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fiji / SPIM_Registration

Deprecated, instead check out: https://github.com/preibischLab/multiview-reconstruction & https://github.com/PreibischLab/BigStitcher
GNU General Public License v2.0
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Error when resaving multichannel CZI to HDF5 #91

Open lacan opened 8 years ago

lacan commented 8 years ago

Seems that the channel indexes are 0-based and that the resave plugin is 1-based

java.lang.RuntimeException: File 'BOB.czi' has only channels [0 ... 1], but you want to open channel 2. Stopping. at spim.fiji.spimdata.imgloaders.LegacyStackImgLoaderLOCI.openLOCI(LegacyStackImgLoaderLOCI.java:290) at spim.fiji.spimdata.imgloaders.LegacyStackImgLoaderLOCI.getImage(LegacyStackImgLoaderLOCI.java:125) at mpicbg.spim.data.legacy.LegacyImgLoaderWrapper$SetupImgLoaderWrapper.getImage(LegacyImgLoaderWrapper.java:79) at bdv.export.WriteSequenceToHdf5.writeHdf5PartitionFile(WriteSequenceToHdf5.java:441) at bdv.export.WriteSequenceToHdf5.writeHdf5File(WriteSequenceToHdf5.java:154) at spim.fiji.plugin.resave.Generic_Resave_HDF5.writeHDF5(Generic_Resave_HDF5.java:220) at spim.fiji.plugin.resave.Resave_HDF5.run(Resave_HDF5.java:88) at ij.IJ.runUserPlugIn(IJ.java:212) at ij.IJ.runPlugIn(IJ.java:176) at ij.Executer.runCommand(Executer.java:136) at ij.Executer.run(Executer.java:65) at java.lang.Thread.run(Thread.java:662)

tpietzsch commented 8 years ago

@lacan Can you provide example data that shows the problem?

lacan commented 8 years ago

@tpietzsch I could. The whole multiangle dataset is 65Gb, but a single angle is 10GB. Is there some service you would know that can accept this size?

spimager commented 8 years ago

Google Drive comes with 15GB storage by default.