3d registration across multiple stacks
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Hi,
Could anyone kindly give some advice on how to registered multiple 3d stacks and extract the transformation information to adjust another channel of these stacks. It seems the Descriptor-based registration (2d/3d) could register 2 3d stacks, but I don't know how to scale that up to >10 stacks. Also is there a way to extract the transformation information and apply each to the other channels of corresponding stack. Thanks! Kevin -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Hey Kevin,
When I want to apply the registration transforms from one stack to another, I use the Plugins>Registration>Register Virtual Stack Slices on the initial stack and make sure to select save transforms. Then to apply the transforms to another stack, use Plugins>Transform>Transform Virtual Stack Slices Mike On Monday, March 30, 2020, 09:27:59 AM EDT, Kevin <[hidden email]> wrote: Hi, Could anyone kindly give some advice on how to registered multiple 3d stacks and extract the transformation information to adjust another channel of these stacks. It seems the Descriptor-based registration (2d/3d) could register 2 3d stacks, but I don't know how to scale that up to >10 stacks. Also is there a way to extract the transformation information and apply each to the other channels of corresponding stack. Thanks! Kevin -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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In reply to this post by aget
Thanks Mike for your reply. I may not describe the problem clear. The question is to register one 3d stack to another 3d stack, instead of registering the slices in one stack. Also need to extract the transformation for each slice in a stack. Any idea any plugin for this purpose? Thanks!
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For registering multiple 3D stacks, I use another free program called Dream.3D (http://dream3d.bluequartz.net <http://dream3d.bluequartz.net/>). I haven’t had much luck trying to do these types of registrations inside of ImageJ.
Mike > On Mar 30, 2020, at 2:43 PM, Yajie Liang <[hidden email]> wrote: > > Thanks Mike for your reply. I may not describe the problem clear. The question is to register one 3d stack to another 3d stack, instead of registering the slices in one stack. Also need to extract the transformation for each slice in a stack. Any idea any plugin for this purpose? Thanks! > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Thanks Mike, I have installed the Dream.3D, but found it hard to start
with. The tutorial does not tell much about its use. Any suggestions about where to find learning materials? Thank you! On Tue, Mar 31, 2020 at 10:56 AM mike chapman <[hidden email]> wrote: > For registering multiple 3D stacks, I use another free program called > Dream.3D (http://dream3d.bluequartz.net <http://dream3d.bluequartz.net/>). > I haven’t had much luck trying to do these types of registrations inside of > ImageJ. > > Mike > > > On Mar 30, 2020, at 2:43 PM, Yajie Liang <[hidden email]> wrote: > > > > Thanks Mike for your reply. I may not describe the problem clear. The > question is to register one 3d stack to another 3d stack, instead of > registering the slices in one stack. Also need to extract the > transformation for each slice in a stack. Any idea any plugin for this > purpose? Thanks! > > > > -- > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- Truth Shall Make You Free -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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There is a webinar introduction from a few years ago posted on youtube (https://www.youtube.com/watch?v=CIYC1nPWb-g <https://www.youtube.com/watch?v=CIYC1nPWb-g>) which would be a good place to start that highlights how to use the software (there is a demo of using the software in the second half).
There are some example pipelines if you go under bookmarks>prebuilt pipelines>Examples inside the gui There is also a forum (https://groups.google.com/forum/#!forum/dream3d-users <https://groups.google.com/forum/#!forum/dream3d-users>) which may be useful. Mike Jackson (the lead on the software) is very responsive on the forum. Mike > On Apr 1, 2020, at 10:32 AM, aget liang <[hidden email]> wrote: > > Thanks Mike, I have installed the Dream.3D, but found it hard to start > with. The tutorial does not tell much about its use. Any suggestions about > where to find learning materials? Thank you! > > On Tue, Mar 31, 2020 at 10:56 AM mike chapman <[hidden email] <mailto:[hidden email]>> > wrote: > >> For registering multiple 3D stacks, I use another free program called >> Dream.3D (http://dream3d.bluequartz.net <http://dream3d.bluequartz.net/> <http://dream3d.bluequartz.net/ <http://dream3d.bluequartz.net/>>). >> I haven’t had much luck trying to do these types of registrations inside of >> ImageJ. >> >> Mike >> >>> On Mar 30, 2020, at 2:43 PM, Yajie Liang <[hidden email]> wrote: >>> >>> Thanks Mike for your reply. I may not describe the problem clear. The >> question is to register one 3d stack to another 3d stack, instead of >> registering the slices in one stack. Also need to extract the >> transformation for each slice in a stack. Any idea any plugin for this >> purpose? Thanks! >>> >>> -- >>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >> >> >> -- >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html <http://imagej.nih.gov/ij/list.html> >> > > > -- > Truth Shall Make You Free > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html <http://imagej.nih.gov/ij/list.html> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Thank you Mike, that's very helpful. I posted a question in the forum. Also
opened some examples, and realized that this software cannot visualize output, right? so we have to use Paraview? On Wed, Apr 1, 2020 at 10:51 AM mike chapman <[hidden email]> wrote: > There is a webinar introduction from a few years ago posted on youtube ( > https://www.youtube.com/watch?v=CIYC1nPWb-g < > https://www.youtube.com/watch?v=CIYC1nPWb-g>) which would be a good place > to start that highlights how to use the software (there is a demo of using > the software in the second half). > > There are some example pipelines if you go under bookmarks>prebuilt > pipelines>Examples inside the gui > > There is also a forum ( > https://groups.google.com/forum/#!forum/dream3d-users < > https://groups.google.com/forum/#!forum/dream3d-users>) which may be > useful. Mike Jackson (the lead on the software) is very responsive on the > forum. > > Mike > > > On Apr 1, 2020, at 10:32 AM, aget liang <[hidden email]> wrote: > > > > Thanks Mike, I have installed the Dream.3D, but found it hard to start > > with. The tutorial does not tell much about its use. Any suggestions > about > > where to find learning materials? Thank you! > > > > On Tue, Mar 31, 2020 at 10:56 AM mike chapman <[hidden email] > <mailto:[hidden email]>> > > wrote: > > > >> For registering multiple 3D stacks, I use another free program called > >> Dream.3D (http://dream3d.bluequartz.net <http://dream3d.bluequartz.net/> > <http://dream3d.bluequartz.net/ <http://dream3d.bluequartz.net/>>). > >> I haven’t had much luck trying to do these types of registrations > inside of > >> ImageJ. > >> > >> Mike > >> > >>> On Mar 30, 2020, at 2:43 PM, Yajie Liang <[hidden email]> wrote: > >>> > >>> Thanks Mike for your reply. I may not describe the problem clear. The > >> question is to register one 3d stack to another 3d stack, instead of > >> registering the slices in one stack. Also need to extract the > >> transformation for each slice in a stack. Any idea any plugin for this > >> purpose? Thanks! > >>> > >>> -- > >>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html > >> > >> > >> -- > >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html < > http://imagej.nih.gov/ij/list.html> > >> > > > > > > -- > > Truth Shall Make You Free > > > > -- > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html < > http://imagej.nih.gov/ij/list.html> > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- Truth Shall Make You Free -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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That is correct. All of the visualizations that I make using Dream3D are done in Paraview.
Mike > On Apr 1, 2020, at 12:06 PM, aget liang <[hidden email]> wrote: > > Thank you Mike, that's very helpful. I posted a question in the forum. Also > opened some examples, and realized that this software cannot visualize > output, right? so we have to use Paraview? > > On Wed, Apr 1, 2020 at 10:51 AM mike chapman <[hidden email]> > wrote: > >> There is a webinar introduction from a few years ago posted on youtube ( >> https://www.youtube.com/watch?v=CIYC1nPWb-g < >> https://www.youtube.com/watch?v=CIYC1nPWb-g>) which would be a good place >> to start that highlights how to use the software (there is a demo of using >> the software in the second half). >> >> There are some example pipelines if you go under bookmarks>prebuilt >> pipelines>Examples inside the gui >> >> There is also a forum ( >> https://groups.google.com/forum/#!forum/dream3d-users < >> https://groups.google.com/forum/#!forum/dream3d-users>) which may be >> useful. Mike Jackson (the lead on the software) is very responsive on the >> forum. >> >> Mike >> >>> On Apr 1, 2020, at 10:32 AM, aget liang <[hidden email]> wrote: >>> >>> Thanks Mike, I have installed the Dream.3D, but found it hard to start >>> with. The tutorial does not tell much about its use. Any suggestions >> about >>> where to find learning materials? Thank you! >>> >>> On Tue, Mar 31, 2020 at 10:56 AM mike chapman <[hidden email] >> <mailto:[hidden email]>> >>> wrote: >>> >>>> For registering multiple 3D stacks, I use another free program called >>>> Dream.3D (http://dream3d.bluequartz.net <http://dream3d.bluequartz.net/> >> <http://dream3d.bluequartz.net/ <http://dream3d.bluequartz.net/>>). >>>> I haven’t had much luck trying to do these types of registrations >> inside of >>>> ImageJ. >>>> >>>> Mike >>>> >>>>> On Mar 30, 2020, at 2:43 PM, Yajie Liang <[hidden email]> wrote: >>>>> >>>>> Thanks Mike for your reply. I may not describe the problem clear. The >>>> question is to register one 3d stack to another 3d stack, instead of >>>> registering the slices in one stack. Also need to extract the >>>> transformation for each slice in a stack. Any idea any plugin for this >>>> purpose? Thanks! >>>>> >>>>> -- >>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >>>> >>>> >>>> -- >>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html < >> http://imagej.nih.gov/ij/list.html> >>>> >>> >>> >>> -- >>> Truth Shall Make You Free >>> >>> -- >>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html < >> http://imagej.nih.gov/ij/list.html> >> >> -- >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >> > > > -- > Truth Shall Make You Free > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Got it, will dig it more; but in the meantime, I found "Correct 3D drift"
plugin of ImageJ could do nice 4D registration, though it only addresses translation at xy plane. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4166950/ On Wed, Apr 1, 2020 at 12:26 PM mike chapman <[hidden email]> wrote: > That is correct. All of the visualizations that I make using Dream3D are > done in Paraview. > > Mike > > > On Apr 1, 2020, at 12:06 PM, aget liang <[hidden email]> wrote: > > > > Thank you Mike, that's very helpful. I posted a question in the forum. > Also > > opened some examples, and realized that this software cannot visualize > > output, right? so we have to use Paraview? > > > > On Wed, Apr 1, 2020 at 10:51 AM mike chapman <[hidden email]> > > wrote: > > > >> There is a webinar introduction from a few years ago posted on youtube ( > >> https://www.youtube.com/watch?v=CIYC1nPWb-g < > >> https://www.youtube.com/watch?v=CIYC1nPWb-g>) which would be a good > place > >> to start that highlights how to use the software (there is a demo of > using > >> the software in the second half). > >> > >> There are some example pipelines if you go under bookmarks>prebuilt > >> pipelines>Examples inside the gui > >> > >> There is also a forum ( > >> https://groups.google.com/forum/#!forum/dream3d-users < > >> https://groups.google.com/forum/#!forum/dream3d-users>) which may be > >> useful. Mike Jackson (the lead on the software) is very responsive on > the > >> forum. > >> > >> Mike > >> > >>> On Apr 1, 2020, at 10:32 AM, aget liang <[hidden email]> wrote: > >>> > >>> Thanks Mike, I have installed the Dream.3D, but found it hard to start > >>> with. The tutorial does not tell much about its use. Any suggestions > >> about > >>> where to find learning materials? Thank you! > >>> > >>> On Tue, Mar 31, 2020 at 10:56 AM mike chapman <[hidden email] > >> <mailto:[hidden email]>> > >>> wrote: > >>> > >>>> For registering multiple 3D stacks, I use another free program called > >>>> Dream.3D (http://dream3d.bluequartz.net < > http://dream3d.bluequartz.net/> > >> <http://dream3d.bluequartz.net/ <http://dream3d.bluequartz.net/>>). > >>>> I haven’t had much luck trying to do these types of registrations > >> inside of > >>>> ImageJ. > >>>> > >>>> Mike > >>>> > >>>>> On Mar 30, 2020, at 2:43 PM, Yajie Liang <[hidden email]> > wrote: > >>>>> > >>>>> Thanks Mike for your reply. I may not describe the problem clear. The > >>>> question is to register one 3d stack to another 3d stack, instead of > >>>> registering the slices in one stack. Also need to extract the > >>>> transformation for each slice in a stack. Any idea any plugin for this > >>>> purpose? Thanks! > >>>>> > >>>>> -- > >>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html > >>>> > >>>> > >>>> -- > >>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html < > >> http://imagej.nih.gov/ij/list.html> > >>>> > >>> > >>> > >>> -- > >>> Truth Shall Make You Free > >>> > >>> -- > >>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html < > >> http://imagej.nih.gov/ij/list.html> > >> > >> -- > >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html > >> > > > > > > -- > > Truth Shall Make You Free > > > > -- > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- Truth Shall Make You Free -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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It might also be worth looking into BigStitcher (https://imagej.net/BigStitcher <https://imagej.net/BigStitcher>) I believe that it can multidimensional registrations, but I have never pushed it past 2D.
Mike > On Apr 1, 2020, at 2:00 PM, aget liang <[hidden email]> wrote: > > Got it, will dig it more; but in the meantime, I found "Correct 3D drift" > plugin of ImageJ could do nice 4D registration, though it only addresses > translation at xy plane. > https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4166950/ > > On Wed, Apr 1, 2020 at 12:26 PM mike chapman <[hidden email]> > wrote: > >> That is correct. All of the visualizations that I make using Dream3D are >> done in Paraview. >> >> Mike >> >>> On Apr 1, 2020, at 12:06 PM, aget liang <[hidden email]> wrote: >>> >>> Thank you Mike, that's very helpful. I posted a question in the forum. >> Also >>> opened some examples, and realized that this software cannot visualize >>> output, right? so we have to use Paraview? >>> >>> On Wed, Apr 1, 2020 at 10:51 AM mike chapman <[hidden email]> >>> wrote: >>> >>>> There is a webinar introduction from a few years ago posted on youtube ( >>>> https://www.youtube.com/watch?v=CIYC1nPWb-g < >>>> https://www.youtube.com/watch?v=CIYC1nPWb-g>) which would be a good >> place >>>> to start that highlights how to use the software (there is a demo of >> using >>>> the software in the second half). >>>> >>>> There are some example pipelines if you go under bookmarks>prebuilt >>>> pipelines>Examples inside the gui >>>> >>>> There is also a forum ( >>>> https://groups.google.com/forum/#!forum/dream3d-users < >>>> https://groups.google.com/forum/#!forum/dream3d-users>) which may be >>>> useful. Mike Jackson (the lead on the software) is very responsive on >> the >>>> forum. >>>> >>>> Mike >>>> >>>>> On Apr 1, 2020, at 10:32 AM, aget liang <[hidden email]> wrote: >>>>> >>>>> Thanks Mike, I have installed the Dream.3D, but found it hard to start >>>>> with. The tutorial does not tell much about its use. Any suggestions >>>> about >>>>> where to find learning materials? Thank you! >>>>> >>>>> On Tue, Mar 31, 2020 at 10:56 AM mike chapman <[hidden email] >>>> <mailto:[hidden email]>> >>>>> wrote: >>>>> >>>>>> For registering multiple 3D stacks, I use another free program called >>>>>> Dream.3D (http://dream3d.bluequartz.net < >> http://dream3d.bluequartz.net/> >>>> <http://dream3d.bluequartz.net/ <http://dream3d.bluequartz.net/>>). >>>>>> I haven’t had much luck trying to do these types of registrations >>>> inside of >>>>>> ImageJ. >>>>>> >>>>>> Mike >>>>>> >>>>>>> On Mar 30, 2020, at 2:43 PM, Yajie Liang <[hidden email]> >> wrote: >>>>>>> >>>>>>> Thanks Mike for your reply. I may not describe the problem clear. The >>>>>> question is to register one 3d stack to another 3d stack, instead of >>>>>> registering the slices in one stack. Also need to extract the >>>>>> transformation for each slice in a stack. Any idea any plugin for this >>>>>> purpose? Thanks! >>>>>>> >>>>>>> -- >>>>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >>>>>> >>>>>> >>>>>> -- >>>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html < >>>> http://imagej.nih.gov/ij/list.html> >>>>>> >>>>> >>>>> >>>>> -- >>>>> Truth Shall Make You Free >>>>> >>>>> -- >>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html < >>>> http://imagej.nih.gov/ij/list.html> >>>> >>>> -- >>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >>>> >>> >>> >>> -- >>> Truth Shall Make You Free >>> >>> -- >>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >> >> -- >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >> > > > -- > Truth Shall Make You Free > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Hi Mike, get some updates on this question: I have figured out that Correct
3D drift could correct shifts along xy or z. now it works fine. I should have used high quality test dataset in the beginning:) So you could give it try for registrating multiple timepoints z stacks On Wed, Apr 1, 2020 at 2:07 PM mike chapman <[hidden email]> wrote: > It might also be worth looking into BigStitcher ( > https://imagej.net/BigStitcher <https://imagej.net/BigStitcher>) I > believe that it can multidimensional registrations, but I have never pushed > it past 2D. > > Mike > > > On Apr 1, 2020, at 2:00 PM, aget liang <[hidden email]> wrote: > > > > Got it, will dig it more; but in the meantime, I found "Correct 3D drift" > > plugin of ImageJ could do nice 4D registration, though it only addresses > > translation at xy plane. > > https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4166950/ > > > > On Wed, Apr 1, 2020 at 12:26 PM mike chapman <[hidden email]> > > wrote: > > > >> That is correct. All of the visualizations that I make using Dream3D > are > >> done in Paraview. > >> > >> Mike > >> > >>> On Apr 1, 2020, at 12:06 PM, aget liang <[hidden email]> wrote: > >>> > >>> Thank you Mike, that's very helpful. I posted a question in the forum. > >> Also > >>> opened some examples, and realized that this software cannot visualize > >>> output, right? so we have to use Paraview? > >>> > >>> On Wed, Apr 1, 2020 at 10:51 AM mike chapman <[hidden email]> > >>> wrote: > >>> > >>>> There is a webinar introduction from a few years ago posted on > youtube ( > >>>> https://www.youtube.com/watch?v=CIYC1nPWb-g < > >>>> https://www.youtube.com/watch?v=CIYC1nPWb-g>) which would be a good > >> place > >>>> to start that highlights how to use the software (there is a demo of > >> using > >>>> the software in the second half). > >>>> > >>>> There are some example pipelines if you go under bookmarks>prebuilt > >>>> pipelines>Examples inside the gui > >>>> > >>>> There is also a forum ( > >>>> https://groups.google.com/forum/#!forum/dream3d-users < > >>>> https://groups.google.com/forum/#!forum/dream3d-users>) which may be > >>>> useful. Mike Jackson (the lead on the software) is very responsive on > >> the > >>>> forum. > >>>> > >>>> Mike > >>>> > >>>>> On Apr 1, 2020, at 10:32 AM, aget liang <[hidden email]> wrote: > >>>>> > >>>>> Thanks Mike, I have installed the Dream.3D, but found it hard to > start > >>>>> with. The tutorial does not tell much about its use. Any suggestions > >>>> about > >>>>> where to find learning materials? Thank you! > >>>>> > >>>>> On Tue, Mar 31, 2020 at 10:56 AM mike chapman < > [hidden email] > >>>> <mailto:[hidden email]>> > >>>>> wrote: > >>>>> > >>>>>> For registering multiple 3D stacks, I use another free program > called > >>>>>> Dream.3D (http://dream3d.bluequartz.net < > >> http://dream3d.bluequartz.net/> > >>>> <http://dream3d.bluequartz.net/ <http://dream3d.bluequartz.net/>>). > >>>>>> I haven’t had much luck trying to do these types of registrations > >>>> inside of > >>>>>> ImageJ. > >>>>>> > >>>>>> Mike > >>>>>> > >>>>>>> On Mar 30, 2020, at 2:43 PM, Yajie Liang <[hidden email]> > >> wrote: > >>>>>>> > >>>>>>> Thanks Mike for your reply. I may not describe the problem clear. > The > >>>>>> question is to register one 3d stack to another 3d stack, instead of > >>>>>> registering the slices in one stack. Also need to extract the > >>>>>> transformation for each slice in a stack. Any idea any plugin for > this > >>>>>> purpose? Thanks! > >>>>>>> > >>>>>>> -- > >>>>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html > >>>>>> > >>>>>> > >>>>>> -- > >>>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html < > >>>> http://imagej.nih.gov/ij/list.html> > >>>>>> > >>>>> > >>>>> > >>>>> -- > >>>>> Truth Shall Make You Free > >>>>> > >>>>> -- > >>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html < > >>>> http://imagej.nih.gov/ij/list.html> > >>>> > >>>> -- > >>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html > >>>> > >>> > >>> > >>> -- > >>> Truth Shall Make You Free > >>> > >>> -- > >>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html > >> > >> -- > >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html > >> > > > > > > -- > > Truth Shall Make You Free > > > > -- > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- Truth Shall Make You Free -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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