 4.824561403508772
> >
> > channel 0 takes it from channel 0
> >
> > Cannot find CUDA JNA library: java.lang.UnsatisfiedLinkError: Unable to
> > load library 'Convolution3D_fftCUDAlib': The specified module could not
> be
> > found.
> >
> >
> >
> > I’ve downloaded the CUDA_code_conv3d files from the Nature Methods
> website
> > and placed all of the files from the ‘precompiled’ folder into the
> > ‘Fiji.app’ folder or the ‘Fiji.app\plugins’ but I get the same error no
> > matter which location the files are in.
> >
> >
> >
> > Any ideas as to what I’m doing wrong?  I'm still running v1.49b on a
> > Windows 7 64bit machine.
> >
> >
> >
> > Thanks for the help!
> >
> >
> >
> > -Doug
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Stephan Preibisch]

Hi Doug,

there are two reasons (that I can see right now) why it doesn’t work:

1) The precompiled version that I put online was compiled for CUDA5.5, thanks to Liren Zhu for compiling and sharing the Windows DLL with me!
2) You have to put the DLL into the Fiji directory directly, not the plugins directory (see http://www.nature.com/nmeth/journal/v11/n6/full/nmeth.2929.html#supplementary-information, chapter Implementation Details).

After placing the DLL in the right location, it might still not run due to the version mismatch. You have a few options now. You could downgrade to CUDA 5.5. Alternatively, I could nicely ask Liren if he maybe did compile it for CUDA6 already and cc you on this one? I do not have a Windows computer with CUDA running, so I cannot really compile it. You could also install Ubuntu 14.04 where I have a working library.

Maybe there is also a way to adapt the compiler call for Linux as shown in the paper to Windows so that you can do it yourself.

Cheers,
Stephan
---

Dr. Stephan Preibisch
HFSP Fellow
Robert H. Singer / Eugene Myers lab

Albert Einstein College of Medicine / HHMI Janelia Farm / MPI-CBG

email: [hidden email] / [hidden email] / [hidden email]
web: http://www.preibisch.net/

On Jun 9, 2014, at 12:24 , Douglas Richardson <[hidden email]> wrote:

> Hi Stephan,
>
> 6.0.1
>
> -Doug
>
>
> On Mon, Jun 9, 2014 at 11:37 AM, Stephan Preibisch <[hidden email]>
> wrote:
>
>> Hi Doug,
>>
>> which version of CUDA do you have installed on your machine?
>>
>> Cheers,
>> Stephan
>>
>> On Jun 9, 2014, at 11:30 , Douglas Richardson <[hidden email]>
>> wrote:
>>
>>> Hello all,
>>>
>>>
>>> Sorry to bother everyone as I know you're busy with ImageJ 2.0 questions,
>>> but here's a hopefully small issue I've been having:
>>>
>>>
>>>
>>> I recently just installed a processing station with an NVIDIA Titan Black
>>> GPU. I'm trying to run the "SPIM multi-view deconvolution" algorithm on
>> the
>>> it but am having some problems.
>>>
>>> Whenever I try to run deconvolution on the GPU I receive the following
>>> error:
>>>
>>>
>>>
>>> ChannelPattern:
>>>
>>> Channels: (0)
>>>
>>> ChannelsToRegister:
>>>
>>> ChannelsRegister: (0)
>>>
>>> ChannelsToFuse:
>>>
>>> ChannelsFuse: (0)
>>>
>>> Z-stretching = 4.824561403508772
>>>
>>> channel 0 takes it from channel 0
>>>
>>> Cannot find CUDA JNA library: java.lang.UnsatisfiedLinkError: Unable to
>>> load library 'Convolution3D_fftCUDAlib': The specified module could not
>> be
>>> found.
>>>
>>>
>>>
>>> I’ve downloaded the CUDA_code_conv3d files from the Nature Methods
>> website
>>> and placed all of the files from the ‘precompiled’ folder into the
>>> ‘Fiji.app’ folder or the ‘Fiji.app\plugins’ but I get the same error no
>>> matter which location the files are in.
>>>
>>>
>>>
>>> Any ideas as to what I’m doing wrong?  I'm still running v1.49b on a
>>> Windows 7 64bit machine.
>>>
>>>
>>>
>>> Thanks for the help!
>>>
>>>
>>>
>>> -Doug
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Douglas Richardson]

Thanks for the suggestions Stephan,

I tried to downgrade to CUDA 5.5, but it won't recognize the GPU anymore,
so this doesn't look like an option.  We have a system with an older CUDA
GPU in it that's just being upgraded to Windows 7.  Once the upgrade is
completed, I'll try to run it with CUDA 5.5 on that system and see what
happens.

Any other suggestions are welcome.

Wayne: Sorry, I'll stick to the Fiji bug reporter from now on.......I knew
Stephan keeps a close eye on this one though!

-Doug


On Mon, Jun 9, 2014 at 12:38 PM, Stephan Preibisch <[hidden email]>
wrote:

> Hi Doug,
>
> there are two reasons (that I can see right now) why it doesn’t work:
>
> 1) The precompiled version that I put online was compiled for CUDA5.5,
> thanks to Liren Zhu for compiling and sharing the Windows DLL with me!
> 2) You have to put the DLL into the Fiji directory directly, not the
> plugins directory (see
> http://www.nature.com/nmeth/journal/v11/n6/full/nmeth.2929.html#supplementary-information,
> chapter Implementation Details).
>
> After placing the DLL in the right location, it might still not run due to
> the version mismatch. You have a few options now. You could downgrade to
> CUDA 5.5. Alternatively, I could nicely ask Liren if he maybe did compile
> it for CUDA6 already and cc you on this one? I do not have a Windows
> computer with CUDA running, so I cannot really compile it. You could also
> install Ubuntu 14.04 where I have a working library.
>
> Maybe there is also a way to adapt the compiler call for Linux as shown in
> the paper to Windows so that you can do it yourself.
>
> Cheers,
> Stephan
> ---
>
> Dr. Stephan Preibisch
> HFSP Fellow
> Robert H. Singer / Eugene Myers lab
>
> Albert Einstein College of Medicine / HHMI Janelia Farm / MPI-CBG
>
> email: [hidden email] / [hidden email] /
> [hidden email]
> web: http://www.preibisch.net/
>
> On Jun 9, 2014, at 12:24 , Douglas Richardson <[hidden email]>
> wrote:
>
> > Hi Stephan,
> >
> > 6.0.1
> >
> > -Doug
> >
> >
> > On Mon, Jun 9, 2014 at 11:37 AM, Stephan Preibisch <[hidden email]
> >
> > wrote:
> >
> >> Hi Doug,
> >>
> >> which version of CUDA do you have installed on your machine?
> >>
> >> Cheers,
> >> Stephan
> >>
> >> On Jun 9, 2014, at 11:30 , Douglas Richardson <[hidden email]>
> >> wrote:
> >>
> >>> Hello all,
> >>>
> >>>
> >>> Sorry to bother everyone as I know you're busy with ImageJ 2.0
> questions,
> >>> but here's a hopefully small issue I've been having:
> >>>
> >>>
> >>>
> >>> I recently just installed a processing station with an NVIDIA Titan
> Black
> >>> GPU. I'm trying to run the "SPIM multi-view deconvolution" algorithm on
> >> the
> >>> it but am having some problems.
> >>>
> >>> Whenever I try to run deconvolution on the GPU I receive the following
> >>> error:
> >>>
> >>>
> >>>
> >>> ChannelPattern:
> >>>
> >>> Channels: (0)
> >>>
> >>> ChannelsToRegister:
> >>>
> >>> ChannelsRegister: (0)
> >>>
> >>> ChannelsToFuse:
> >>>
> >>> ChannelsFuse: (0)
> >>>
> >>> Z-stretching = 4.824561403508772
> >>>
> >>> channel 0 takes it from channel 0
> >>>
> >>> Cannot find CUDA JNA library: java.lang.UnsatisfiedLinkError: Unable to
> >>> load library 'Convolution3D_fftCUDAlib': The specified module could not
> >> be
> >>> found.
> >>>
> >>>
> >>>
> >>> I’ve downloaded the CUDA_code_conv3d files from the Nature Methods
> >> website
> >>> and placed all of the files from the ‘precompiled’ folder into the
> >>> ‘Fiji.app’ folder or the ‘Fiji.app\plugins’ but I get the same error no
> >>> matter which location the files are in.
> >>>
> >>>
> >>>
> >>> Any ideas as to what I’m doing wrong?  I'm still running v1.49b on a
> >>> Windows 7 64bit machine.
> >>>
> >>>
> >>>
> >>> Thanks for the help!
> >>>
> >>>
> >>>
> >>> -Doug
> >>>
> >>> --
> >>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >>
> >> --
> >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >>
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[dscho]

Hi Douglas,

On Mon, 9 Jun 2014, Douglas Richardson wrote:

> Wayne: Sorry, I'll stick to the Fiji bug reporter from now on.......

The ImageJ mailing list is the best place to discuss these things: as you
pointed out, Stephan keeps an eye on this list. He does not keep an eye on
the Fiji bugzilla. SPIM registration is an ImageJ plugin after all, a
plugin that just happens to be available in the Fiji distribution of
ImageJ for users' convenience.

There are other users of the SPIM deconvolution plugin that will benefit
from seeing this discussion and its outcome. There is a lot of expertise
on this mailing list and the use of CUDA is on the rise in biological
image processing. I think this is in fact a perfect place to discuss this.

The strength of the ImageJ mailing list has always been that it is a
friendly place with a wide range of expertise about everything related to
ImageJ, and sometimes even beyond.

Let's continue to keep it that way,
Johannes

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[bnorthan]

Hi Douglas

Any luck fixing your problem?  I had a similar problem working with a cuda
plugin.

First I was getting an error something like "can't find library.so"

1.  I had to put the native libraries in a "lib" directory directly under
the Fiji directory.  So perhaps put the .dll in the "lib" directory.

Then I got an error something like "can't find cudart.so"

2.  I had to add the location of the Cuda library to my system library
path.  The ubuntu cuda installer didn't do this automatically.  Not sure
the behaviour is the same in Windows or not.  But you might want to check
and see if the location of the cuda libaries has been added to the system
path.

3.  You mention you couldn't get the newest graphics card to work with Cuda
5.5.  I think that might be because cuda 5.5 installs an older version of
the nvidia drivers.  I think you can get the newer cards working with Cuda
5.5.  This info is for GTX 750 Ti but perhaps relevant for you as well.

"The GTX 750 Ti is not supported by the driver (319.37) that is included
with the cuda 5.5 toolkit installer package. Download the latest driver
installer package for GeForce 750 Ti from www.nvidia.com and run that to
replace your 319.37 driver (only). You should have better results. Yes,
CUDA 5.5 is compatible with the newer driver you are installing."




On Tue, Jun 10, 2014 at 11:17 AM, Johannes Schindelin <
[hidden email]> wrote:

> Hi Douglas,
>
> On Mon, 9 Jun 2014, Douglas Richardson wrote:
>
> > Wayne: Sorry, I'll stick to the Fiji bug reporter from now on.......
>
> The ImageJ mailing list is the best place to discuss these things: as you
> pointed out, Stephan keeps an eye on this list. He does not keep an eye on
> the Fiji bugzilla. SPIM registration is an ImageJ plugin after all, a
> plugin that just happens to be available in the Fiji distribution of
> ImageJ for users' convenience.
>
> There are other users of the SPIM deconvolution plugin that will benefit
> from seeing this discussion and its outcome. There is a lot of expertise
> on this mailing list and the use of CUDA is on the rise in biological
> image processing. I think this is in fact a perfect place to discuss this.
>
> The strength of the ImageJ mailing list has always been that it is a
> friendly place with a wide range of expertise about everything related to
> ImageJ, and sometimes even beyond.
>
> Let's continue to keep it that way,
> Johannes
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Stephan Preibisch]

Thanks a lot Brian for the help!

the behavior is unfortunately very different under Windows and Linux as we figured out.

The new version of my plugin that is currently developed handles it much better I think, it actively looks for it and you can change the path. It will be released very soon, if you want to try it ahead of time let me know, I can send you jars (or here is the source https://github.com/fiji/spimreconstruction/tree/revised-spimdata)! It is much more flexible and powerful and iterates with the BigDataViewer.

Cheers,
Stephan

On Jun 11, 2014, at 17:11 , Brian Northan <[hidden email]> wrote:

> Hi Douglas
>
> Any luck fixing your problem?  I had a similar problem working with a cuda
> plugin.
>
> First I was getting an error something like "can't find library.so"
>
> 1.  I had to put the native libraries in a "lib" directory directly under
> the Fiji directory.  So perhaps put the .dll in the "lib" directory.
>
> Then I got an error something like "can't find cudart.so"
>
> 2.  I had to add the location of the Cuda library to my system library
> path.  The ubuntu cuda installer didn't do this automatically.  Not sure
> the behaviour is the same in Windows or not.  But you might want to check
> and see if the location of the cuda libaries has been added to the system
> path.
>
> 3.  You mention you couldn't get the newest graphics card to work with Cuda
> 5.5.  I think that might be because cuda 5.5 installs an older version of
> the nvidia drivers.  I think you can get the newer cards working with Cuda
> 5.5.  This info is for GTX 750 Ti but perhaps relevant for you as well.
>
> "The GTX 750 Ti is not supported by the driver (319.37) that is included
> with the cuda 5.5 toolkit installer package. Download the latest driver
> installer package for GeForce 750 Ti from www.nvidia.com and run that to
> replace your 319.37 driver (only). You should have better results. Yes,
> CUDA 5.5 is compatible with the newer driver you are installing."
>
>
>
>
> On Tue, Jun 10, 2014 at 11:17 AM, Johannes Schindelin <
> [hidden email]> wrote:
>
>> Hi Douglas,
>>
>> On Mon, 9 Jun 2014, Douglas Richardson wrote:
>>
>>> Wayne: Sorry, I'll stick to the Fiji bug reporter from now on.......
>>
>> The ImageJ mailing list is the best place to discuss these things: as you
>> pointed out, Stephan keeps an eye on this list. He does not keep an eye on
>> the Fiji bugzilla. SPIM registration is an ImageJ plugin after all, a
>> plugin that just happens to be available in the Fiji distribution of
>> ImageJ for users' convenience.
>>
>> There are other users of the SPIM deconvolution plugin that will benefit
>> from seeing this discussion and its outcome. There is a lot of expertise
>> on this mailing list and the use of CUDA is on the rise in biological
>> image processing. I think this is in fact a perfect place to discuss this.
>>
>> The strength of the ImageJ mailing list has always been that it is a
>> friendly place with a wide range of expertise about everything related to
>> ImageJ, and sometimes even beyond.
>>
>> Let's continue to keep it that way,
>> Johannes
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[bnorthan]

Hi Stephan

Thanks, I will try it out.  Also, looking at your code in
"Multi_View_Deconvolution.java" I saw a comment (around line 825 where it
loads the libary) "under linux automatically checks lib/linux64".  So that
mean it only checks the Fiji/lib directory under linux??


On Wed, Jun 11, 2014 at 5:20 PM, Stephan Preibisch <[hidden email]>
wrote:

> Thanks a lot Brian for the help!
>
> the behavior is unfortunately very different under Windows and Linux as we
> figured out.
>
> The new version of my plugin that is currently developed handles it much
> better I think, it actively looks for it and you can change the path. It
> will be released very soon, if you want to try it ahead of time let me
> know, I can send you jars (or here is the source
> https://github.com/fiji/spimreconstruction/tree/revised-spimdata)! It is
> much more flexible and powerful and iterates with the BigDataViewer.
>
> Cheers,
> Stephan
>
> On Jun 11, 2014, at 17:11 , Brian Northan <[hidden email]> wrote:
>
> > Hi Douglas
> >
> > Any luck fixing your problem?  I had a similar problem working with a
> cuda
> > plugin.
> >
> > First I was getting an error something like "can't find library.so"
> >
> > 1.  I had to put the native libraries in a "lib" directory directly under
> > the Fiji directory.  So perhaps put the .dll in the "lib" directory.
> >
> > Then I got an error something like "can't find cudart.so"
> >
> > 2.  I had to add the location of the Cuda library to my system library
> > path.  The ubuntu cuda installer didn't do this automatically.  Not sure
> > the behaviour is the same in Windows or not.  But you might want to check
> > and see if the location of the cuda libaries has been added to the system
> > path.
> >
> > 3.  You mention you couldn't get the newest graphics card to work with
> Cuda
> > 5.5.  I think that might be because cuda 5.5 installs an older version of
> > the nvidia drivers.  I think you can get the newer cards working with
> Cuda
> > 5.5.  This info is for GTX 750 Ti but perhaps relevant for you as well.
> >
> > "The GTX 750 Ti is not supported by the driver (319.37) that is included
> > with the cuda 5.5 toolkit installer package. Download the latest driver
> > installer package for GeForce 750 Ti from www.nvidia.com and run that to
> > replace your 319.37 driver (only). You should have better results. Yes,
> > CUDA 5.5 is compatible with the newer driver you are installing."
> >
> >
> >
> >
> > On Tue, Jun 10, 2014 at 11:17 AM, Johannes Schindelin <
> > [hidden email]> wrote:
> >
> >> Hi Douglas,
> >>
> >> On Mon, 9 Jun 2014, Douglas Richardson wrote:
> >>
> >>> Wayne: Sorry, I'll stick to the Fiji bug reporter from now on.......
> >>
> >> The ImageJ mailing list is the best place to discuss these things: as
> you
> >> pointed out, Stephan keeps an eye on this list. He does not keep an eye
> on
> >> the Fiji bugzilla. SPIM registration is an ImageJ plugin after all, a
> >> plugin that just happens to be available in the Fiji distribution of
> >> ImageJ for users' convenience.
> >>
> >> There are other users of the SPIM deconvolution plugin that will benefit
> >> from seeing this discussion and its outcome. There is a lot of expertise
> >> on this mailing list and the use of CUDA is on the rise in biological
> >> image processing. I think this is in fact a perfect place to discuss
> this.
> >>
> >> The strength of the ImageJ mailing list has always been that it is a
> >> friendly place with a wide range of expertise about everything related
> to
> >> ImageJ, and sometimes even beyond.
> >>
> >> Let's continue to keep it that way,
> >> Johannes
> >>
> >> --
> >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >>
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Stephan Preibisch]

Hi Brian,

it seemed to be a somewhat inconsistent behavior between platforms and versions, that’s why I changed it to the manual selection in the new version. I would try lib/linux64, lib, folder directly. One of them should work. At least it did back then on Windows and Ubuntu.

I was under time pressure because of the paper when I finished that code, so it is not that well done. I am mostly working on the new version now which should not have these problems any more.

I hope by the end of next week it can be released.

Cheers,
Stephan

On Jun 11, 2014, at 17:48 , Brian Northan <[hidden email]> wrote:

> Hi Stephan
>
> Thanks, I will try it out.  Also, looking at your code in
> "Multi_View_Deconvolution.java" I saw a comment (around line 825 where it
> loads the libary) "under linux automatically checks lib/linux64".  So that
> mean it only checks the Fiji/lib directory under linux??
>
>
> On Wed, Jun 11, 2014 at 5:20 PM, Stephan Preibisch <[hidden email]>
> wrote:
>
>> Thanks a lot Brian for the help!
>>
>> the behavior is unfortunately very different under Windows and Linux as we
>> figured out.
>>
>> The new version of my plugin that is currently developed handles it much
>> better I think, it actively looks for it and you can change the path. It
>> will be released very soon, if you want to try it ahead of time let me
>> know, I can send you jars (or here is the source
>> https://github.com/fiji/spimreconstruction/tree/revised-spimdata)! It is
>> much more flexible and powerful and iterates with the BigDataViewer.
>>
>> Cheers,
>> Stephan
>>
>> On Jun 11, 2014, at 17:11 , Brian Northan <[hidden email]> wrote:
>>
>>> Hi Douglas
>>>
>>> Any luck fixing your problem?  I had a similar problem working with a
>> cuda
>>> plugin.
>>>
>>> First I was getting an error something like "can't find library.so"
>>>
>>> 1.  I had to put the native libraries in a "lib" directory directly under
>>> the Fiji directory.  So perhaps put the .dll in the "lib" directory.
>>>
>>> Then I got an error something like "can't find cudart.so"
>>>
>>> 2.  I had to add the location of the Cuda library to my system library
>>> path.  The ubuntu cuda installer didn't do this automatically.  Not sure
>>> the behaviour is the same in Windows or not.  But you might want to check
>>> and see if the location of the cuda libaries has been added to the system
>>> path.
>>>
>>> 3.  You mention you couldn't get the newest graphics card to work with
>> Cuda
>>> 5.5.  I think that might be because cuda 5.5 installs an older version of
>>> the nvidia drivers.  I think you can get the newer cards working with
>> Cuda
>>> 5.5.  This info is for GTX 750 Ti but perhaps relevant for you as well.
>>>
>>> "The GTX 750 Ti is not supported by the driver (319.37) that is included
>>> with the cuda 5.5 toolkit installer package. Download the latest driver
>>> installer package for GeForce 750 Ti from www.nvidia.com and run that to
>>> replace your 319.37 driver (only). You should have better results. Yes,
>>> CUDA 5.5 is compatible with the newer driver you are installing."
>>>
>>>
>>>
>>>
>>> On Tue, Jun 10, 2014 at 11:17 AM, Johannes Schindelin <
>>> [hidden email]> wrote:
>>>
>>>> Hi Douglas,
>>>>
>>>> On Mon, 9 Jun 2014, Douglas Richardson wrote:
>>>>
>>>>> Wayne: Sorry, I'll stick to the Fiji bug reporter from now on.......
>>>>
>>>> The ImageJ mailing list is the best place to discuss these things: as
>> you
>>>> pointed out, Stephan keeps an eye on this list. He does not keep an eye
>> on
>>>> the Fiji bugzilla. SPIM registration is an ImageJ plugin after all, a
>>>> plugin that just happens to be available in the Fiji distribution of
>>>> ImageJ for users' convenience.
>>>>
>>>> There are other users of the SPIM deconvolution plugin that will benefit
>>>> from seeing this discussion and its outcome. There is a lot of expertise
>>>> on this mailing list and the use of CUDA is on the rise in biological
>>>> image processing. I think this is in fact a perfect place to discuss
>> this.
>>>>
>>>> The strength of the ImageJ mailing list has always been that it is a
>>>> friendly place with a wide range of expertise about everything related
>> to
>>>> ImageJ, and sometimes even beyond.
>>>>
>>>> Let's continue to keep it that way,
>>>> Johannes
>>>>
>>>> --
>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>>
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Douglas Richardson]

Sorry it took me awhile to reply, I didn't have a lot of time to work on
this this week.  Here is the good news, everything seems to be working well
now.  Thanks to both Stephan and Brian for your suggestions.  Here's what I
discovered in the end:

The current code is not compatible with CUDA6.0 as Stephan had suggested.
CUDA5.5 is needed.  As Brian had recomended, I was able to instal CUDA5.5,
then update the driver for the GTX Titan Black GPU (I'm now using Graphics
Driver 337.88)

Another note for others trying this: For a complete instal of the CUDA5.5
(or 6.0) toolbox, an installed copy of Visual Studio 2012 (not 2013!) is
required.  (I currently only have the 30 day trial, hopefully everything
doesn't crash after 30 days.)

The .dll and .so files only needed to be placed in the /Fiji.app directory,
not their own lib folder

The CUDA library is added to the system path upon installation in Windows 7.

I now have this running on two systems:

1) Windows 7 (64bit), 16GB RAM, GTX 285 GPU, CUDA 5.5, Graphics Driver
320.57, Visual Studio 2012
2) Windows 7 (64bit), 196GB RAM, GTX Titan Black GPU, CUDA 5.5, Graphics
Driver 337.88, Visual Studio 2012

Thanks again for all the help!

-Doug


On Wed, Jun 11, 2014 at 8:04 PM, Stephan Preibisch <[hidden email]>
wrote:

> Hi Brian,
>
> it seemed to be a somewhat inconsistent behavior between platforms and
> versions, that’s why I changed it to the manual selection in the new
> version. I would try lib/linux64, lib, folder directly. One of them should
> work. At least it did back then on Windows and Ubuntu.
>
> I was under time pressure because of the paper when I finished that code,
> so it is not that well done. I am mostly working on the new version now
> which should not have these problems any more.
>
> I hope by the end of next week it can be released.
>
> Cheers,
> Stephan
>
> On Jun 11, 2014, at 17:48 , Brian Northan <[hidden email]> wrote:
>
> > Hi Stephan
> >
> > Thanks, I will try it out.  Also, looking at your code in
> > "Multi_View_Deconvolution.java" I saw a comment (around line 825 where it
> > loads the libary) "under linux automatically checks lib/linux64".  So
> that
> > mean it only checks the Fiji/lib directory under linux??
> >
> >
> > On Wed, Jun 11, 2014 at 5:20 PM, Stephan Preibisch <[hidden email]
> >
> > wrote:
> >
> >> Thanks a lot Brian for the help!
> >>
> >> the behavior is unfortunately very different under Windows and Linux as
> we
> >> figured out.
> >>
> >> The new version of my plugin that is currently developed handles it much
> >> better I think, it actively looks for it and you can change the path. It
> >> will be released very soon, if you want to try it ahead of time let me
> >> know, I can send you jars (or here is the source
> >> https://github.com/fiji/spimreconstruction/tree/revised-spimdata)! It
> is
> >> much more flexible and powerful and iterates with the BigDataViewer.
> >>
> >> Cheers,
> >> Stephan
> >>
> >> On Jun 11, 2014, at 17:11 , Brian Northan <[hidden email]> wrote:
> >>
> >>> Hi Douglas
> >>>
> >>> Any luck fixing your problem?  I had a similar problem working with a
> >> cuda
> >>> plugin.
> >>>
> >>> First I was getting an error something like "can't find library.so"
> >>>
> >>> 1.  I had to put the native libraries in a "lib" directory directly
> under
> >>> the Fiji directory.  So perhaps put the .dll in the "lib" directory.
> >>>
> >>> Then I got an error something like "can't find cudart.so"
> >>>
> >>> 2.  I had to add the location of the Cuda library to my system library
> >>> path.  The ubuntu cuda installer didn't do this automatically.  Not
> sure
> >>> the behaviour is the same in Windows or not.  But you might want to
> check
> >>> and see if the location of the cuda libaries has been added to the
> system
> >>> path.
> >>>
> >>> 3.  You mention you couldn't get the newest graphics card to work with
> >> Cuda
> >>> 5.5.  I think that might be because cuda 5.5 installs an older version
> of
> >>> the nvidia drivers.  I think you can get the newer cards working with
> >> Cuda
> >>> 5.5.  This info is for GTX 750 Ti but perhaps relevant for you as well.
> >>>
> >>> "The GTX 750 Ti is not supported by the driver (319.37) that is
> included
> >>> with the cuda 5.5 toolkit installer package. Download the latest driver
> >>> installer package for GeForce 750 Ti from www.nvidia.com and run that
> to
> >>> replace your 319.37 driver (only). You should have better results. Yes,
> >>> CUDA 5.5 is compatible with the newer driver you are installing."
> >>>
> >>>
> >>>
> >>>
> >>> On Tue, Jun 10, 2014 at 11:17 AM, Johannes Schindelin <
> >>> [hidden email]> wrote:
> >>>
> >>>> Hi Douglas,
> >>>>
> >>>> On Mon, 9 Jun 2014, Douglas Richardson wrote:
> >>>>
> >>>>> Wayne: Sorry, I'll stick to the Fiji bug reporter from now on.......
> >>>>
> >>>> The ImageJ mailing list is the best place to discuss these things: as
> >> you
> >>>> pointed out, Stephan keeps an eye on this list. He does not keep an
> eye
> >> on
> >>>> the Fiji bugzilla. SPIM registration is an ImageJ plugin after all, a
> >>>> plugin that just happens to be available in the Fiji distribution of
> >>>> ImageJ for users' convenience.
> >>>>
> >>>> There are other users of the SPIM deconvolution plugin that will
> benefit
> >>>> from seeing this discussion and its outcome. There is a lot of
> expertise
> >>>> on this mailing list and the use of CUDA is on the rise in biological
> >>>> image processing. I think this is in fact a perfect place to discuss
> >> this.
> >>>>
> >>>> The strength of the ImageJ mailing list has always been that it is a
> >>>> friendly place with a wide range of expertise about everything related
> >> to
> >>>> ImageJ, and sometimes even beyond.
> >>>>
> >>>> Let's continue to keep it that way,
> >>>> Johannes
> >>>>
> >>>> --
> >>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >>>>
> >>>
> >>> --
> >>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >>
> >>
> >> --
> >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >>
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Stephan Preibisch]

Hi Doug,

that’s great! Did you check if maybe the free Visual Studio Redistributable package (http://www.microsoft.com/en-us/download/details.aspx?id=30679) is sufficient for running it?

Cheers,
Stephan

On Jun 13, 2014, at 16:42 , Douglas Richardson <[hidden email]> wrote:

> Sorry it took me awhile to reply, I didn't have a lot of time to work on
> this this week.  Here is the good news, everything seems to be working well
> now.  Thanks to both Stephan and Brian for your suggestions.  Here's what I
> discovered in the end:
>
> The current code is not compatible with CUDA6.0 as Stephan had suggested.
> CUDA5.5 is needed.  As Brian had recomended, I was able to instal CUDA5.5,
> then update the driver for the GTX Titan Black GPU (I'm now using Graphics
> Driver 337.88)
>
> Another note for others trying this: For a complete instal of the CUDA5.5
> (or 6.0) toolbox, an installed copy of Visual Studio 2012 (not 2013!) is
> required.  (I currently only have the 30 day trial, hopefully everything
> doesn't crash after 30 days.)
>
> The .dll and .so files only needed to be placed in the /Fiji.app directory,
> not their own lib folder
>
> The CUDA library is added to the system path upon installation in Windows 7.
>
> I now have this running on two systems:
>
> 1) Windows 7 (64bit), 16GB RAM, GTX 285 GPU, CUDA 5.5, Graphics Driver
> 320.57, Visual Studio 2012
> 2) Windows 7 (64bit), 196GB RAM, GTX Titan Black GPU, CUDA 5.5, Graphics
> Driver 337.88, Visual Studio 2012
>
> Thanks again for all the help!
>
> -Doug
>
>
> On Wed, Jun 11, 2014 at 8:04 PM, Stephan Preibisch <[hidden email]>
> wrote:
>
>> Hi Brian,
>>
>> it seemed to be a somewhat inconsistent behavior between platforms and
>> versions, that’s why I changed it to the manual selection in the new
>> version. I would try lib/linux64, lib, folder directly. One of them should
>> work. At least it did back then on Windows and Ubuntu.
>>
>> I was under time pressure because of the paper when I finished that code,
>> so it is not that well done. I am mostly working on the new version now
>> which should not have these problems any more.
>>
>> I hope by the end of next week it can be released.
>>
>> Cheers,
>> Stephan
>>
>> On Jun 11, 2014, at 17:48 , Brian Northan <[hidden email]> wrote:
>>
>>> Hi Stephan
>>>
>>> Thanks, I will try it out.  Also, looking at your code in
>>> "Multi_View_Deconvolution.java" I saw a comment (around line 825 where it
>>> loads the libary) "under linux automatically checks lib/linux64".  So
>> that
>>> mean it only checks the Fiji/lib directory under linux??
>>>
>>>
>>> On Wed, Jun 11, 2014 at 5:20 PM, Stephan Preibisch <[hidden email]
>>>
>>> wrote:
>>>
>>>> Thanks a lot Brian for the help!
>>>>
>>>> the behavior is unfortunately very different under Windows and Linux as
>> we
>>>> figured out.
>>>>
>>>> The new version of my plugin that is currently developed handles it much
>>>> better I think, it actively looks for it and you can change the path. It
>>>> will be released very soon, if you want to try it ahead of time let me
>>>> know, I can send you jars (or here is the source
>>>> https://github.com/fiji/spimreconstruction/tree/revised-spimdata)! It
>> is
>>>> much more flexible and powerful and iterates with the BigDataViewer.
>>>>
>>>> Cheers,
>>>> Stephan
>>>>
>>>> On Jun 11, 2014, at 17:11 , Brian Northan <[hidden email]> wrote:
>>>>
>>>>> Hi Douglas
>>>>>
>>>>> Any luck fixing your problem?  I had a similar problem working with a
>>>> cuda
>>>>> plugin.
>>>>>
>>>>> First I was getting an error something like "can't find library.so"
>>>>>
>>>>> 1.  I had to put the native libraries in a "lib" directory directly
>> under
>>>>> the Fiji directory.  So perhaps put the .dll in the "lib" directory.
>>>>>
>>>>> Then I got an error something like "can't find cudart.so"
>>>>>
>>>>> 2.  I had to add the location of the Cuda library to my system library
>>>>> path.  The ubuntu cuda installer didn't do this automatically.  Not
>> sure
>>>>> the behaviour is the same in Windows or not.  But you might want to
>> check
>>>>> and see if the location of the cuda libaries has been added to the
>> system
>>>>> path.
>>>>>
>>>>> 3.  You mention you couldn't get the newest graphics card to work with
>>>> Cuda
>>>>> 5.5.  I think that might be because cuda 5.5 installs an older version
>> of
>>>>> the nvidia drivers.  I think you can get the newer cards working with
>>>> Cuda
>>>>> 5.5.  This info is for GTX 750 Ti but perhaps relevant for you as well.
>>>>>
>>>>> "The GTX 750 Ti is not supported by the driver (319.37) that is
>> included
>>>>> with the cuda 5.5 toolkit installer package. Download the latest driver
>>>>> installer package for GeForce 750 Ti from www.nvidia.com and run that
>> to
>>>>> replace your 319.37 driver (only). You should have better results. Yes,
>>>>> CUDA 5.5 is compatible with the newer driver you are installing."
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Tue, Jun 10, 2014 at 11:17 AM, Johannes Schindelin <
>>>>> [hidden email]> wrote:
>>>>>
>>>>>> Hi Douglas,
>>>>>>
>>>>>> On Mon, 9 Jun 2014, Douglas Richardson wrote:
>>>>>>
>>>>>>> Wayne: Sorry, I'll stick to the Fiji bug reporter from now on.......
>>>>>>
>>>>>> The ImageJ mailing list is the best place to discuss these things: as
>>>> you
>>>>>> pointed out, Stephan keeps an eye on this list. He does not keep an
>> eye
>>>> on
>>>>>> the Fiji bugzilla. SPIM registration is an ImageJ plugin after all, a
>>>>>> plugin that just happens to be available in the Fiji distribution of
>>>>>> ImageJ for users' convenience.
>>>>>>
>>>>>> There are other users of the SPIM deconvolution plugin that will
>> benefit
>>>>>> from seeing this discussion and its outcome. There is a lot of
>> expertise
>>>>>> on this mailing list and the use of CUDA is on the rise in biological
>>>>>> image processing. I think this is in fact a perfect place to discuss
>>>> this.
>>>>>>
>>>>>> The strength of the ImageJ mailing list has always been that it is a
>>>>>> friendly place with a wide range of expertise about everything related
>>>> to
>>>>>> ImageJ, and sometimes even beyond.
>>>>>>
>>>>>> Let's continue to keep it that way,
>>>>>> Johannes
>>>>>>
>>>>>> --
>>>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>>>>
>>>>>
>>>>> --
>>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>>
>>>>
>>>> --
>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>>
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Richard Mort-2]

Can anyone advise me on a way to make measurements on orthogonal views?
I hvae a number of large stacks of 3D scans of embryos. I would like to
navigate them using orthogonal views and then make simple measurements
(body circumference, body length etc) at a number of positions. Does any
plugin provide this functionality?
Cheers
Richard

--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Douglas Richardson]

Hi Stephan,

I did not check that package.  I did check the free Visual Studio Express,
but that was unable to support CUDA installation.  If I have any problems
at the end of the 30 day trial for Visual Studio 2012, I will give the
redistributable package a try and report back.

I'm very impressed at how fast this is, thanks for all the hard work!

-Doug


On Mon, Jun 16, 2014 at 10:27 AM, Stephan Preibisch <[hidden email]>
wrote:

> Hi Doug,
>
> that’s great! Did you check if maybe the free Visual Studio
> Redistributable package (
> http://www.microsoft.com/en-us/download/details.aspx?id=30679) is
> sufficient for running it?
>
> Cheers,
> Stephan
>
> On Jun 13, 2014, at 16:42 , Douglas Richardson <[hidden email]>
> wrote:
>
> > Sorry it took me awhile to reply, I didn't have a lot of time to work on
> > this this week.  Here is the good news, everything seems to be working
> well
> > now.  Thanks to both Stephan and Brian for your suggestions.  Here's
> what I
> > discovered in the end:
> >
> > The current code is not compatible with CUDA6.0 as Stephan had suggested.
> > CUDA5.5 is needed.  As Brian had recomended, I was able to instal
> CUDA5.5,
> > then update the driver for the GTX Titan Black GPU (I'm now using
> Graphics
> > Driver 337.88)
> >
> > Another note for others trying this: For a complete instal of the CUDA5.5
> > (or 6.0) toolbox, an installed copy of Visual Studio 2012 (not 2013!) is
> > required.  (I currently only have the 30 day trial, hopefully everything
> > doesn't crash after 30 days.)
> >
> > The .dll and .so files only needed to be placed in the /Fiji.app
> directory,
> > not their own lib folder
> >
> > The CUDA library is added to the system path upon installation in
> Windows 7.
> >
> > I now have this running on two systems:
> >
> > 1) Windows 7 (64bit), 16GB RAM, GTX 285 GPU, CUDA 5.5, Graphics Driver
> > 320.57, Visual Studio 2012
> > 2) Windows 7 (64bit), 196GB RAM, GTX Titan Black GPU, CUDA 5.5, Graphics
> > Driver 337.88, Visual Studio 2012
> >
> > Thanks again for all the help!
> >
> > -Doug
> >
> >
> > On Wed, Jun 11, 2014 at 8:04 PM, Stephan Preibisch <[hidden email]
> >
> > wrote:
> >
> >> Hi Brian,
> >>
> >> it seemed to be a somewhat inconsistent behavior between platforms and
> >> versions, that’s why I changed it to the manual selection in the new
> >> version. I would try lib/linux64, lib, folder directly. One of them
> should
> >> work. At least it did back then on Windows and Ubuntu.
> >>
> >> I was under time pressure because of the paper when I finished that
> code,
> >> so it is not that well done. I am mostly working on the new version now
> >> which should not have these problems any more.
> >>
> >> I hope by the end of next week it can be released.
> >>
> >> Cheers,
> >> Stephan
> >>
> >> On Jun 11, 2014, at 17:48 , Brian Northan <[hidden email]> wrote:
> >>
> >>> Hi Stephan
> >>>
> >>> Thanks, I will try it out.  Also, looking at your code in
> >>> "Multi_View_Deconvolution.java" I saw a comment (around line 825 where
> it
> >>> loads the libary) "under linux automatically checks lib/linux64".  So
> >> that
> >>> mean it only checks the Fiji/lib directory under linux??
> >>>
> >>>
> >>> On Wed, Jun 11, 2014 at 5:20 PM, Stephan Preibisch <
> [hidden email]
> >>>
> >>> wrote:
> >>>
> >>>> Thanks a lot Brian for the help!
> >>>>
> >>>> the behavior is unfortunately very different under Windows and Linux
> as
> >> we
> >>>> figured out.
> >>>>
> >>>> The new version of my plugin that is currently developed handles it
> much
> >>>> better I think, it actively looks for it and you can change the path.
> It
> >>>> will be released very soon, if you want to try it ahead of time let me
> >>>> know, I can send you jars (or here is the source
> >>>> https://github.com/fiji/spimreconstruction/tree/revised-spimdata)! It
> >> is
> >>>> much more flexible and powerful and iterates with the BigDataViewer.
> >>>>
> >>>> Cheers,
> >>>> Stephan
> >>>>
> >>>> On Jun 11, 2014, at 17:11 , Brian Northan <[hidden email]> wrote:
> >>>>
> >>>>> Hi Douglas
> >>>>>
> >>>>> Any luck fixing your problem?  I had a similar problem working with a
> >>>> cuda
> >>>>> plugin.
> >>>>>
> >>>>> First I was getting an error something like "can't find library.so"
> >>>>>
> >>>>> 1.  I had to put the native libraries in a "lib" directory directly
> >> under
> >>>>> the Fiji directory.  So perhaps put the .dll in the "lib" directory.
> >>>>>
> >>>>> Then I got an error something like "can't find cudart.so"
> >>>>>
> >>>>> 2.  I had to add the location of the Cuda library to my system
> library
> >>>>> path.  The ubuntu cuda installer didn't do this automatically.  Not
> >> sure
> >>>>> the behaviour is the same in Windows or not.  But you might want to
> >> check
> >>>>> and see if the location of the cuda libaries has been added to the
> >> system
> >>>>> path.
> >>>>>
> >>>>> 3.  You mention you couldn't get the newest graphics card to work
> with
> >>>> Cuda
> >>>>> 5.5.  I think that might be because cuda 5.5 installs an older
> version
> >> of
> >>>>> the nvidia drivers.  I think you can get the newer cards working with
> >>>> Cuda
> >>>>> 5.5.  This info is for GTX 750 Ti but perhaps relevant for you as
> well.
> >>>>>
> >>>>> "The GTX 750 Ti is not supported by the driver (319.37) that is
> >> included
> >>>>> with the cuda 5.5 toolkit installer package. Download the latest
> driver
> >>>>> installer package for GeForce 750 Ti from www.nvidia.com and run
> that
> >> to
> >>>>> replace your 319.37 driver (only). You should have better results.
> Yes,
> >>>>> CUDA 5.5 is compatible with the newer driver you are installing."
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>> On Tue, Jun 10, 2014 at 11:17 AM, Johannes Schindelin <
> >>>>> [hidden email]> wrote:
> >>>>>
> >>>>>> Hi Douglas,
> >>>>>>
> >>>>>> On Mon, 9 Jun 2014, Douglas Richardson wrote:
> >>>>>>
> >>>>>>> Wayne: Sorry, I'll stick to the Fiji bug reporter from now
> on.......
> >>>>>>
> >>>>>> The ImageJ mailing list is the best place to discuss these things:
> as
> >>>> you
> >>>>>> pointed out, Stephan keeps an eye on this list. He does not keep an
> >> eye
> >>>> on
> >>>>>> the Fiji bugzilla. SPIM registration is an ImageJ plugin after all,
> a
> >>>>>> plugin that just happens to be available in the Fiji distribution of
> >>>>>> ImageJ for users' convenience.
> >>>>>>
> >>>>>> There are other users of the SPIM deconvolution plugin that will
> >> benefit
> >>>>>> from seeing this discussion and its outcome. There is a lot of
> >> expertise
> >>>>>> on this mailing list and the use of CUDA is on the rise in
> biological
> >>>>>> image processing. I think this is in fact a perfect place to discuss
> >>>> this.
> >>>>>>
> >>>>>> The strength of the ImageJ mailing list has always been that it is a
> >>>>>> friendly place with a wide range of expertise about everything
> related
> >>>> to
> >>>>>> ImageJ, and sometimes even beyond.
> >>>>>>
> >>>>>> Let's continue to keep it that way,
> >>>>>> Johannes
> >>>>>>
> >>>>>> --
> >>>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >>>>>>
> >>>>>
> >>>>> --
> >>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >>>>
> >>>>
> >>>> --
> >>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >>>>
> >>>
> >>> --
> >>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >>
> >> --
> >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >>
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
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