ome / bioformats

Bio-Formats is a Java library for reading and writing data in life sciences image file formats. It is developed by the Open Microscopy Environment. Bio-Formats is released under the GNU General Public License (GPL); commercial licenses are available from Glencoe Software.
https://www.openmicroscopy.org/bio-formats
GNU General Public License v2.0
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MATLAB: "loci.formats.in.*Reader" is not valid. #3225

Closed erjel closed 6 years ago

erjel commented 6 years ago

I would like to use the Bio-Format MATLAB Toolbox for automatically convert .nd2to .tif files with a small script. Unfortunately I could not even mange to read the files. The script:

filename = './nd2file.nd2';

addpath('./bfmatlab');
[status,version] = bfCheckJavaPath()

data = bfopen(filename);

produces the error message

status =

  logical

   1

version =

    '5.1.1'

"loci.formats.in.FilePatternReader" is not valid.
"loci.formats.in.ZipReader" is not valid.
"loci.formats.in.APNGReader" is not valid.
"loci.formats.in.JPEGReader" is not valid.
"loci.formats.in.PGMReader" is not valid.
"loci.formats.in.FitsReader" is not valid.
"loci.formats.in.PCXReader" is not valid.
"loci.formats.in.GIFReader" is not valid.
"loci.formats.in.BMPReader" is not valid.
"loci.formats.in.IPLabReader" is not valid.
"loci.formats.in.IvisionReader" is not valid.
"loci.formats.in.DeltavisionReader" is not valid.
"loci.formats.in.MRCReader" is not valid.
"loci.formats.in.GatanReader" is not valid.
"loci.formats.in.GatanDM2Reader" is not valid.
"loci.formats.in.ImarisReader" is not valid.
"loci.formats.in.OpenlabRawReader" is not valid.
"loci.formats.in.OMEXMLReader" is not valid.
"loci.formats.in.LIFReader" is not valid.
"loci.formats.in.AVIReader" is not valid.
"loci.formats.in.PictReader" is not valid.
"loci.formats.in.SDTReader" is not valid.
"loci.formats.in.EPSReader" is not valid.
"loci.formats.in.SlidebookReader" is not valid.
"loci.formats.in.AliconaReader" is not valid.
"loci.formats.in.MNGReader" is not valid.
"loci.formats.in.KhorosReader" is not valid.
"loci.formats.in.VisitechReader" is not valid.
"loci.formats.in.LIMReader" is not valid.
"loci.formats.in.PSDReader" is not valid.
"loci.formats.in.InCellReader" is not valid.
"loci.formats.in.L2DReader" is not valid.
"loci.formats.in.FEIReader" is not valid.
"loci.formats.in.NAFReader" is not valid.
"loci.formats.in.MINCReader" is not valid.
"loci.formats.in.QTReader" is not valid.
"loci.formats.in.MRWReader" is not valid.
"loci.formats.in.TillVisionReader" is not valid.
"loci.formats.in.ARFReader" is not valid.
"loci.formats.in.CellomicsReader" is not valid.
"loci.formats.in.LiFlimReader" is not valid.
"loci.formats.in.TargaReader" is not valid.
"loci.formats.in.OxfordInstrumentsReader" is not valid.
"loci.formats.in.VGSAMReader" is not valid.
"loci.formats.in.HISReader" is not valid.
"loci.formats.in.WATOPReader" is not valid.
"loci.formats.in.SeikoReader" is not valid.
"loci.formats.in.TopometrixReader" is not valid.
"loci.formats.in.UBMReader" is not valid.
"loci.formats.in.QuesantReader" is not valid.
"loci.formats.in.BioRadGelReader" is not valid.
"loci.formats.in.RHKReader" is not valid.
"loci.formats.in.MolecularImagingReader" is not valid.
"loci.formats.in.CellWorxReader" is not valid.
"loci.formats.in.Ecat7Reader" is not valid.
"loci.formats.in.VarianFDFReader" is not valid.
"loci.formats.in.AIMReader" is not valid.
"loci.formats.in.InCell3000Reader" is not valid.
"loci.formats.in.SpiderReader" is not valid.
"loci.formats.in.VolocityReader" is not valid.
"loci.formats.in.ImagicReader" is not valid.
"loci.formats.in.HamamatsuVMSReader" is not valid.
"loci.formats.in.CellSensReader" is not valid.
"loci.formats.in.INRReader" is not valid.
"loci.formats.in.KodakReader" is not valid.
"loci.formats.in.VolocityClippingReader" is not valid.
"loci.formats.in.ZeissCZIReader" is not valid.
"loci.formats.in.SIFReader" is not valid.
"loci.formats.in.NDPISReader" is not valid.
"loci.formats.in.PovrayReader" is not valid.
"loci.formats.in.IMODReader" is not valid.
"loci.formats.in.FakeReader" is not valid.
"loci.formats.in.AFIReader" is not valid.
"loci.formats.in.ImspectorReader" is not valid.
"loci.formats.in.BioRadSCNReader" is not valid.
"loci.formats.in.ZeissLMSReader" is not valid.
"loci.formats.in.PQBinReader" is not valid.
"loci.formats.in.FlowSightReader" is not valid.
"loci.formats.in.IM3Reader" is not valid.
"loci.formats.in.I2IReader" is not valid.
"loci.formats.in.JEOLReader" is not valid.
"loci.formats.in.NiftiReader" is not valid.
"loci.formats.in.AnalyzeReader" is not valid.
"loci.formats.in.APLReader" is not valid.
"loci.formats.in.NRRDReader" is not valid.
"loci.formats.in.ICSReader" is not valid.
"loci.formats.in.PerkinElmerReader" is not valid.
"loci.formats.in.AmiraReader" is not valid.
"loci.formats.in.ScanrReader" is not valid.
"loci.formats.in.BDReader" is not valid.
"loci.formats.in.UnisokuReader" is not valid.
"loci.formats.in.PDSReader" is not valid.
"loci.formats.in.FujiReader" is not valid.
"loci.formats.in.OperettaReader" is not valid.
"loci.formats.in.InveonReader" is not valid.
"loci.formats.in.CellVoyagerReader" is not valid.
"loci.formats.in.BioRadReader" is not valid.
"loci.formats.in.FV1000Reader" is not valid.
"loci.formats.in.ZeissZVIReader" is not valid.
"loci.formats.in.IPWReader" is not valid.
"loci.formats.in.JPEG2000Reader" is not valid.
"loci.formats.in.JPXReader" is not valid.
"loci.formats.in.ND2Reader" is not valid.
"loci.formats.in.PCIReader" is not valid.
"loci.formats.in.ImarisHDFReader" is not valid.
"loci.formats.in.CellH5Reader" is not valid.
"loci.formats.in.WlzReader" is not valid.
"loci.formats.in.VeecoReader" is not valid.
"loci.formats.in.ZeissLSMReader" is not valid.
"loci.formats.in.SEQReader" is not valid.
"loci.formats.in.GelReader" is not valid.
"loci.formats.in.ImarisTiffReader" is not valid.
"loci.formats.in.FlexReader" is not valid.
"loci.formats.in.SVSReader" is not valid.
"loci.formats.in.ImaconReader" is not valid.
"loci.formats.in.LEOReader" is not valid.
"loci.formats.in.JPKReader" is not valid.
"loci.formats.in.NDPIReader" is not valid.
"loci.formats.in.PCORAWReader" is not valid.
"loci.formats.in.OMETiffReader" is not valid.
"loci.formats.in.PyramidTiffReader" is not valid.
"loci.formats.in.MIASReader" is not valid.
"loci.formats.in.TCSReader" is not valid.
"loci.formats.in.LeicaReader" is not valid.
"loci.formats.in.NikonReader" is not valid.
"loci.formats.in.FluoviewReader" is not valid.
"loci.formats.in.PrairieReader" is not valid.
"loci.formats.in.MetamorphReader" is not valid.
"loci.formats.in.MicromanagerReader" is not valid.
"loci.formats.in.ImprovisionTiffReader" is not valid.
"loci.formats.in.MetamorphTiffReader" is not valid.
"loci.formats.in.NikonTiffReader" is not valid.
"loci.formats.in.PhotoshopTiffReader" is not valid.
"loci.formats.in.FEITiffReader" is not valid.
"loci.formats.in.SimplePCITiffReader" is not valid.
"loci.formats.in.NikonElementsTiffReader" is not valid.
"loci.formats.in.TrestleReader" is not valid.
"loci.formats.in.SISReader" is not valid.
"loci.formats.in.DNGReader" is not valid.
"loci.formats.in.ZeissTIFFReader" is not valid.
"loci.formats.in.LeicaSCNReader" is not valid.
"loci.formats.in.SlidebookTiffReader" is not valid.
"loci.formats.in.TiffDelegateReader" is not valid.
"loci.formats.in.TextReader" is not valid.
"loci.formats.in.BurleighReader" is not valid.
"loci.formats.in.OpenlabReader" is not valid.
"loci.formats.in.DicomReader" is not valid.
"loci.formats.in.SMCameraReader" is not valid.
"loci.formats.in.SBIGReader" is not valid.
"loci.formats.in.HRDGDFReader" is not valid.
"loci.formats.in.HitachiReader" is not valid.
"loci.formats.in.BrukerReader" is not valid.
"loci.formats.in.CanonRawReader" is not valid.
"loci.formats.in.OBFReader" is not valid.
Error using bfGetReader (line 85)
Java exception occurred:
loci.formats.UnknownFormatException: Unknown file format: /home/###/Development/Matlab/BioFormats/nd2file.nd2
    at loci.formats.ImageReader.getReader(ImageReader.java:190)
    at loci.formats.ImageReader.setId(ImageReader.java:832)
    at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
    at loci.formats.ChannelFiller.setId(ChannelFiller.java:223)
    at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
    at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:291)

Error in bfopen (line 114)
r = bfGetReader(id, stitchFiles);

Error in convert_nd2_tif (line 6)
data = bfopen(filename);

The first thing which puzzles me is the version number '5.1.1': I downloaded bioformats_package.jar several times either bundled in the MATLAB Toolbox, as Java Bio-Formats Package and copy-pasted it in the toolbox folder and finally even downloaded legacy versions (5.7.0) just to check whether the version number changes. It does not ...

Since I only care about a working script and not so much about a single version number, I focused on the error message: It seems like no reader can be connected to the .nd2 file type in line 181 in ImageReader.java. But if manually check it

r = javaObject('loci.formats.in.ND2Reader');
r.isThisType(filename, true)

I get a positiv result:

ans =

  logical

   1

On the other hand a

r.setId(filename)

will result in the same error message like above.

I thought that I have followed the documentation as closely as possible. But somewhere I missed something out. I already tested it on two systems: MATLAB 2017b with WIndows 10 64-bit and the latest Java JDK 10 (binary directory C:\Program Files\java\jre-10.0.2\bin added to PATH environment variable) MATLAB 2017a with Debian 9 stretch 64-bit with openjdk version "1.8.0_181"

Can anyone help me?

sbesson commented 6 years ago

Hi @erjel,

sorry to hear about these issues. I agree that the reported version number is suspicious. To help troubleshooting this issue, could you send us the content of

>> javaclasspath

in order to confirm there is nothing in the static of the dynamic Java class path that would shadow the content of bioformats_package you downloaded?

erjel commented 6 years ago

Hi @sbesson ,

>> javaclasspath

        STATIC JAVA PATH

    C:\Micro-Manager-2.0beta\plugins\Micro-Manager\guava-17.0.jar                                             
    C:\Program Files\MATLAB\R2017b\java\patch                                                                 
    C:\Program Files\MATLAB\R2017b\java\jarext\ant.jar                                                        
    C:\Program Files\MATLAB\R2017b\java\jarext\ant-launcher.jar                                               
    C:\Program Files\MATLAB\R2017b\java\jarext\antlr.jar                                                      
    C:\Program Files\MATLAB\R2017b\java\jarext\felix.jar                                                      
    C:\Program Files\MATLAB\R2017b\java\jarext\scr.jar                                                        
    C:\Program Files\MATLAB\R2017b\java\jarext\axis2\activation.jar                                           
    C:\Program Files\MATLAB\R2017b\java\jarext\axis2\axiom-api.jar                                            
    C:\Program Files\MATLAB\R2017b\java\jarext\axis2\axiom-impl.jar                                           
    C:\Program Files\MATLAB\R2017b\java\jarext\axis2\axis2-adb.jar                                            
    C:\Program Files\MATLAB\R2017b\java\jarext\axis2\axis2-kernel.jar                                         
    C:\Program Files\MATLAB\R2017b\java\jarext\axis2\axis2-transport-http.jar                                 
    C:\Program Files\MATLAB\R2017b\java\jarext\axis2\axis2-transport-local.jar                                
    C:\Program Files\MATLAB\R2017b\java\jarext\axis2\commons-httpclient.jar                                   
    C:\Program Files\MATLAB\R2017b\java\jarext\axis2\geronimo-stax-api.jar                                    
    C:\Program Files\MATLAB\R2017b\java\jarext\axis2\httpcore.jar                                             
    C:\Program Files\MATLAB\R2017b\java\jarext\axis2\mail.jar                                                 
    C:\Program Files\MATLAB\R2017b\java\jarext\axis2\neethi.jar                                               
    C:\Program Files\MATLAB\R2017b\java\jarext\axis2\wsdl4j.jar                                               
    C:\Program Files\MATLAB\R2017b\java\jarext\axis2\wstx-asl.jar                                             
    C:\Program Files\MATLAB\R2017b\java\jarext\axis2\XmlSchema.jar                                            
    C:\Program Files\MATLAB\R2017b\java\jarext\batik-anim.jar                                                 
    C:\Program Files\MATLAB\R2017b\java\jarext\batik-extension.jar                                            
    C:\Program Files\MATLAB\R2017b\java\jarext\batik-dom.jar                                                  
    C:\Program Files\MATLAB\R2017b\java\jarext\batik-transcoder.jar                                           
    C:\Program Files\MATLAB\R2017b\java\jarext\batik-awt-util.jar                                             
    C:\Program Files\MATLAB\R2017b\java\jarext\batik-bridge.jar                                               
    C:\Program Files\MATLAB\R2017b\java\jarext\batik-gvt.jar                                                  
    C:\Program Files\MATLAB\R2017b\java\jarext\batik-css.jar                                                  
    C:\Program Files\MATLAB\R2017b\java\jarext\batik-parser.jar                                               
    C:\Program Files\MATLAB\R2017b\java\jarext\batik-ext.jar                                                  
    C:\Program Files\MATLAB\R2017b\java\jarext\batik-gui-util.jar                                             
    C:\Program Files\MATLAB\R2017b\java\jarext\batik-svggen.jar                                               
    C:\Program Files\MATLAB\R2017b\java\jarext\batik-codec.jar                                                
    C:\Program Files\MATLAB\R2017b\java\jarext\batik-svg-dom.jar                                              
    C:\Program Files\MATLAB\R2017b\java\jarext\batik-script.jar                                               
    C:\Program Files\MATLAB\R2017b\java\jarext\batik-util.jar                                                 
    C:\Program Files\MATLAB\R2017b\java\jarext\batik-swing.jar                                                
    C:\Program Files\MATLAB\R2017b\java\jarext\batik-xml.jar                                                  
    C:\Program Files\MATLAB\R2017b\java\jarext\bluecove-emu.jar                                               
    C:\Program Files\MATLAB\R2017b\java\jarext\bluecove.jar                                                   
    C:\Program Files\MATLAB\R2017b\java\jarext\commons-cli.jar                                                
    C:\Program Files\MATLAB\R2017b\java\jarext\commons-codec.jar                                              
    C:\Program Files\MATLAB\R2017b\java\jarext\commons-collections-generic.jar                                
    C:\Program Files\MATLAB\R2017b\java\jarext\commons-collections.jar                                        
    C:\Program Files\MATLAB\R2017b\java\jarext\commons-compress.jar                                           
    C:\Program Files\MATLAB\R2017b\java\jarext\commons-io.jar                                                 
    C:\Program Files\MATLAB\R2017b\java\jarext\commons-lang.jar                                               
    C:\Program Files\MATLAB\R2017b\java\jarext\commons-logging.jar                                            
    C:\Program Files\MATLAB\R2017b\java\jarext\commons-net.jar                                                
    C:\Program Files\MATLAB\R2017b\java\jarext\dom4j.jar                                                      
    C:\Program Files\MATLAB\R2017b\java\jarext\fop-pdf-images.jar                                             
    C:\Program Files\MATLAB\R2017b\java\jarext\fop.jar                                                        
    C:\Program Files\MATLAB\R2017b\java\jarext\avalon-framework-api.jar                                       
    C:\Program Files\MATLAB\R2017b\java\jarext\avalon-framework-impl.jar                                      
    C:\Program Files\MATLAB\R2017b\java\jarext\foxtrot.jar                                                    
    C:\Program Files\MATLAB\R2017b\java\jarext\geotools\geoapi-nogenerics.jar                                 
    C:\Program Files\MATLAB\R2017b\java\jarext\geotools\gt2-api.jar                                           
    C:\Program Files\MATLAB\R2017b\java\jarext\geotools\gt2-coverage.jar                                      
    C:\Program Files\MATLAB\R2017b\java\jarext\geotools\gt2-main.jar                                          
    C:\Program Files\MATLAB\R2017b\java\jarext\geotools\gt2-referencing.jar                                   
    C:\Program Files\MATLAB\R2017b\java\jarext\geotools\gt2-referencing3D.jar                                 
    C:\Program Files\MATLAB\R2017b\java\jarext\geotools\gt2-wms.jar                                           
    C:\Program Files\MATLAB\R2017b\java\jarext\geotools\jts.jar                                               
    C:\Program Files\MATLAB\R2017b\java\jarext\glazedlists_java15.jar                                         
    C:\Program Files\MATLAB\R2017b\java\jarext\google-collect.jar                                             
    C:\Program Files\MATLAB\R2017b\java\jarext\gson.jar                                                       
    C:\Program Files\MATLAB\R2017b\java\jarext\guice\aopalliance.jar                                          
    C:\Program Files\MATLAB\R2017b\java\jarext\guice\guice.jar                                                
    C:\Program Files\MATLAB\R2017b\java\jarext\guice\guice-assistedinject.jar                                 
    C:\Program Files\MATLAB\R2017b\java\jarext\guice\javax.inject.jar                                         
    C:\Program Files\MATLAB\R2017b\java\jarext\distcomp\h2mig_pagestore_addon.jar                             
    C:\Program Files\MATLAB\R2017b\java\jarext\distcomp\h2.jar                                                
    C:\Program Files\MATLAB\R2017b\java\jarext\ice\ice.jar                                                    
    C:\Program Files\MATLAB\R2017b\java\jarext\ice\ib6core.jar                                                
    C:\Program Files\MATLAB\R2017b\java\jarext\ice\ib6extra.jar                                               
    C:\Program Files\MATLAB\R2017b\java\jarext\ice\ib6http.jar                                                
    C:\Program Files\MATLAB\R2017b\java\jarext\ice\ib6https.jar                                               
    C:\Program Files\MATLAB\R2017b\java\jarext\ice\ib6js.jar                                                  
    C:\Program Files\MATLAB\R2017b\java\jarext\ice\ib6swing.jar                                               
    C:\Program Files\MATLAB\R2017b\java\jarext\ice\ib6util.jar                                                
    C:\Program Files\MATLAB\R2017b\java\jarext\ice\ib6xalan.jar                                               
    C:\Program Files\MATLAB\R2017b\java\jarext\ice\icessl.jar                                                 
    C:\Program Files\MATLAB\R2017b\java\jarext\jackson\jackson-annotations.jar                                
    C:\Program Files\MATLAB\R2017b\java\jarext\jackson\jackson-core.jar                                       
    C:\Program Files\MATLAB\R2017b\java\jarext\jackson\jackson-databind.jar                                   
    C:\Program Files\MATLAB\R2017b\java\jarext\jackson\jackson-jaxrs-base.jar                                 
    C:\Program Files\MATLAB\R2017b\java\jarext\jackson\jackson-jaxrs-json-provider.jar                        
    C:\Program Files\MATLAB\R2017b\java\jarext\jackson\jackson-module-jaxb-annotations.jar                    
    C:\Program Files\MATLAB\R2017b\java\jarext\access-bridge.jar                                              
    C:\Program Files\MATLAB\R2017b\java\jarext\jaccess-1_4.jar                                                
    C:\Program Files\MATLAB\R2017b\java\jarext\jaxen.jar                                                      
    C:\Program Files\MATLAB\R2017b\java\jarext\jdom.jar                                                       
    C:\Program Files\MATLAB\R2017b\java\jarext\annotations.jar                                                
    C:\Program Files\MATLAB\R2017b\java\jarext\jgit\jgit.jar                                                  
    C:\Program Files\MATLAB\R2017b\java\jarext\jgit\jgitui.jar                                                
    C:\Program Files\MATLAB\R2017b\java\jarext\jgoodies-forms.jar                                             
    C:\Program Files\MATLAB\R2017b\java\jarext\jgoodies-looks.jar                                             
    C:\Program Files\MATLAB\R2017b\java\jarext\jide\jide-action.jar                                           
    C:\Program Files\MATLAB\R2017b\java\jarext\jide\jide-charts.jar                                           
    C:\Program Files\MATLAB\R2017b\java\jarext\jide\jide-common.jar                                           
    C:\Program Files\MATLAB\R2017b\java\jarext\jide\jide-components.jar                                       
    C:\Program Files\MATLAB\R2017b\java\jarext\jide\jide-dialogs.jar                                          
    C:\Program Files\MATLAB\R2017b\java\jarext\jide\jide-dock.jar                                             
    C:\Program Files\MATLAB\R2017b\java\jarext\jide\jide-properties.jar                                       
    C:\Program Files\MATLAB\R2017b\java\jarext\jide\jide-grids.jar                                            
    C:\Program Files\MATLAB\R2017b\java\jarext\jide\jide-shortcut.jar                                         
    C:\Program Files\MATLAB\R2017b\java\jarext\distcomp\jini2\lib\fiddler-dl.jar                              
    C:\Program Files\MATLAB\R2017b\java\jarext\distcomp\jini2\lib\phoenix-dl.jar                              
    C:\Program Files\MATLAB\R2017b\java\jarext\distcomp\jini2\lib\mahalo.jar                                  
    C:\Program Files\MATLAB\R2017b\java\jarext\distcomp\jini2\lib\destroy.jar                                 
    C:\Program Files\MATLAB\R2017b\java\jarext\distcomp\jini2\lib\jsk-platform.jar                            
    C:\Program Files\MATLAB\R2017b\java\jarext\distcomp\jini2\lib\jini-ext.jar                                
    C:\Program Files\MATLAB\R2017b\java\jarext\distcomp\jini2\lib\jini-core.jar                               
    C:\Program Files\MATLAB\R2017b\java\jarext\distcomp\jini2\lib\reggie-dl.jar                               
    C:\Program Files\MATLAB\R2017b\java\jarext\distcomp\jini2\lib\norm-dl.jar                                 
    C:\Program Files\MATLAB\R2017b\java\jarext\distcomp\jini2\lib\browser-dl.jar                              
    C:\Program Files\MATLAB\R2017b\java\jarext\distcomp\jini2\lib\sdm-dl.jar                                  
    C:\Program Files\MATLAB\R2017b\java\jarext\distcomp\jini2\lib\norm.jar                                    
    C:\Program Files\MATLAB\R2017b\java\jarext\distcomp\jini2\lib\mahalo-dl.jar                               
    C:\Program Files\MATLAB\R2017b\java\jarext\distcomp\jini2\lib\group.jar                                   
    C:\Program Files\MATLAB\R2017b\java\jarext\distcomp\jini2\lib\phoenix-init.jar                            
    C:\Program Files\MATLAB\R2017b\java\jarext\distcomp\jini2\lib\browser.jar                                 
    C:\Program Files\MATLAB\R2017b\java\jarext\distcomp\jini2\lib\reggie.jar                                  
    C:\Program Files\MATLAB\R2017b\java\jarext\distcomp\jini2\lib\fiddler.jar                                 
    C:\Program Files\MATLAB\R2017b\java\jarext\distcomp\jini2\lib\phoenix-group.jar                           
    C:\Program Files\MATLAB\R2017b\java\jarext\distcomp\jini2\lib\sun-util.jar                                
    C:\Program Files\MATLAB\R2017b\java\jarext\distcomp\jini2\lib\jsk-policy.jar                              
    C:\Program Files\MATLAB\R2017b\java\jarext\distcomp\jini2\lib\group-dl.jar                                
    C:\Program Files\MATLAB\R2017b\java\jarext\distcomp\jini2\lib\sharedvm.jar                                
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    C:\Micro-Manager-2.0beta\ij.jar                                                                           
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    C:\Micro-Manager-2.0beta\plugins\Micro-Manager\formats-api-5.1.1.jar                                      
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    C:\Micro-Manager-2.0beta\plugins\Micro-Manager\kryo-2.24.0.jar                                            
    C:\Micro-Manager-2.0beta\plugins\Micro-Manager\logback-classic-1.1.1.jar                                  
    C:\Micro-Manager-2.0beta\plugins\Micro-Manager\logback-core-1.1.1.jar                                     
    C:\Micro-Manager-2.0beta\plugins\Micro-Manager\miglayout-core-4.2.jar                                     
    C:\Micro-Manager-2.0beta\plugins\Micro-Manager\miglayout-swing-4.2.jar                                    
    C:\Micro-Manager-2.0beta\plugins\Micro-Manager\minlog-1.2.jar                                             
    C:\Micro-Manager-2.0beta\plugins\Micro-Manager\objenesis-2.1.jar                                          
    C:\Micro-Manager-2.0beta\plugins\Micro-Manager\ome-xml-5.1.1.jar                                          
    C:\Micro-Manager-2.0beta\plugins\Micro-Manager\protobuf-java-2.5.0.jar                                    
    C:\Micro-Manager-2.0beta\plugins\Micro-Manager\rsyntaxtextarea-2.5.2.jar                                  
    C:\Micro-Manager-2.0beta\plugins\Micro-Manager\scijava-common-2.46.0.jar                                  
    C:\Micro-Manager-2.0beta\plugins\Micro-Manager\serializer-2.7.1.jar                                       
    C:\Micro-Manager-2.0beta\plugins\Micro-Manager\slf4j-api-1.7.6.jar                                        
    C:\Micro-Manager-2.0beta\plugins\Micro-Manager\swingx-0.9.5.jar                                           
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    C:\Micro-Manager-2.0beta\plugins\Micro-Manager\xml-apis-1.3.04.jar                                        

        DYNAMIC JAVA PATH

    F:\###\z_MATLAB_Analysis\bfmatlab\bioformats_package.jar

Thank you for your help! Eric

sbesson commented 6 years ago

Hi @erjel

    C:\Micro-Manager-2.0beta\plugins\Micro-Manager\formats-api-5.1.1.jar                                      
    C:\Micro-Manager-2.0beta\plugins\Micro-Manager\formats-common-5.1.1.jar  

largely explains the issue you are describing. Micro-Manager 1.4 and 2.0-beta both use and ship an older version of Bio-Formats. If you want to use a recent version of Bio-Formats for reading files, you will need to remove the Micro-Manager JARs (at least the Bio-Formats ones) from your static Java path.

erjel commented 6 years ago

Thank you for your quick response! I commented the corresponding lines in javaclasspath.txt. As expected this solved the problem with the used bioformats version:

version =

    '5.9.2'

Unfortunately I ran into a different problem:

Error using bfGetReader (line 75)
Java exception occurred:
java.lang.NoSuchFieldError: MICROMETER

    at loci.formats.in.NiftiReader.<init>(NiftiReader.java:78)

    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)

    at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)

    at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)

    at java.lang.reflect.Constructor.newInstance(Constructor.java:423)

    at java.lang.Class.newInstance(Class.java:442)

    at loci.formats.ImageReader.<init>(ImageReader.java:129)

    at loci.formats.in.FilePatternReader.<init>(FilePatternReader.java:77)

    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)

    at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)

    at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)

    at java.lang.reflect.Constructor.newInstance(Constructor.java:423)

    at java.lang.Class.newInstance(Class.java:442)

    at loci.formats.ImageReader.<init>(ImageReader.java:129)

    at loci.formats.ImageReader.<init>(ImageReader.java:116)

    at loci.formats.ReaderWrapper.<init>(ReaderWrapper.java:61)

    at loci.formats.ChannelFiller.<init>(ChannelFiller.java:71)

Do you have any idea why the NiftiReader is used? I tested bfopen also with a matlab-generated .tif-file to make sure that my .nd2 file is not corrupted. It produces the same error message.

sbesson commented 6 years ago

The above is actually related to the same problem. The Bio-Formats 5.1.1 JARs shipped with Micro-Manager depend on the ome-xml:5.1.1component which is an older version of the OME model. Removing:

    C:\Micro-Manager-2.0beta\plugins\Micro-Manager\ome-xml-5.1.1.jar                                          

should allow to import the latest classes included in bioformats_package.

erjel commented 6 years ago

Thank you a lot! It solved the problem.

Summary: 1.) Inspect the javaclasspath in matlab

>> javaclasspath

2.) In case multiple versions of bioformats are present comment/ delete them.

>> cd(prefdir)
>> edit javaclasspath.txt

In my case we changed corresponding lines to:

[...]
#C:\Micro-Manager-2.0beta\plugins\Micro-Manager\formats-api-5.1.1.jar
#C:\Micro-Manager-2.0beta\plugins\Micro-Manager\formats-common-5.1.1.jar
[...]
#C:\Micro-Manager-2.0beta\plugins\Micro-Manager\ome-xml-5.1.1.jar
[...]