Re: Fiji _is_ "conventional ImageJ", was Make images overlap
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Re: Fiji _is_ "conventional ImageJ", was Make images overlap
 
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Hi Joel and all,
On Jun 13, 2011, at 6:00 AM, IMAGEJ automatic digest system wrote: > Date: Sun, 12 Jun 2011 21:48:29 -0400 > From: "JOEL B. SHEFFIELD" <[hidden email]> > Subject: Re: Make images overlap > > It should also be possible to use the "Turbo Reg" plugin in conventional > ImageJ. You can search for it on the plugins page. But the point is, you dont need to bother to look for it, download it and install it manually. Just download fiji, update it and the latest StackReg version is already there ;-) Fiji is _not_ a competitor for ImageJ: Fiji IS just imageJ, with a bunch of stuff added on to make it nicer to use, eg the updater and much more. The same people all work together on ImageJ, ImageJA, ImageJ2, imglib and Fiji If anyone has a good reason to use plain ImageJ instead of the Fiji "distribution" of imageJ (that would be like building your own car from scratch, instead of buying a finished one) then we would really like to find out how and why, so we in the Fiji team can provide an ImageJ distribution that you _will_ use. cheers Dan > > Joel > > > On Sun, Jun 12, 2011 at 5:45 PM, Stephan Saalfeld <[hidden email]>wrote: > >> Hi Tomas, >> >> using Fiji, you have at least two options: >> >> 1. >> Open both images and mark corresponding points in both using the point >> selection tool (index number must match) and use the plugin: >> >> http://pacific.mpi-cbg.de/wiki/index.php/Landmark_Correspondences >> >> to map one image into the other using a transformation model of your >> choice (translation + rotation is rigid). >> >> >> 2. >> Import the slides into TrakEM2 and use either of the manual >> alignment/transformation modes. That is less trivial in terms of the >> learning the program and less easy to script but provides a much nicer >> user interface (interactive overlay supporting various overlay modes). >> The underlying engine is the same: >> >> http://www.ini.uzh.ch/~acardona/trakem2_manual.html#transform_patch >> >> http://www.ini.uzh.ch/~acardona/trakem2_manual.html#landmarks >> >> Good luck and best regards, >> Stephan >> > Dr. Daniel James White BSc. (Hons.) PhD Senior Microscopist / Image Processing and Analysis Light Microscopy Facility Max Planck Institute of Molecular Cell Biology and Genetics Pfotenhauerstrasse 108 01307 DRESDEN Germany +49 (0)15114966933 (German Mobile) +49 (0)351 210 2627 (Work phone at MPI-CBG) +49 (0)351 210 1078 (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 [hidden email] ( [hidden email] ) |
Fiji _is_ "conventional ImageJ", was Make images overlap
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From: JOEL B. SHEFFIELD <[hidden email]>
Date: Mon, Jun 13, 2011 at 10:23 AM Subject: Re: Fiji _is_ "conventional ImageJ", was Make images overlap To: Dan White <[hidden email]> Hi Dan, and the rest of the dedicated Fiji project contributors, I certainly appreciate the work that you all have done in making ImageJ more convenient. I apologize for my poor choice of words --perhaps I should have said "original", although that would ignore all of the upgrades, etc. My thought in posting was that I have the impression that there are many users who are, indeed, using the non-Fiji version, and who may still be interested in specific projects that require a given plugin. For many new users, especially, "ImageJ" means the program that is downloaded from rsb.nih.gov, or imagej.nih.gov, since that is where Google leads them. Joel On Mon, Jun 13, 2011 at 6:13 AM, Dan White <[hidden email]> wrote: > Hi Joel and all, > > > On Jun 13, 2011, at 6:00 AM, IMAGEJ automatic digest system wrote: > > > Date: Sun, 12 Jun 2011 21:48:29 -0400 > > From: "JOEL B. SHEFFIELD" <[hidden email]> > > Subject: Re: Make images overlap > > > > It should also be possible to use the "Turbo Reg" plugin in conventional > > ImageJ. You can search for it on the plugins page. > > But the point is, you dont need to bother to look for it, download it and > install it manually. > > Just download fiji, update it and the latest StackReg version is already > there ;-) > > Fiji is _not_ a competitor for ImageJ: > Fiji IS just imageJ, with a bunch of stuff added on to make it nicer to > use, > eg the updater and much more. > > The same people all work together on ImageJ, ImageJA, ImageJ2, imglib and > Fiji > > If anyone has a good reason to use plain ImageJ instead of the > Fiji "distribution" of imageJ > (that would be like building your own car from scratch, instead of buying a > finished one) > then we would really like to find out how and why, > so we in the Fiji team can provide an ImageJ distribution that you _will_ > use. > > cheers > > Dan > > > > > > > Joel > > > > > > On Sun, Jun 12, 2011 at 5:45 PM, Stephan Saalfeld <[hidden email] > >wrote: > > > >> Hi Tomas, > >> > >> using Fiji, you have at least two options: > >> > >> 1. > >> Open both images and mark corresponding points in both using the point > >> selection tool (index number must match) and use the plugin: > >> > >> http://pacific.mpi-cbg.de/wiki/index.php/Landmark_Correspondences > >> > >> to map one image into the other using a transformation model of your > >> choice (translation + rotation is rigid). > >> > >> > >> 2. > >> Import the slides into TrakEM2 and use either of the manual > >> alignment/transformation modes. That is less trivial in terms of the > >> learning the program and less easy to script but provides a much nicer > >> user interface (interactive overlay supporting various overlay modes). > >> The underlying engine is the same: > >> > >> http://www.ini.uzh.ch/~acardona/trakem2_manual.html#transform_patch > >> > >> http://www.ini.uzh.ch/~acardona/trakem2_manual.html#landmarks > >> > >> Good luck and best regards, > >> Stephan > >> > > > > Dr. Daniel James White BSc. (Hons.) PhD > Senior Microscopist / Image Processing and Analysis > Light Microscopy Facility > Max Planck Institute of Molecular Cell Biology and Genetics > Pfotenhauerstrasse 108 > 01307 DRESDEN > Germany > > +49 (0)15114966933 (German Mobile) > +49 (0)351 210 2627 (Work phone at MPI-CBG) > +49 (0)351 210 1078 (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 > [hidden email] > ( [hidden email] ) > > > > > > > -- Joel B. Sheffield, Ph.D Department of Biology Temple University Philadelphia, PA 19122 Voice: 215 204 8839 e-mail: [hidden email] URL: http://astro.temple.edu/~jbs -- Joel B. Sheffield, Ph.D Department of Biology Temple University Philadelphia, PA 19122 Voice: 215 204 8839 e-mail: [hidden email] URL: http://astro.temple.edu/~jbs |
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Hi everyone,
My thought in posting was that I have the impression that there are many > users who are, indeed, using the non-Fiji version, and who may still be > interested in specific projects that require a given plugin. For many new > users, especially, "ImageJ" means the program that is downloaded from > rsb.nih.gov, or imagej.nih.gov, since that is where Google leads them. > Difficulty with the ImageJ "alphabet soup" of names is understandable, given how many relevant projects there are within the ImageJ community. We recently posted a FAQ question to help people understand the difference between the names: http://imagejdev.org/faq#n141 That said, we hope to reduce the confusion with the release of ImageJ2 later this fall. We are working toward an IJ2 that includes an automatic update feature (adopted from Fiji) that allows people to host their own plugin sites. Users can then select plugins for installation from known update sites, rather than manually searching, downloading and installing them—though the manual install will still be possible too, of course. Once IJ2 has built-in support for automatic updates, the current "Fiji" suite of plugins can become available through one or more update sites. If someone then tells you (e.g.) "I got my result with TrakEM2" then you can just choose "Add plugin" from the IJ2 menu, click the Fiji update site, and select TrakEM2 from the list to add it. There will likely continue to be a standalone Fiji program available from the Fiji web site, but our goal is for it to be exactly the same as a copy of ImageJ2 with all the Fiji plugins pre-installed. As always, there are some technical challenges to making this vision into a reality, but it is very doable, and the ImageJDev and Fiji developers will be working together to make it happen. Regards, Curtis Rueden ImageJDev project lead http://imagejdev.org/ On Mon, Jun 13, 2011 at 9:49 AM, JOEL B. SHEFFIELD <[hidden email]> wrote: > From: JOEL B. SHEFFIELD <[hidden email]> > Date: Mon, Jun 13, 2011 at 10:23 AM > Subject: Re: Fiji _is_ "conventional ImageJ", was Make images overlap > To: Dan White <[hidden email]> > > > Hi Dan, and the rest of the dedicated Fiji project contributors, > > I certainly appreciate the work that you all have done in making ImageJ > more > convenient. I apologize for my poor choice of words --perhaps I should > have said "original", although that would ignore all of the upgrades, etc. > > My thought in posting was that I have the impression that there are many > users who are, indeed, using the non-Fiji version, and who may still be > interested in specific projects that require a given plugin. For many new > users, especially, "ImageJ" means the program that is downloaded from > rsb.nih.gov, or imagej.nih.gov, since that is where Google leads them. > > > Joel > > > On Mon, Jun 13, 2011 at 6:13 AM, Dan White <[hidden email]> wrote: > > > Hi Joel and all, > > > > > > On Jun 13, 2011, at 6:00 AM, IMAGEJ automatic digest system wrote: > > > > > Date: Sun, 12 Jun 2011 21:48:29 -0400 > > > From: "JOEL B. SHEFFIELD" <[hidden email]> > > > Subject: Re: Make images overlap > > > > > > It should also be possible to use the "Turbo Reg" plugin in > conventional > > > ImageJ. You can search for it on the plugins page. > > > > But the point is, you dont need to bother to look for it, download it and > > install it manually. > > > > Just download fiji, update it and the latest StackReg version is already > > there ;-) > > > > Fiji is _not_ a competitor for ImageJ: > > Fiji IS just imageJ, with a bunch of stuff added on to make it nicer to > > use, > > eg the updater and much more. > > > > The same people all work together on ImageJ, ImageJA, ImageJ2, imglib and > > Fiji > > > > If anyone has a good reason to use plain ImageJ instead of the > > Fiji "distribution" of imageJ > > (that would be like building your own car from scratch, instead of buying > a > > finished one) > > then we would really like to find out how and why, > > so we in the Fiji team can provide an ImageJ distribution that you _will_ > > use. > > > > cheers > > > > Dan > > > > > > > > > > > > Joel > > > > > > > > > On Sun, Jun 12, 2011 at 5:45 PM, Stephan Saalfeld <[hidden email] > > >wrote: > > > > > >> Hi Tomas, > > >> > > >> using Fiji, you have at least two options: > > >> > > >> 1. > > >> Open both images and mark corresponding points in both using the point > > >> selection tool (index number must match) and use the plugin: > > >> > > >> http://pacific.mpi-cbg.de/wiki/index.php/Landmark_Correspondences > > >> > > >> to map one image into the other using a transformation model of your > > >> choice (translation + rotation is rigid). > > >> > > >> > > >> 2. > > >> Import the slides into TrakEM2 and use either of the manual > > >> alignment/transformation modes. That is less trivial in terms of the > > >> learning the program and less easy to script but provides a much nicer > > >> user interface (interactive overlay supporting various overlay modes). > > >> The underlying engine is the same: > > >> > > >> http://www.ini.uzh.ch/~acardona/trakem2_manual.html#transform_patch > > >> > > >> http://www.ini.uzh.ch/~acardona/trakem2_manual.html#landmarks > > >> > > >> Good luck and best regards, > > >> Stephan > > >> > > > > > > > Dr. Daniel James White BSc. (Hons.) PhD > > Senior Microscopist / Image Processing and Analysis > > Light Microscopy Facility > > Max Planck Institute of Molecular Cell Biology and Genetics > > Pfotenhauerstrasse 108 > > 01307 DRESDEN > > Germany > > > > +49 (0)15114966933 (German Mobile) > > +49 (0)351 210 2627 (Work phone at MPI-CBG) > > +49 (0)351 210 1078 (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 > > [hidden email] > > ( [hidden email] ) > > > > > > > > > > > > > > > > > -- > > > Joel B. Sheffield, Ph.D > Department of Biology > Temple University > Philadelphia, PA 19122 > Voice: 215 204 8839 > e-mail: [hidden email] > URL: http://astro.temple.edu/~jbs > > > > > -- > > > Joel B. Sheffield, Ph.D > Department of Biology > Temple University > Philadelphia, PA 19122 > Voice: 215 204 8839 > e-mail: [hidden email] > URL: http://astro.temple.edu/~jbs > |
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Hi,
On Mon, 13 Jun 2011, Curtis Rueden wrote: > > My thought in posting was that I have the impression that there are > > many users who are, indeed, using the non-Fiji version, and who may > > still be interested in specific projects that require a given plugin. > > For many new users, especially, "ImageJ" means the program that is > > downloaded from rsb.nih.gov, or imagej.nih.gov, since that is where > > Google leads them. Right, but then, Fiji was created to make it unnecessary to download things from multiple sites (and still end up with obsolete versions of plugins, because you looked in the wrong place). > Difficulty with the ImageJ "alphabet soup" of names is understandable, > given how many relevant projects there are within the ImageJ community. > We recently posted a FAQ question to help people understand the > difference between the names: > > http://imagejdev.org/faq#n141 > > That said, we hope to reduce the confusion with the release of ImageJ2 > later this fall. We are working toward an IJ2 that includes an automatic > update feature (adopted from Fiji) that allows people to host their own > plugin sites. taking away a lot of the repetitive, cumbersome discussions revolving around "I want ImageJ, not Fiji! -- But you want easy, right? So download Fiji. -- But I don't want to!" :-) So: just to state it once more, in crystal-clear words: Fiji does not want to compete with ImageJ. Fiji wants to make ImageJ easier to use for people who do not want to learn e.g. what a "heap" is. The work on Fiji has been made slightly tedious by the insistence of some that there is a huge difference between the two projects when it is not. That was never the intention of Fiji. But those problems not stop us (at least yours truly) from continuing to work on making the two projects converge (but I admit that I spent more time on working toward that goal than to refute the misconceptions). The real difference between Fiji and ImageJ is actually in the subtitle "batteries included". If you want to go to the shop and buy the appropriate batteries, sure, go ahead. But if you don't want to need to care which types of batteries are needed, if you are more interested in playing with the toy right away, just take the package that has "batteries included". > Users can then select plugins for installation from known update sites, > rather than manually searching, downloading and installing them—though > the manual install will still be possible too, of course. > > Once IJ2 has built-in support for automatic updates, the current "Fiji" > suite of plugins can become available through one or more update sites. > If someone then tells you (e.g.) "I got my result with TrakEM2" then you > can just choose "Add plugin" from the IJ2 menu, click the Fiji update > site, and select TrakEM2 from the list to add it. We still have to figure out how we want to handle the difference with the Fiji launcher (which is still required in order to update plugins). But eventually everybody will benefit from Fiji -- even the ones clinging to the name "ImageJ" :-) > There will likely continue to be a standalone Fiji program available > from the Fiji web site, but our goal is for it to be exactly the same as > a copy of ImageJ2 with all the Fiji plugins pre-installed. > > As always, there are some technical challenges to making this vision > into a reality, but it is very doable, and the ImageJDev and Fiji > developers will be working together to make it happen. The good thing is that the ImageJ2 and Fiji developers share that common vision (even if users are often fully unaware). And soon, we will also share some office space, too :-) Ciao, Johannes |
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