Problem opening Leica SP1 .lei file
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Problem opening Leica SP1 .lei file
 
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Hi all
I tried to open someone else's images taken on a Leica SP1 confocal microscope by dragging and dropping the .lei file (which describes the imaging session) onto ImageJ, but I got an error that the directory couldn't be found - it looked as though the plugin was duplicating the directory name string then confusing itself by looking for ~/images/directory_1directory_1/ instead of just ~/images/directory_1/ I don't have access to the images right now so can't give exact details of the error message. Can anyone else confirm this behaviour? This is ij 1.41e on 32-bit Ubuntu 8.04, using the IJ-bundled JRE. Mike |
Re: Problem opening Leica SP1 .lei file
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I have had the same problem on our system. It may be
something that happened in one of the IJ upgrades. Joel ---- Original message ---- >Date: Fri, 20 Jun 2008 09:30:49 +0100 >From: Michael Doube <[hidden email]> >Subject: Problem opening Leica SP1 .lei file >To: [hidden email] > >Hi all > >I tried to open someone else's images taken on a Leica SP1 confocal >microscope by dragging and dropping the .lei file (which describes the >imaging session) onto ImageJ, but I got an error that the directory >couldn't be found - it looked as though the plugin was duplicating the >directory name string then confusing itself by looking for >~/images/directory_1directory_1/ instead of just ~/images/directory_1/ > >I don't have access to the images right now so can't give exact details >of the error message. Can anyone else confirm this behaviour? > >This is ij 1.41e on 32-bit Ubuntu 8.04, using the IJ-bundled JRE. > >Mike Joel B. Sheffield Professor, Department of Biology Temple University Philadelphia, PA 19122 [hidden email] http://astro.temple.edu/~jbs |
Re: Problem opening Leica SP1 .lei file
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In reply to this post by Michael Doube
Mike,
a very general answer, but: did you try the Bio-Formats plugin? Michael Michael Doube wrote: > Hi all > > I tried to open someone else's images taken on a Leica SP1 confocal > microscope by dragging and dropping the .lei file (which describes the > imaging session) onto ImageJ, but I got an error that the directory > couldn't be found - it looked as though the plugin was duplicating the > directory name string then confusing itself by looking for > ~/images/directory_1directory_1/ instead of just ~/images/directory_1/ > > I don't have access to the images right now so can't give exact details > of the error message. Can anyone else confirm this behaviour? > > This is ij 1.41e on 32-bit Ubuntu 8.04, using the IJ-bundled JRE. > > Mike |
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Hi,
I am not sure, but I thought ImageJ did not support reading LEI files without the Bio-Formats plugin. So I'm guessing Mike & Joel have Bio-Formats installed, and ImageJ is calling it when they drag and drop? If so, then I'm guessing there is a bug in Bio-Formats with LEI, in which case I would be glad to fix the problem, if someone can send me a stack trace and/or sample data that demonstrates the problem. -Curtis On Fri, Jun 20, 2008 at 3:04 PM, Michael Weber <[hidden email]> wrote: > Mike, > > a very general answer, but: did you try the Bio-Formats plugin? > > Michael > > > > Michael Doube wrote: > >> Hi all >> >> I tried to open someone else's images taken on a Leica SP1 confocal >> microscope by dragging and dropping the .lei file (which describes the >> imaging session) onto ImageJ, but I got an error that the directory couldn't >> be found - it looked as though the plugin was duplicating the directory name >> string then confusing itself by looking for ~/images/directory_1directory_1/ >> instead of just ~/images/directory_1/ >> >> I don't have access to the images right now so can't give exact details of >> the error message. Can anyone else confirm this behaviour? >> >> This is ij 1.41e on 32-bit Ubuntu 8.04, using the IJ-bundled JRE. >> >> Mike >> > |
Re: Problem opening Leica SP1 .lei file
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In reply to this post by Michael Weber-4
Michael, Curtis
I just used IJ in its 'natural' state, without the Bio-Formats plugin - actually very freshly installed straight from Wayne's website, no extra plugins added and running the jre from the ImageJ subdirectory. It looked as though IJ was handling the .lei file but was stopped by a bug which meant it couldn't find the images that the .lei referred to. I will see if I can get permission to send the files through to you Curtis. Mike Michael Weber wrote: > Mike, > > a very general answer, but: did you try the Bio-Formats plugin? > > Michael > > > Michael Doube wrote: >> Hi all >> >> I tried to open someone else's images taken on a Leica SP1 confocal >> microscope by dragging and dropping the .lei file (which describes >> the imaging session) onto ImageJ, but I got an error that the >> directory couldn't be found - it looked as though the plugin was >> duplicating the directory name string then confusing itself by >> looking for ~/images/directory_1directory_1/ instead of just >> ~/images/directory_1/ >> >> I don't have access to the images right now so can't give exact >> details of the error message. Can anyone else confirm this behaviour? >> >> This is ij 1.41e on 32-bit Ubuntu 8.04, using the IJ-bundled JRE. >> >> Mike -- Michael Doube BPhil BVSc PhD MRCVS Research Associate Department of Bioengineering Imperial College London South Kensington Campus London SW7 2AZ United Kingdom |
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Hi Mike,
I would suggest giving Bio-Formats a try. The LEI reader in Bio-Formats notices if any of the TIFF files have been renamed, tries to guess at what happened, and sometimes even succeeds (though not always). -Curtis On Fri, Jun 20, 2008 at 3:49 PM, Michael Doube <[hidden email]> wrote: > Michael, Curtis > > I just used IJ in its 'natural' state, without the Bio-Formats plugin - > actually very freshly installed straight from Wayne's website, no extra > plugins added and running the jre from the ImageJ subdirectory. It looked > as though IJ was handling the .lei file but was stopped by a bug which meant > it couldn't find the images that the .lei referred to. I will see if I can > get permission to send the files through to you Curtis. > > Mike > > > Michael Weber wrote: > >> Mike, >> >> a very general answer, but: did you try the Bio-Formats plugin? >> >> Michael >> >> >> Michael Doube wrote: >> >>> Hi all >>> >>> I tried to open someone else's images taken on a Leica SP1 confocal >>> microscope by dragging and dropping the .lei file (which describes the >>> imaging session) onto ImageJ, but I got an error that the directory couldn't >>> be found - it looked as though the plugin was duplicating the directory name >>> string then confusing itself by looking for ~/images/directory_1directory_1/ >>> instead of just ~/images/directory_1/ >>> >>> I don't have access to the images right now so can't give exact details >>> of the error message. Can anyone else confirm this behaviour? >>> >>> This is ij 1.41e on 32-bit Ubuntu 8.04, using the IJ-bundled JRE. >>> >>> Mike >>> >> > -- > Michael Doube BPhil BVSc PhD MRCVS > Research Associate > Department of Bioengineering > Imperial College London > South Kensington Campus > London SW7 2AZ > United Kingdom > |
Re: Problem opening Leica SP1 .lei file
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In reply to this post by Michael Doube
Actually, I have been using some plugins that were developed
by Tony Collins some time ago. I don't know if they are included in the macphotonics set or not. However, these are the ones that are not working for me, with precisely the error that Mike described. Joel ---- Original message ---- >Date: Fri, 20 Jun 2008 15:17:15 +0100 >From: Curtis Rueden <[hidden email]> >Subject: Re: Problem opening Leica SP1 .lei file >To: [hidden email] > >Hi, > >I am not sure, but I thought ImageJ did not support reading LEI files >without the Bio-Formats plugin. So I'm guessing Mike & Joel have Bio-Formats >installed, and ImageJ is calling it when they drag and drop? > >If so, then I'm guessing there is a bug in Bio-Formats with LEI, in which >case I would be glad to fix the problem, if someone can send me a stack >trace and/or sample data that demonstrates the problem. > >-Curtis > >On Fri, Jun 20, 2008 at 3:04 PM, Michael Weber <[hidden email]> wrote: > >> Mike, >> >> a very general answer, but: did you try the Bio-Formats plugin? >> >> Michael >> >> >> >> Michael Doube wrote: >> >>> Hi all >>> >>> I tried to open someone else's images taken on a Leica SP1 >>> microscope by dragging and dropping the .lei file (which describes the >>> imaging session) onto ImageJ, but I got an error that the directory couldn't >>> be found - it looked as though the plugin was duplicating the directory name >>> string then confusing itself by looking for ~/images/directory_1directory_1/ >>> instead of just ~/images/directory_1/ >>> >>> I don't have access to the images right now so can't give exact details of >>> the error message. Can anyone else confirm this behaviour? >>> >>> This is ij 1.41e on 32-bit Ubuntu 8.04, using the IJ-bundled JRE. >>> >>> Mike >>> >> Joel B. Sheffield Professor, Department of Biology Temple University Philadelphia, PA 19122 [hidden email] http://astro.temple.edu/~jbs |
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In reply to this post by Michael Doube
I have almost exactly the same problem. I am trying to open an image stack
made on a Leica SP1 confocal microscope. I have ImageJ v1.40g running on Windows XP. I have installed the latest HAndleExtraFileTypes.class plugin. When opening the .lei file, I get an error saying that the accompanying txt file could not be found. However, the path to the .txt file in the error message is incorrect. It has the format C:\pathNAME.txt . The backslash behind the directory name and the .txt file name (NAME) is missing. I copied the .txt file to one directory lower and renamed it to fit the error message and tried again. I then got a different error message -"Plugin or class not found Leica_TIFF_sequence". I double checked that my HAndleExtraFileTypes.class was up to date, then I found this forum online. I installed the Bio-Formats plug-in and tried again. I got the following error message: java.lang.ArrayIndexOutOfBoundsException: 0 at loci.formats.in.LeicaReader.initFile(LeicaReader.java:491) at loci.formats.FormatReader.setId(FormatReader.java:633) at loci.formats.FormatHandler.setId(FormatHandler.java:134) at loci.plugins.Importer.run(Importer.java:145) at loci.plugins.LociImporter.run(LociImporter.java:74) at ij.IJ.runUserPlugIn(IJ.java:158) at ij.IJ.runPlugIn(IJ.java:124) at ij.IJ.runPlugIn(IJ.java:113) at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:253) at HandleExtraFileTypes.run(HandleExtraFileTypes.java:37) at ij.IJ.runUserPlugIn(IJ.java:158) at ij.IJ.runPlugIn(IJ.java:124) at ij.IJ.runPlugIn(IJ.java:113) at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:304) at ij.io.Opener.openImage(Opener.java:233) at ij.io.Opener.openImage(Opener.java:249) at ij.io.Opener.open(Opener.java:116) at ij.io.Opener.open(Opener.java:55) at ij.plugin.Commands.run(Commands.java:23) at ij.IJ.runPlugIn(IJ.java:131) at ij.Executer.runCommand(Executer.java:104) at ij.Executer.run(Executer.java:58) at java.lang.Thread.run(Unknown Source) Needless to say, I am pretty much lost at this point. Any help would be greatly appreciated. Matija
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Hi Matija,
It looks like you found a bug in Bio-Formats. First, please try the latest trunk build, available for download from the Bio-Formats web site at http://www.loci.wisc.edu/ome/formats-download.html. If you still experience this error with the latest version, and would be able to provide a sample dataset demonstrating the problem, it would be extremely helpful to us for debugging. Files less than 15 MB can be sent as to me directly as email attachments, or if you need a place to put larger files you can use our FTP server -- just let us know and I'll send you the connection details off-list. Thanks, Curtis On Sun, Jun 29, 2008 at 5:49 PM, matijac <[hidden email]> wrote: > I have almost exactly the same problem. I am trying to open an image stack > made on a Leica SP1 confocal microscope. I have ImageJ v1.40g running on > Windows XP. I have installed the latest HAndleExtraFileTypes.class plugin. > When opening the .lei file, I get an error saying that the accompanying txt > file could not be found. However, the path to the .txt file in the error > message is incorrect. It has the format C:\pathNAME.txt . The backslash > behind the directory name and the .txt file name (NAME) is missing. I copied > the .txt file to one directory lower and renamed it to fit the error message > and tried again. I then got a different error message -"Plugin or class not > found > Leica_TIFF_sequence". I double checked that my > HAndleExtraFileTypes.class was up to date, then I found this forum online. I > installed the Bio-Formats plug-in and tried again. I got the following error > message: > > java.lang.ArrayIndexOutOfBoundsException: 0 > at loci.formats.in.LeicaReader.initFile(LeicaReader.java:491) > at loci.formats.FormatReader.setId(FormatReader.java:633) > at loci.formats.FormatHandler.setId(FormatHandler.java:134) > at loci.plugins.Importer.run(Importer.java:145) > at loci.plugins.LociImporter.run(LociImporter.java:74) > at ij.IJ.runUserPlugIn(IJ.java:158) > at ij.IJ.runPlugIn(IJ.java:124) > at ij.IJ.runPlugIn(IJ.java:113) > at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:253) > at HandleExtraFileTypes.run(HandleExtraFileTypes.java:37) > at ij.IJ.runUserPlugIn(IJ.java:158) > at ij.IJ.runPlugIn(IJ.java:124) > at ij.IJ.runPlugIn(IJ.java:113) > at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:304) > at ij.io.Opener.openImage(Opener.java:233) > at ij.io.Opener.openImage(Opener.java:249) > at ij.io.Opener.open(Opener.java:116) > at ij.io.Opener.open(Opener.java:55) > at ij.plugin.Commands.run(Commands.java:23) > at ij.IJ.runPlugIn(IJ.java:131) > at ij.Executer.runCommand(Executer.java:104) > at ij.Executer.run(Executer.java:58) > at java.lang.Thread.run(Unknown Source) > > > Needless to say, I am pretty much lost at this point. > > Any help would be greatly appreciated. > > Matija > > > Michael Doube-3 wrote: >> >> Hi all >> >> I tried to open someone else's images taken on a Leica SP1 confocal >> microscope by dragging and dropping the .lei file (which describes the >> imaging session) onto ImageJ, but I got an error that the directory >> couldn't be found - it looked as though the plugin was duplicating the >> directory name string then confusing itself by looking for >> ~/images/directory_1directory_1/ instead of just ~/images/directory_1/ >> >> I don't have access to the images right now so can't give exact details >> of the error message. Can anyone else confirm this behaviour? >> >> This is ij 1.41e on 32-bit Ubuntu 8.04, using the IJ-bundled JRE. >> >> Mike >> >> > > -- > View this message in context: http://www.nabble.com/Problem-opening-Leica-SP1-.lei-file-tp18025302p18186267.html > Sent from the ImageJ mailing list archive at Nabble.com. > |
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Thanks to everyone who helped on this!
Wayne Rasband has fixed the HandleExtraFileTypes.class. Curtis Rueden and everyone else at LOCI, who maintain the Bio-Formats plug-in, have updated the plug-in and the import now works seamlessly. All you have to do is click on the .lei file which has to be in the same directory as the image stack. Also, thanks to Joel Sheffield for writing a new plug-in that also works. However, the Bio-Formats provides a simpler solution for the user. Sorry if this sounds like spamming the board, just wanted to notify everyone that the issue has been fixed and point out the best solution in my opinion. Matija
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