1) Use Fiji [1]. It comes with the stitching plugins, and is already
JAR files of Bio-Formats [1] into your plugins folder. This is what Fiji
3) Remove slf4j-api-1.7.1.jar, as you have done. This is actually OK as
slf4j-api-1.5.10. (But I am really not sure whether it does! Does
> 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>
>>>>
>>>
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>>>
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>>
>>
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>