cell image analyzer
Locked
 
|
Dear all,
The cell image analyzer described in Baeker and Travo seems to be a very interesting interface, which I would very much like to use for comparing intensity ratios. I downloaded the MRI-toolbox, but it did not have an extension. I tried several things -naming it as a .jar file and trying to run it (not valid/or no main method) -naming it as a .jar file and placing it in the plugin directory of ImageJ -naming it as a .class file and trying to compile and run it None of the above worked. Is the package already avaible for use? The name is 'mri-toolbox-imagejconf-edition', so it ocurret to me that it might just be put online for demo purposes. Any information about the 'cell image analyzer' would be appreciated very much. Greetings, Edwin Commandeur P.S. I don't want to be annoying, but I find the name MRI-toolbox a bit confusing, given that MRI reminds me of magnetic reasonance imaging. |
|
|
Dear all,
According to the Linux console 'file' commando, the file 'mri-toolbox-imagejconf-edition' (which is the file you get when you extract the 'mri-toolbox-imagejconf-edition.zip' download) is a POSIX tar archive. On Linux it can be untarred by doing: tar --extract --file=mri-toolbox-imagejconf-edition On windows I just had to add .tar to the filename and then it was noticed by WinRAR, and easy to extract using WinRAR additions to the right click menu. (by the way: TugZIP will also do the job and is free) The file 'mri-toolbox-imagejconf-edition' contained another 4 zip files: MRI_LookupTableTool.zip MRI_SlideShowControl.zip MRI_Toolbox.zip MRI_VisualScripting.zip These zip files contained the eventual plugins and help files. That way I had to uncompress 3 times (easy when you know it). When I renamed the 'mri-toolbox-imagejconf-edition' to 'mri-toolbox-imagejconf-edition.zip' (after deleting the zip file I downloaded) I could also extract the file, but in that case I did not got 4 zip files, but a five directories, and a html file 'About MRI Cell Image Analyzer.html'. The five directories are: _applications _help _lut _operations plugins It could well be that this is the way the authors intended the file to be uncompressed. Greetings, Edwin > Dear all, > > The cell image analyzer described in Baeker and Travo seems > to be a very interesting interface, which I would very much > like to use for comparing intensity ratios. > > I downloaded the MRI-toolbox, but it did not have an > extension. I tried several things > > -naming it as a .jar file and trying to run it (not valid/or > no main method) > -naming it as a .jar file and placing it in the plugin > directory of ImageJ > -naming it as a .class file and trying to compile and run it > > None of the above worked. Is the package already avaible for > use? The name is 'mri-toolbox-imagejconf-edition', so it > ocurret to me that it might just be put online for demo > purposes. > > Any information about the 'cell image analyzer' would be > appreciated very much. > > Greetings, > Edwin Commandeur > > P.S. I don't want to be annoying, but I find the name > MRI-toolbox a bit confusing, given that MRI reminds me of > magnetic reasonance imaging. > |
|
|
Hello,
you are right for the name. Our imaging facility is called Montpellier RIO Imaging (short MRI). And magnetic resonance imaging is IRM in French. We recognized the possible confusion with ourselves, but it is too late to change now. Did you get it to run? You should unzip the zip-files in the ImageJ base folder. You can find some further information on http://www.mri.cnrs.fr/mriwiki/index.php?pagename=Links%20and%20Readings I'll try to fix the archive on the ImageJ documentation wiki and write some installation instructions, as well. I've you have any questions, don't hesitate to ask me. Volker Commandeur a écrit : > Dear all, > > According to the Linux console 'file' commando, the file > 'mri-toolbox-imagejconf-edition' (which is the file you get > when you extract the 'mri-toolbox-imagejconf-edition.zip' > download) is a POSIX tar archive. > > On Linux it can be untarred by doing: > tar --extract --file=mri-toolbox-imagejconf-edition > > On windows I just had to add .tar to the filename and then > it was noticed by WinRAR, and easy to extract using WinRAR > additions to the right click menu. (by the way: TugZIP will > also do the job and is free) > > The file 'mri-toolbox-imagejconf-edition' contained another > 4 zip files: > MRI_LookupTableTool.zip > MRI_SlideShowControl.zip > MRI_Toolbox.zip > MRI_VisualScripting.zip > > These zip files contained the eventual plugins and help files. > > That way I had to uncompress 3 times (easy when you know it). > > When I renamed the 'mri-toolbox-imagejconf-edition' to > 'mri-toolbox-imagejconf-edition.zip' (after deleting the zip > file I downloaded) I could also extract the file, but in > that case I did not got 4 zip files, but a five directories, > and a html file 'About MRI Cell Image Analyzer.html'. The > five directories are: > > _applications > _help > _lut > _operations > plugins > > It could well be that this is the way the authors intended > the file to be uncompressed. > > Greetings, > Edwin > > > > > > > >> Dear all, >> >> The cell image analyzer described in Baeker and Travo seems >> to be a very interesting interface, which I would very much >> like to use for comparing intensity ratios. >> >> I downloaded the MRI-toolbox, but it did not have an >> extension. I tried several things >> >> -naming it as a .jar file and trying to run it (not valid/or >> no main method) >> -naming it as a .jar file and placing it in the plugin >> directory of ImageJ >> -naming it as a .class file and trying to compile and run it >> >> None of the above worked. Is the package already avaible for >> use? The name is 'mri-toolbox-imagejconf-edition', so it >> ocurret to me that it might just be put online for demo >> purposes. >> >> Any information about the 'cell image analyzer' would be >> appreciated very much. >> >> Greetings, >> Edwin Commandeur >> >> P.S. I don't want to be annoying, but I find the name >> MRI-toolbox a bit confusing, given that MRI reminds me of >> magnetic reasonance imaging. >> >> > > -- passerelle antivirus du campus CNRS de Montpellier -- |
|
|
Hello Volker,
Thank you for the kind reply. Once I had the MRI-toolbox unzipped I indeed got it to work. It did matter how I unzipped it for the files that I managed to extract. Only by untarring I got the four zip files I mentioned earlier. By unzipping (after changing the extension to .zip in windows) I got the directories as mentioned, but I could not find the MRI Tools palette jar and other files, so it seems to matter how the files are extracted. Also a lot of thanks for the url, which I had not found by googling. The 'compare intensities' applications were the kind of applications I was looking for. I will try them out and will contact you if I still have questions after that. A big thanks to all who worked on the cell image analyzer. ImageJ keeps on surprising me with all the functionality that is available for it. Greetings, Edwin Volker Bäcker schreef: > Hello, > > you are right for the name. Our imaging facility is called Montpellier > RIO Imaging (short MRI). > And magnetic resonance imaging is IRM in French. We recognized the > possible confusion with > ourselves, but it is too late to change now. > > Did you get it to run? You should unzip the zip-files in the ImageJ base > folder. > You can find some further information on > http://www.mri.cnrs.fr/mriwiki/index.php?pagename=Links%20and%20Readings > > I'll try to fix the archive on the ImageJ documentation wiki and write > some installation instructions, as well. > I've you have any questions, don't hesitate to ask me. > > Volker > > > Commandeur a écrit : >> Dear all, >> >> According to the Linux console 'file' commando, the file >> 'mri-toolbox-imagejconf-edition' (which is the file you get >> when you extract the 'mri-toolbox-imagejconf-edition.zip' >> download) is a POSIX tar archive. >> >> On Linux it can be untarred by doing: >> tar --extract --file=mri-toolbox-imagejconf-edition >> >> On windows I just had to add .tar to the filename and then >> it was noticed by WinRAR, and easy to extract using WinRAR >> additions to the right click menu. (by the way: TugZIP will >> also do the job and is free) >> >> The file 'mri-toolbox-imagejconf-edition' contained another >> 4 zip files: >> MRI_LookupTableTool.zip >> MRI_SlideShowControl.zip >> MRI_Toolbox.zip >> MRI_VisualScripting.zip >> >> These zip files contained the eventual plugins and help files. >> >> That way I had to uncompress 3 times (easy when you know it). >> >> When I renamed the 'mri-toolbox-imagejconf-edition' to >> 'mri-toolbox-imagejconf-edition.zip' (after deleting the zip >> file I downloaded) I could also extract the file, but in >> that case I did not got 4 zip files, but a five directories, >> and a html file 'About MRI Cell Image Analyzer.html'. The >> five directories are: >> >> _applications >> _help >> _lut >> _operations >> plugins >> >> It could well be that this is the way the authors intended >> the file to be uncompressed. >> >> Greetings, >> Edwin >> >> >> >> >> >> >> >>> Dear all, >>> >>> The cell image analyzer described in Baeker and Travo seems >>> to be a very interesting interface, which I would very much >>> like to use for comparing intensity ratios. >>> >>> I downloaded the MRI-toolbox, but it did not have an >>> extension. I tried several things >>> >>> -naming it as a .jar file and trying to run it (not valid/or >>> no main method) >>> -naming it as a .jar file and placing it in the plugin >>> directory of ImageJ >>> -naming it as a .class file and trying to compile and run it >>> >>> None of the above worked. Is the package already avaible for >>> use? The name is 'mri-toolbox-imagejconf-edition', so it >>> ocurret to me that it might just be put online for demo >>> purposes. >>> Any information about the 'cell image analyzer' would be >>> appreciated very much. >>> Greetings, >>> Edwin Commandeur >>> >>> P.S. I don't want to be annoying, but I find the name >>> MRI-toolbox a bit confusing, given that MRI reminds me of >>> magnetic reasonance imaging. >>> >>> >> >> > |
|
|
In reply to this post by Volker Baecker
Hello,
It also seems I downloaded the MRI toolbox from the wrong place. I downloaded the MRI toolbox from: http://imagejdocu.tudor.lu/imagej-documenation-wiki/plugins/mri-cell-image-analyzer That is the first url that pops up when googling on 'cell image analyzer'. It shows how googling can be deceptive at times. In the url Volker gave in his mail there is a download to the complete MRI Cell Image analyzer, that I now realize is not just a plugin, but a complete wrapper around ImageJ, adding all kinds of functionality. So I should have gone to: http://www.mri.cnrs.fr/mriwiki/uploads/download-mri-cia.htm The zip files on that page work just fine! Greetings, Edwin Volker Bäcker schreef: > Hello, > > you are right for the name. Our imaging facility is called Montpellier > RIO Imaging (short MRI). > And magnetic resonance imaging is IRM in French. We recognized the > possible confusion with > ourselves, but it is too late to change now. > > Did you get it to run? You should unzip the zip-files in the ImageJ base > folder. > You can find some further information on > http://www.mri.cnrs.fr/mriwiki/index.php?pagename=Links%20and%20Readings > > I'll try to fix the archive on the ImageJ documentation wiki and write > some installation instructions, as well. > I've you have any questions, don't hesitate to ask me. > > Volker > |
«
Return to ImageJ
|
1 view|%1 views
| Free forum by Nabble | Edit this page |