segmentation
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Hello,
I would like to do a segmentation of a microscopy image using ImageJ. I want to divide the picture into three labels: bone (originally more or less yellow), cartilage (originally green) and connective tissue which has other colors. Then Id like to measure these three areas. What tool/plugin should I use? The contrast between the tissues is not so good..... I would really appreciate any help Magda -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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This post was updated on .
Hello,
maybe good choice for you could be the Weka segmentation plugin in Fiji. See its webpage - http://fiji.sc/Trainable_Weka_Segmentation JB On 15 August 2013 16:04, Jędrzejas, Magdalena < magdalena.jedrzejas@izi.fraunhofer.de> wrote: > Hello, > > I would like to do a segmentation of a microscopy image using ImageJ. I > want to divide the picture into three labels: bone (originally more or less > yellow), cartilage (originally green) and connective tissue which has other > colors. Then Id like to measure these three areas. What tool/plugin should > I use? The contrast between the tissues is not so good..... > > I would really appreciate any help > > Magda > > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- Best regards and wishes of a nice day, Jiří Borovec ---------------------------------------------------------------------------------------------------- Jiří Borovec <jiri.borovec@fel.cvut.cz> PhD student at CMP CTU, ISC member http://cmp.felk.cvut.cz/~borovji3 -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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In reply to this post by Jędrzejas, Magdalena
Hi,
Normally, go to image>adjust>color threshold. However, doing this successfully depends rather a lot on staining /image quality. Do you have an example? Also is your section from demineralised bone, or undemineralised? In the latter case there are a number of stains (such as von Kossa or Aniline blue) that nicely stain only the mineralised tissue. For more difficult segmentation have a look at the trainable WEKA segmentation plugin. This is included in the Fiji distribution of ImageJ. bye, Rob On 15/08/2013 15:04, Jędrzejas, Magdalena wrote: > Hello, > > I would like to do a segmentation of a microscopy image using ImageJ. I want to divide the picture into three labels: bone (originally more or less yellow), cartilage (originally green) and connective tissue which has other colors. Then Id like to measure these three areas. What tool/plugin should I use? The contrast between the tissues is not so good..... > > I would really appreciate any help > > Magda > > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- _____________________________ Dr. Rob van 't Hof Reader Centre for Molecular Medicine MRC IGMM University of Edinburgh Western General Hospital Crewe Road, Edinburgh EH4 2XU United Kingdom Phone: (+44)-131-6511031 email: [hidden email] _____________________________ 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 |
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In reply to this post by Jędrzejas, Magdalena
Hi,
Normally, go to image>adjust>color threshold. However, doing this successfully depends rather a lot on staining /image quality. Do you have an example? Also is your section from demineralised bone, or undemineralised? In the latter case there are a number of stains (such as von Kossa or Aniline blue) that nicely stain only the mineralised tissue. For more difficult segmentation have a look at the trainable WEKA segmentation plugin. This is included in the Fiji distribution of ImageJ. bye, Rob On 15/08/2013 15:04, Jędrzejas, Magdalena wrote: > Hello, > > I would like to do a segmentation of a microscopy image using ImageJ. I want to divide the picture into three labels: bone (originally more or less yellow), cartilage (originally green) and connective tissue which has other colors. Then Id like to measure these three areas. What tool/plugin should I use? The contrast between the tissues is not so good..... > > I would really appreciate any help > > Magda > > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- _____________________________ Dr. Rob van 't Hof Reader Centre for Molecular Medicine MRC IGMM University of Edinburgh Western General Hospital Crewe Road, Edinburgh EH4 2XU United Kingdom Phone: (+44)-131-6511031 email: [hidden email] _____________________________ 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 |
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In reply to this post by Jirka
Hi Magda,
> I would like to do a segmentation of a microscopy image using ImageJ. I agree with Jiří that the Trainable Weka Segmentation plugin is likely your easiest path to success. That said, if you want an overview of how segmentation typically works in ImageJ in general, see this page: http://fiji.sc/Segmentation Regards, Curtis On Thu, Aug 15, 2013 at 9:48 AM, Jiří Borovec <[hidden email]>wrote: > Hello, > maybe good choice for you could be the Weka segmentation plugin in Fiji. > See its webpage - http://fiji.sc/Trainable_Weka_Segmentation > > JB > > > On 15 August 2013 16:04, Jędrzejas, Magdalena < > [hidden email]> wrote: > > > Hello, > > > > I would like to do a segmentation of a microscopy image using ImageJ. I > > want to divide the picture into three labels: bone (originally more or > less > > yellow), cartilage (originally green) and connective tissue which has > other > > colors. Then Id like to measure these three areas. What tool/plugin > should > > I use? The contrast between the tissues is not so good..... > > > > I would really appreciate any help > > > > Magda > > > > > > -- > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > > > > > -- > Best regards and wishes of a nice day, Jiří Borovec > > ---------------------------------------------------------------------------------------------------- > Jiří Borovec | < > [hidden email]> > PhD student at CMP, ISC member, CTU | tel.: +420 2 2435 7590 > http://cmp.felk.cvut.cz/~borovji3 | mobile: +420 728480285 > > -- > 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 Rob van 't Hof-2
Hello,
Thank you, this plugin works really good. I only have one question: is there some kind of 'tool' which works like 'fill holes' or sth like that? After segmentation I obtained a segmented image, but I cannot get rid of really small areas of another label in the middle of large area of the basic one. I worked before with BZ II Analyzer, and there I used a 'fill holes' effect, where you could define the maximal size of the holes inside the larger area of other label, which should be covered. How can I do it in Fiji? Thanks in advance Regards Magda -----Ursprüngliche Nachricht----- Von: ImageJ Interest Group [mailto:[hidden email]] Im Auftrag von Rob van 't Hof Gesendet: Donnerstag, 15. August 2013 16:56 An: [hidden email] Betreff: Re: segmentation Hi, Normally, go to image>adjust>color threshold. However, doing this successfully depends rather a lot on staining /image quality. Do you have an example? Also is your section from demineralised bone, or undemineralised? In the latter case there are a number of stains (such as von Kossa or Aniline blue) that nicely stain only the mineralised tissue. For more difficult segmentation have a look at the trainable WEKA segmentation plugin. This is included in the Fiji distribution of ImageJ. bye, Rob On 15/08/2013 15:04, Jędrzejas, Magdalena wrote: > Hello, > > I would like to do a segmentation of a microscopy image using ImageJ. I want to divide the picture into three labels: bone (originally more or less yellow), cartilage (originally green) and connective tissue which has other colors. Then Id like to measure these three areas. What tool/plugin should I use? The contrast between the tissues is not so good..... > > I would really appreciate any help > > Magda > > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- _____________________________ Dr. Rob van 't Hof Reader Centre for Molecular Medicine MRC IGMM University of Edinburgh Western General Hospital Crewe Road, Edinburgh EH4 2XU United Kingdom Phone: (+44)-131-6511031 email: [hidden email] _____________________________ 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 -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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In ImageJ, there are standard binary operations such as Closing (which
would help you with small holes), or even a "Fill Holes" under Process>Binary. Be aware though, that the foreground will be affected, i.e. take care whether you define your objects to be white or rather black (defined in the binary options menu). Johannes *Dr. Johannes Koch* *Tissue Med Biosciences GmbH* Magnesitstrasse1 | A-3500 Krems T: +43/2732/87470-300 | M: [hidden email] <mailto:[hidden email]> *www.tmbiosciences.com <http://www.tmbiosciences.com/>* Diese E-Mail enthält vertrauliche und/oder rechtlich geschützte Information. Wenn Sie nicht der richtige Adressat sind oder diese E-Mail irrtümlich erhalten haben, informieren Sie bitte unverzüglich den Absender und vernichten Sie diese E-Mail sofort. Das unerlaubte Kopieren sowie die unbefugte Weitergabe dieser E-Mail sind nicht gestattet. This e-mail may contain confidential and/or privileged information. If you are not the intended recipient or have received this e-mail in error please notify the sender immediately and destroy this e-mail. Any unauthorized copying, disclosure or distribution of the material in this e-mail is strictly forbidden. Am 19.08.2013 11:51, schrieb Jędrzejas, Magdalena: > Hello, > Thank you, this plugin works really good. I only have one question: is there some kind of 'tool' which works like 'fill holes' or sth like that? After segmentation I obtained a segmented image, but I cannot get rid of really small areas of another label in the middle of large area of the basic one. I worked before with BZ II Analyzer, and there I used a 'fill holes' effect, where you could define the maximal size of the holes inside the larger area of other label, which should be covered. How can I do it in Fiji? > Thanks in advance > Regards > Magda > > -----Ursprüngliche Nachricht----- > Von: ImageJ Interest Group [mailto:[hidden email]] Im Auftrag von Rob van 't Hof > Gesendet: Donnerstag, 15. August 2013 16:56 > An: [hidden email] > Betreff: Re: segmentation > > Hi, > Normally, go to image>adjust>color threshold. However, doing this successfully depends rather a lot on staining /image quality. Do you have an example? > Also is your section from demineralised bone, or undemineralised? In the latter case there are a number of stains (such as von Kossa or Aniline > blue) that nicely stain only the mineralised tissue. > For more difficult segmentation have a look at the trainable WEKA segmentation plugin. This is included in the Fiji distribution of ImageJ. > > bye, > Rob > > On 15/08/2013 15:04, Jędrzejas, Magdalena wrote: >> Hello, >> >> I would like to do a segmentation of a microscopy image using ImageJ. I want to divide the picture into three labels: bone (originally more or less yellow), cartilage (originally green) and connective tissue which has other colors. Then Id like to measure these three areas. What tool/plugin should I use? The contrast between the tissues is not so good..... >> >> I would really appreciate any help >> >> Magda >> >> >> -- >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Unfortunately the functions you mentioned only work with the black and white image. I have an image with black, white and two different shades of grey, is there an option to fill the holes in such image?
Magda -----Ursprüngliche Nachricht----- Von: ImageJ Interest Group [mailto:[hidden email]] Im Auftrag von Johannes Koch Gesendet: Montag, 19. August 2013 11:59 An: [hidden email] Betreff: Re: segmentation In ImageJ, there are standard binary operations such as Closing (which would help you with small holes), or even a "Fill Holes" under Process>Binary. Be aware though, that the foreground will be affected, i.e. take care whether you define your objects to be white or rather black (defined in the binary options menu). Johannes *Dr. Johannes Koch* *Tissue Med Biosciences GmbH* Magnesitstrasse1 | A-3500 Krems T: +43/2732/87470-300 | M: [hidden email] <mailto:[hidden email]> *www.tmbiosciences.com <http://www.tmbiosciences.com/>* Diese E-Mail enthält vertrauliche und/oder rechtlich geschützte Information. Wenn Sie nicht der richtige Adressat sind oder diese E-Mail irrtümlich erhalten haben, informieren Sie bitte unverzüglich den Absender und vernichten Sie diese E-Mail sofort. Das unerlaubte Kopieren sowie die unbefugte Weitergabe dieser E-Mail sind nicht gestattet. This e-mail may contain confidential and/or privileged information. If you are not the intended recipient or have received this e-mail in error please notify the sender immediately and destroy this e-mail. Any unauthorized copying, disclosure or distribution of the material in this e-mail is strictly forbidden. Am 19.08.2013 11:51, schrieb Jędrzejas, Magdalena: > Hello, > Thank you, this plugin works really good. I only have one question: is there some kind of 'tool' which works like 'fill holes' or sth like that? After segmentation I obtained a segmented image, but I cannot get rid of really small areas of another label in the middle of large area of the basic one. I worked before with BZ II Analyzer, and there I used a 'fill holes' effect, where you could define the maximal size of the holes inside the larger area of other label, which should be covered. How can I do it in Fiji? > Thanks in advance > Regards > Magda > > -----Ursprüngliche Nachricht----- > Von: ImageJ Interest Group [mailto:[hidden email]] Im Auftrag von > Rob van 't Hof > Gesendet: Donnerstag, 15. August 2013 16:56 > An: [hidden email] > Betreff: Re: segmentation > > Hi, > Normally, go to image>adjust>color threshold. However, doing this successfully depends rather a lot on staining /image quality. Do you have an example? > Also is your section from demineralised bone, or undemineralised? In > the latter case there are a number of stains (such as von Kossa or > Aniline > blue) that nicely stain only the mineralised tissue. > For more difficult segmentation have a look at the trainable WEKA segmentation plugin. This is included in the Fiji distribution of ImageJ. > > bye, > Rob > > On 15/08/2013 15:04, Jędrzejas, Magdalena wrote: >> Hello, >> >> I would like to do a segmentation of a microscopy image using ImageJ. I want to divide the picture into three labels: bone (originally more or less yellow), cartilage (originally green) and connective tissue which has other colors. Then Id like to measure these three areas. What tool/plugin should I use? The contrast between the tissues is not so good..... >> >> I would really appreciate any help >> >> Magda >> >> >> -- >> 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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I have one more question. When I'm trying to apply classifier which I created to another image, every time Fiji crashes down. How can I make a classifier once and then only apply it to other images and not to make a new classifier for an every new image?
Magda -----Ursprüngliche Nachricht----- Von: ImageJ Interest Group [mailto:[hidden email]] Im Auftrag von Jedrzejas, Magdalena Gesendet: Montag, 19. August 2013 13:29 An: [hidden email] Betreff: AW: segmentation Unfortunately the functions you mentioned only work with the black and white image. I have an image with black, white and two different shades of grey, is there an option to fill the holes in such image? Magda -----Ursprüngliche Nachricht----- Von: ImageJ Interest Group [mailto:[hidden email]] Im Auftrag von Johannes Koch Gesendet: Montag, 19. August 2013 11:59 An: [hidden email] Betreff: Re: segmentation In ImageJ, there are standard binary operations such as Closing (which would help you with small holes), or even a "Fill Holes" under Process>Binary. Be aware though, that the foreground will be affected, i.e. take care whether you define your objects to be white or rather black (defined in the binary options menu). Johannes *Dr. Johannes Koch* *Tissue Med Biosciences GmbH* Magnesitstrasse1 | A-3500 Krems T: +43/2732/87470-300 | M: [hidden email] <mailto:[hidden email]> *www.tmbiosciences.com <http://www.tmbiosciences.com/>* Diese E-Mail enthält vertrauliche und/oder rechtlich geschützte Information. Wenn Sie nicht der richtige Adressat sind oder diese E-Mail irrtümlich erhalten haben, informieren Sie bitte unverzüglich den Absender und vernichten Sie diese E-Mail sofort. Das unerlaubte Kopieren sowie die unbefugte Weitergabe dieser E-Mail sind nicht gestattet. This e-mail may contain confidential and/or privileged information. If you are not the intended recipient or have received this e-mail in error please notify the sender immediately and destroy this e-mail. Any unauthorized copying, disclosure or distribution of the material in this e-mail is strictly forbidden. Am 19.08.2013 11:51, schrieb Jędrzejas, Magdalena: > Hello, > Thank you, this plugin works really good. I only have one question: is there some kind of 'tool' which works like 'fill holes' or sth like that? After segmentation I obtained a segmented image, but I cannot get rid of really small areas of another label in the middle of large area of the basic one. I worked before with BZ II Analyzer, and there I used a 'fill holes' effect, where you could define the maximal size of the holes inside the larger area of other label, which should be covered. How can I do it in Fiji? > Thanks in advance > Regards > Magda > > -----Ursprüngliche Nachricht----- > Von: ImageJ Interest Group [mailto:[hidden email]] Im Auftrag von > Rob van 't Hof > Gesendet: Donnerstag, 15. August 2013 16:56 > An: [hidden email] > Betreff: Re: segmentation > > Hi, > Normally, go to image>adjust>color threshold. However, doing this successfully depends rather a lot on staining /image quality. Do you have an example? > Also is your section from demineralised bone, or undemineralised? In > the latter case there are a number of stains (such as von Kossa or > Aniline > blue) that nicely stain only the mineralised tissue. > For more difficult segmentation have a look at the trainable WEKA segmentation plugin. This is included in the Fiji distribution of ImageJ. > > bye, > Rob > > On 15/08/2013 15:04, Jędrzejas, Magdalena wrote: >> Hello, >> >> I would like to do a segmentation of a microscopy image using ImageJ. I want to divide the picture into three labels: bone (originally more or less yellow), cartilage (originally green) and connective tissue which has other colors. Then Id like to measure these three areas. What tool/plugin should I use? The contrast between the tissues is not so good..... >> >> I would really appreciate any help >> >> Magda >> >> >> -- >> 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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In reply to this post by Jędrzejas, Magdalena
On Monday 19 Aug 2013 12:28:36 Jędrzejas, Magdalena wrote:
> Unfortunately the functions you mentioned only work with the black and white > image. I have an image with black, white and two different shades of grey, > is there an option to fill the holes in such image? Magda Decompose your labels into binary images, delete holes in each of them and recompose them again. You will have to apply quite a few image operations for this because it is not straightforward with a single command. -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Which tool should I use to decompose and recompose my labels?
-----Ursprüngliche Nachricht----- Von: ImageJ Interest Group [mailto:[hidden email]] Im Auftrag von Gabriel Landini Gesendet: Montag, 19. August 2013 13:54 An: [hidden email] Betreff: Re: AW: segmentation On Monday 19 Aug 2013 12:28:36 Jędrzejas, Magdalena wrote: > Unfortunately the functions you mentioned only work with the black and > white image. I have an image with black, white and two different > shades of grey, is there an option to fill the holes in such image? > Magda Decompose your labels into binary images, delete holes in each of them and recompose them again. You will have to apply quite a few image operations for this because it is not straightforward with a single command. -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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On Monday 19 Aug 2013 13:21:02 Jędrzejas, Magdalena wrote:
> Which tool should I use to decompose and recompose my labels? Maybe the threshold function helps to produce a binary image of each label, but really I can only imagine what your images look like. To recompose you could change the grey value of each label binary image and add them up. Since they are exclusive labels they should not overlap. Cheers Gabriel -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Hi List,
I use the stitching plugin of S. Preibisch (Grid/Collection mode). After switching from 32bit to a 64bit Windows I get an error always when I try to run the plugin out of my IJ installation. The error message is: java.lang.NoSuchMethodError: org.slf4j.helpers.MessageFormatter.format(Ljava/lang/String;Ljava/lang/Object;Ljava/lang/Object;)Ljava/lang/String; at org.slf4j.impl.Log4jLoggerAdapter.debug(Log4jLoggerAdapter.java:246) at loci.common.IniParser.parseINI(IniParser.java:114) at loci.common.IniParser.parseINI(IniParser.java:98) at loci.plugins.prefs.OptionsList.<init>(OptionsList.java:64) at loci.plugins.in.ImporterOptions.<init>(ImporterOptions.java:156) at mpicbg.stitching.ImageCollectionElement.open(ImageCollectionElement.java:81) at Stitching_Grid.run(Stitching_Grid.java:342) at ij.IJ.runUserPlugIn(IJ.java:185) at ij.IJ.runPlugIn(IJ.java:152) at ij.Executer.runCommand(Executer.java:127) at ij.Executer.run(Executer.java:64) at java.lang.Thread.run(Unknown Source) IJ version is 1.47f7 Java version is 1.6.0_31(64bit) - included in the IJ installation I have update the stitching plugin (from http://fly.mpi-cbg.de/~preibisch/software.html#Stitching). The data is ok. (I used a current FIJI installation where everything work as expected.) Does anyone has an idea what to do? Thanks, Peter -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Hi Peter,
you miss something from the LOCI bioformats to open the stacks ... it is available for download here http://loci.wisc.edu/bio-formats/downloads Hope that helps, Stephan On Aug 20, 2013, at 12:25 , Peter Haub wrote: > Hi List, > I use the stitching plugin of S. Preibisch (Grid/Collection mode). > After switching from 32bit to a 64bit Windows I get an error always when I try to run the plugin out of my IJ installation. > The error message is: > java.lang.NoSuchMethodError: org.slf4j.helpers.MessageFormatter.format(Ljava/lang/String;Ljava/lang/Object;Ljava/lang/Object;)Ljava/lang/String; > at org.slf4j.impl.Log4jLoggerAdapter.debug(Log4jLoggerAdapter.java:246) > at loci.common.IniParser.parseINI(IniParser.java:114) > at loci.common.IniParser.parseINI(IniParser.java:98) > at loci.plugins.prefs.OptionsList.<init>(OptionsList.java:64) > at loci.plugins.in.ImporterOptions.<init>(ImporterOptions.java:156) > at mpicbg.stitching.ImageCollectionElement.open(ImageCollectionElement.java:81) > at Stitching_Grid.run(Stitching_Grid.java:342) > at ij.IJ.runUserPlugIn(IJ.java:185) > at ij.IJ.runPlugIn(IJ.java:152) > at ij.Executer.runCommand(Executer.java:127) > at ij.Executer.run(Executer.java:64) > at java.lang.Thread.run(Unknown Source) > IJ version is 1.47f7 > Java version is 1.6.0_31(64bit) - included in the IJ installation > I have update the stitching plugin (from http://fly.mpi-cbg.de/~preibisch/software.html#Stitching). > The data is ok. (I used a current FIJI installation where everything work as expected.) > Does anyone has an idea what to do? > Thanks, > Peter > > -- > 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 Peter,
> After switching from 32bit to a 64bit Windows I get an error always > when I try to run the plugin out of my IJ installation. As Stephan says, something is missing. But it should definitely not be necessary to download anything manually. If you run Help > Update Fiji, then click "Advanced mode" and change the "View Options" to "View uninstalled files only" do you see any entries ending in ".jar"? > java.lang.NoSuchMethodError: org.slf4j.helpers.MessageFormatter.format Your error message suggests you are missing slf4j-api-1.5.10.jar. If indeed you are missing that file (or other JAR files), click the "Status/Action" and change it to "Install / Update". If that doesn't work, you can also try downloading a fresh & up-to-date Fiji from: http://fiji.sc/Downloads. Regards, Curtis On Tue, Aug 20, 2013 at 8:28 AM, Stephan Preibisch <[hidden email]>wrote: > Hi Peter, > > you miss something from the LOCI bioformats to open the stacks ... it is > available for download here http://loci.wisc.edu/bio-formats/downloads > > Hope that helps, > Stephan > > On Aug 20, 2013, at 12:25 , Peter Haub wrote: > > > Hi List, > > I use the stitching plugin of S. Preibisch (Grid/Collection mode). > > After switching from 32bit to a 64bit Windows I get an error always when > I try to run the plugin out of my IJ installation. > > The error message is: > > java.lang.NoSuchMethodError: > org.slf4j.helpers.MessageFormatter.format(Ljava/lang/String;Ljava/lang/Object;Ljava/lang/Object;)Ljava/lang/String; > > at > org.slf4j.impl.Log4jLoggerAdapter.debug(Log4jLoggerAdapter.java:246) > > at loci.common.IniParser.parseINI(IniParser.java:114) > > at loci.common.IniParser.parseINI(IniParser.java:98) > > at loci.plugins.prefs.OptionsList.<init>(OptionsList.java:64) > > at loci.plugins.in.ImporterOptions.<init>(ImporterOptions.java:156) > > at > mpicbg.stitching.ImageCollectionElement.open(ImageCollectionElement.java:81) > > at Stitching_Grid.run(Stitching_Grid.java:342) > > at ij.IJ.runUserPlugIn(IJ.java:185) > > at ij.IJ.runPlugIn(IJ.java:152) > > at ij.Executer.runCommand(Executer.java:127) > > at ij.Executer.run(Executer.java:64) > > at java.lang.Thread.run(Unknown Source) > > IJ version is 1.47f7 > > Java version is 1.6.0_31(64bit) - included in the IJ installation > > I have update the stitching plugin (from > http://fly.mpi-cbg.de/~preibisch/software.html#Stitching). > > The data is ok. (I used a current FIJI installation where everything > work as expected.) > > Does anyone has an idea what to do? > > Thanks, > > Peter > > > > -- > > 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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Hi Stephan,
Hi Curtis, Thanks for your answers. I found the reason for the error message. Stephans stitching plugin comes with a copy of the loci_tools.jar (if manually installed into a IJ configuration). This loci_tools.jar contains a version of slf4j (in \org\slf4j\ in the latest loci_tools.jar, downloaded from the loci web page). This slf4j seems to be in conflict with another version of that library (slf4j-api-1.7.1.jar), located in the ..\plugins\Micro-Manager folder in a default microManager configuration. Removing this slf4j-api-1.7.1.jar solves the problem. The stitching plugin can be used then without error messages. I would prefer to not remove this slf4j-api-1.7.1.jar permanently. Does anyone has an idea how to deal with this conflict? Which version of slf4j is used in loci_tools.jar? Is there any plan to update this to the latest version 1.7.1? Would there be a conflict during Java class loading if the same version of slf4j would be available twice? Maybe someone has a hint. Thanks, Peter On 20.08.2013 16:24, Curtis Rueden wrote: > Hi Peter, > >> After switching from 32bit to a 64bit Windows I get an error always >> when I try to run the plugin out of my IJ installation. > As Stephan says, something is missing. But it should definitely not be > necessary to download anything manually. > > If you run Help > Update Fiji, then click "Advanced mode" and change the > "View Options" to "View uninstalled files only" do you see any entries > ending in ".jar"? > >> java.lang.NoSuchMethodError: org.slf4j.helpers.MessageFormatter.format > Your error message suggests you are missing slf4j-api-1.5.10.jar. > > If indeed you are missing that file (or other JAR files), click the > "Status/Action" and change it to "Install / Update". > > If that doesn't work, you can also try downloading a fresh & up-to-date > Fiji from: http://fiji.sc/Downloads. > > Regards, > Curtis > > > On Tue, Aug 20, 2013 at 8:28 AM, Stephan Preibisch <[hidden email]>wrote: > >> Hi Peter, >> >> you miss something from the LOCI bioformats to open the stacks ... it is >> available for download here http://loci.wisc.edu/bio-formats/downloads >> >> Hope that helps, >> Stephan >> >> On Aug 20, 2013, at 12:25 , Peter Haub wrote: >> >>> Hi List, >>> I use the stitching plugin of S. Preibisch (Grid/Collection mode). >>> After switching from 32bit to a 64bit Windows I get an error always when >> I try to run the plugin out of my IJ installation. >>> The error message is: >>> java.lang.NoSuchMethodError: >> org.slf4j.helpers.MessageFormatter.format(Ljava/lang/String;Ljava/lang/Object;Ljava/lang/Object;)Ljava/lang/String; >>> at >> org.slf4j.impl.Log4jLoggerAdapter.debug(Log4jLoggerAdapter.java:246) >>> at loci.common.IniParser.parseINI(IniParser.java:114) >>> at loci.common.IniParser.parseINI(IniParser.java:98) >>> at loci.plugins.prefs.OptionsList.<init>(OptionsList.java:64) >>> at loci.plugins.in.ImporterOptions.<init>(ImporterOptions.java:156) >>> at >> mpicbg.stitching.ImageCollectionElement.open(ImageCollectionElement.java:81) >>> at Stitching_Grid.run(Stitching_Grid.java:342) >>> at ij.IJ.runUserPlugIn(IJ.java:185) >>> at ij.IJ.runPlugIn(IJ.java:152) >>> at ij.Executer.runCommand(Executer.java:127) >>> at ij.Executer.run(Executer.java:64) >>> at java.lang.Thread.run(Unknown Source) >>> IJ version is 1.47f7 >>> Java version is 1.6.0_31(64bit) - included in the IJ installation >>> I have update the stitching plugin (from >> http://fly.mpi-cbg.de/~preibisch/software.html#Stitching). >>> The data is ok. (I used a current FIJI installation where everything >> work as expected.) >>> Does anyone has an idea what to do? >>> Thanks, >>> Peter >>> >>> -- >>> 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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Hi Peter,
Apologies for the delay in my reply. > I would prefer to not remove this slf4j-api-1.7.1.jar permanently. > Does anyone has an idea how to deal with this conflict? Three options: 1) Use Fiji [1]. It comes with the stitching plugins, and is already structured to avoid this sort of problem. 2) Stop using loci_tools.jar and instead put all the individual component JAR files of Bio-Formats [1] into your plugins folder. This is what Fiji does. 3) Remove slf4j-api-1.7.1.jar, as you have done. This is actually OK as long as Micro-Manager does not use any new API introduced since slf4j-api-1.5.10. (But I am really not sure whether it does! Does Micro-Manager's logging still work for you with that library removed?) > Which version of slf4j is used in loci_tools.jar? Version 4.4.8 of loci_tools.jar uses SLF4J 1.5.10. > Is there any plan to update this to the latest version 1.7.1? The latest development version of Bio-Formats has already been upgraded to 1.7.2 [3], which will be the version used for the next releases: 4.4.9 and 5.0.0-beta2. > Would there be a conflict during Java class loading if the same > version of slf4j would be available twice? It should work, as long as the two versions really are the same. Regards, Curtis [1] http://fiji.sc/ [2] https://www.openmicroscopy.org/site/products/bio-formats/downloads [3] https://github.com/openmicroscopy/bioformats/commit/5b8b5ff83d23012c5805a8420681085244934cb6 On Wed, Aug 21, 2013 at 3:25 AM, Peter Haub <[hidden email]> wrote: > Hi Stephan, > Hi Curtis, > > Thanks for your answers. > I found the reason for the error message. > > Stephans stitching plugin comes with a copy of the loci_tools.jar (if > manually installed into a IJ configuration). > This loci_tools.jar contains a version of slf4j (in \org\slf4j\ in the > latest loci_tools.jar, downloaded from the loci web page). > This slf4j seems to be in conflict with another version of that library > (slf4j-api-1.7.1.jar), located in the ..\plugins\Micro-Manager folder in a > default microManager configuration. > Removing this slf4j-api-1.7.1.jar solves the problem. The stitching plugin > can be used then without error messages. > > I would prefer to not remove this slf4j-api-1.7.1.jar permanently. > Does anyone has an idea how to deal with this conflict? > > Which version of slf4j is used in loci_tools.jar? > Is there any plan to update this to the latest version 1.7.1? > Would there be a conflict during Java class loading if the same version of > slf4j would be available twice? > > Maybe someone has a hint. > Thanks, > Peter > > > > On 20.08.2013 16:24, Curtis Rueden wrote: > >> Hi Peter, >> >> After switching from 32bit to a 64bit Windows I get an error always >>> when I try to run the plugin out of my IJ installation. >>> >> As Stephan says, something is missing. But it should definitely not be >> necessary to download anything manually. >> >> If you run Help > Update Fiji, then click "Advanced mode" and change the >> "View Options" to "View uninstalled files only" do you see any entries >> ending in ".jar"? >> >> java.lang.NoSuchMethodError: org.slf4j.helpers.**MessageFormatter.format >>> >> Your error message suggests you are missing slf4j-api-1.5.10.jar. >> >> If indeed you are missing that file (or other JAR files), click the >> "Status/Action" and change it to "Install / Update". >> >> If that doesn't work, you can also try downloading a fresh & up-to-date >> Fiji from: http://fiji.sc/Downloads. >> >> Regards, >> Curtis >> >> >> On Tue, Aug 20, 2013 at 8:28 AM, Stephan Preibisch <[hidden email] >> >wrote: >> >> Hi Peter, >>> >>> you miss something from the LOCI bioformats to open the stacks ... it is >>> available for download here http://loci.wisc.edu/bio-**formats/downloads<http://loci.wisc.edu/bio-formats/downloads> >>> >>> Hope that helps, >>> Stephan >>> >>> On Aug 20, 2013, at 12:25 , Peter Haub wrote: >>> >>> Hi List, >>>> I use the stitching plugin of S. Preibisch (Grid/Collection mode). >>>> After switching from 32bit to a 64bit Windows I get an error always when >>>> >>> I try to run the plugin out of my IJ installation. >>> >>>> The error message is: >>>> java.lang.NoSuchMethodError: >>>> >>> org.slf4j.helpers.**MessageFormatter.format(Ljava/** >>> lang/String;Ljava/lang/Object;**Ljava/lang/Object;)Ljava/lang/**String; >>> >>>> at >>>> >>> org.slf4j.impl.**Log4jLoggerAdapter.debug(**Log4jLoggerAdapter.java:246) >>> >>>> at loci.common.IniParser.**parseINI(IniParser.java:114) >>>> at loci.common.IniParser.**parseINI(IniParser.java:98) >>>> at loci.plugins.prefs.**OptionsList.<init>(**OptionsList.java:64) >>>> at loci.plugins.in.**ImporterOptions.<init>(** >>>> ImporterOptions.java:156) >>>> at >>>> >>> mpicbg.stitching.**ImageCollectionElement.open(** >>> ImageCollectionElement.java:**81) >>> >>>> at Stitching_Grid.run(Stitching_**Grid.java:342) >>>> at ij.IJ.runUserPlugIn(IJ.java:**185) >>>> at ij.IJ.runPlugIn(IJ.java:152) >>>> at ij.Executer.runCommand(**Executer.java:127) >>>> at ij.Executer.run(Executer.java:**64) >>>> at java.lang.Thread.run(Unknown Source) >>>> IJ version is 1.47f7 >>>> Java version is 1.6.0_31(64bit) - included in the IJ installation >>>> I have update the stitching plugin (from >>>> >>> http://fly.mpi-cbg.de/~**preibisch/software.html#**Stitching<http://fly.mpi-cbg.de/~preibisch/software.html#Stitching> >>> ). >>> >>>> The data is ok. (I used a current FIJI installation where everything >>>> >>> work as expected.) >>> >>>> Does anyone has an idea what to do? >>>> Thanks, >>>> Peter >>>> >>>> -- >>>> 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<http://imagej.nih.gov/ij/list.html> >>> >>> -- >> 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<http://imagej.nih.gov/ij/list.html> > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Hi Curtis,
Thanks for coming back on this and thanks for your detailed asnwers. In the meantime I'm working by removing loci-common.jar ome-xml.jar scifio.jar slf4j-api-1.7.1.jar from the IJ\plugins\Micro-Manager directory and using the versions included in the stitching plugin (without changing storage position). Until now it works fine and we do not see any problems. But we haven't done any specific testing e.g. of the Micro-Managers logging feature. If there will be new information I will post it. Regards, Peter On 10.09.2013 23:14, Curtis Rueden wrote: > Hi Peter, > > Apologies for the delay in my reply. > >> I would prefer to not remove this slf4j-api-1.7.1.jar permanently. >> Does anyone has an idea how to deal with this conflict? > Three options: > > 1) Use Fiji [1]. It comes with the stitching plugins, and is already > structured to avoid this sort of problem. > > 2) Stop using loci_tools.jar and instead put all the individual component > JAR files of Bio-Formats [1] into your plugins folder. This is what Fiji > does. > > 3) Remove slf4j-api-1.7.1.jar, as you have done. This is actually OK as > long as Micro-Manager does not use any new API introduced since > slf4j-api-1.5.10. (But I am really not sure whether it does! Does > Micro-Manager's logging still work for you with that library removed?) > >> Which version of slf4j is used in loci_tools.jar? > Version 4.4.8 of loci_tools.jar uses SLF4J 1.5.10. > >> Is there any plan to update this to the latest version 1.7.1? > The latest development version of Bio-Formats has already been upgraded to > 1.7.2 [3], which will be the version used for the next releases: 4.4.9 and > 5.0.0-beta2. > >> Would there be a conflict during Java class loading if the same >> version of slf4j would be available twice? > It should work, as long as the two versions really are the same. > > Regards, > Curtis > > [1] http://fiji.sc/ > [2] https://www.openmicroscopy.org/site/products/bio-formats/downloads > [3] > https://github.com/openmicroscopy/bioformats/commit/5b8b5ff83d23012c5805a8420681085244934cb6 > > > On Wed, Aug 21, 2013 at 3:25 AM, Peter Haub <[hidden email]> wrote: > >> Hi Stephan, >> Hi Curtis, >> >> Thanks for your answers. >> I found the reason for the error message. >> >> Stephans stitching plugin comes with a copy of the loci_tools.jar (if >> manually installed into a IJ configuration). >> This loci_tools.jar contains a version of slf4j (in \org\slf4j\ in the >> latest loci_tools.jar, downloaded from the loci web page). >> This slf4j seems to be in conflict with another version of that library >> (slf4j-api-1.7.1.jar), located in the ..\plugins\Micro-Manager folder in a >> default microManager configuration. >> Removing this slf4j-api-1.7.1.jar solves the problem. The stitching plugin >> can be used then without error messages. >> >> I would prefer to not remove this slf4j-api-1.7.1.jar permanently. >> Does anyone has an idea how to deal with this conflict? >> >> Which version of slf4j is used in loci_tools.jar? >> Is there any plan to update this to the latest version 1.7.1? >> Would there be a conflict during Java class loading if the same version of >> slf4j would be available twice? >> >> Maybe someone has a hint. >> Thanks, >> Peter >> >> >> >> On 20.08.2013 16:24, Curtis Rueden wrote: >> >>> Hi Peter, >>> >>> After switching from 32bit to a 64bit Windows I get an error always >>>> when I try to run the plugin out of my IJ installation. >>>> >>> As Stephan says, something is missing. But it should definitely not be >>> necessary to download anything manually. >>> >>> If you run Help > Update Fiji, then click "Advanced mode" and change the >>> "View Options" to "View uninstalled files only" do you see any entries >>> ending in ".jar"? >>> >>> java.lang.NoSuchMethodError: org.slf4j.helpers.**MessageFormatter.format >>> Your error message suggests you are missing slf4j-api-1.5.10.jar. >>> >>> If indeed you are missing that file (or other JAR files), click the >>> "Status/Action" and change it to "Install / Update". >>> >>> If that doesn't work, you can also try downloading a fresh & up-to-date >>> Fiji from: http://fiji.sc/Downloads. >>> >>> Regards, >>> Curtis >>> >>> >>> On Tue, Aug 20, 2013 at 8:28 AM, Stephan Preibisch <[hidden email] >>>> wrote: >>> Hi Peter, >>>> you miss something from the LOCI bioformats to open the stacks ... it is >>>> available for download here http://loci.wisc.edu/bio-**formats/downloads<http://loci.wisc.edu/bio-formats/downloads> >>>> >>>> Hope that helps, >>>> Stephan >>>> >>>> On Aug 20, 2013, at 12:25 , Peter Haub wrote: >>>> >>>> Hi List, >>>>> I use the stitching plugin of S. Preibisch (Grid/Collection mode). >>>>> After switching from 32bit to a 64bit Windows I get an error always when >>>>> >>>> I try to run the plugin out of my IJ installation. >>>> >>>>> The error message is: >>>>> java.lang.NoSuchMethodError: >>>>> >>>> org.slf4j.helpers.**MessageFormatter.format(Ljava/** >>>> lang/String;Ljava/lang/Object;**Ljava/lang/Object;)Ljava/lang/**String; >>>> >>>>> at >>>>> >>>> org.slf4j.impl.**Log4jLoggerAdapter.debug(**Log4jLoggerAdapter.java:246) >>>> >>>>> at loci.common.IniParser.**parseINI(IniParser.java:114) >>>>> at loci.common.IniParser.**parseINI(IniParser.java:98) >>>>> at loci.plugins.prefs.**OptionsList.<init>(**OptionsList.java:64) >>>>> at loci.plugins.in.**ImporterOptions.<init>(** >>>>> ImporterOptions.java:156) >>>>> at >>>>> >>>> mpicbg.stitching.**ImageCollectionElement.open(** >>>> ImageCollectionElement.java:**81) >>>> >>>>> at Stitching_Grid.run(Stitching_**Grid.java:342) >>>>> at ij.IJ.runUserPlugIn(IJ.java:**185) >>>>> at ij.IJ.runPlugIn(IJ.java:152) >>>>> at ij.Executer.runCommand(**Executer.java:127) >>>>> at ij.Executer.run(Executer.java:**64) >>>>> at java.lang.Thread.run(Unknown Source) >>>>> IJ version is 1.47f7 >>>>> Java version is 1.6.0_31(64bit) - included in the IJ installation >>>>> I have update the stitching plugin (from >>>>> >>>> http://fly.mpi-cbg.de/~**preibisch/software.html#**Stitching<http://fly.mpi-cbg.de/~preibisch/software.html#Stitching> >>>> ). >>>> >>>>> The data is ok. (I used a current FIJI installation where everything >>>>> >>>> work as expected.) >>>> >>>>> Does anyone has an idea what to do? >>>>> Thanks, >>>>> Peter >>>>> >>>>> -- >>>>> 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<http://imagej.nih.gov/ij/list.html> >>>> >>>> -- >>> 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<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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