Buffer too small error - Opening .nd2 file with Bioformats + BigStitcher

[Eddymorphling]

I am trying to stich an Nikon .nd2 multi-point dataset but get the error below when trying to use BigStitcher to open and read metadata using Bioformats. I am currently running on Bioformats 8.0. I saw folks have also reported similar errors in the past on the ImageJ forums and BigStitcher github pages but I was not able to find a fix to the issue yet. Not sure if this is a Bioformats error or a BigStitcher issue to be honest.. Any suggestions?

loci.formats.FormatException: Buffer too small (got 1572864, expected 2097152).
	at loci.formats.FormatTools.checkBufferSize(FormatTools.java:1048)
	at loci.formats.FormatTools.checkPlaneParameters(FormatTools.java:1004)
	at loci.formats.in.ND2Reader.openBytes(ND2Reader.java:244)
	at loci.formats.FormatReader.openBytes(FormatReader.java:901)
	at loci.formats.ImageReader.openBytes(ImageReader.java:458)
	at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:343)
	at net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyFileMapImgLoaderLOCI.openImg(LegacyFileMapImgLoaderLOCI.java:270)
	at net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyFileMapImgLoaderLOCI.getImage(LegacyFileMapImgLoaderLOCI.java:153)
	at mpicbg.spim.data.legacy.LegacyImgLoaderWrapper$SetupImgLoaderWrapper.getImage(LegacyImgLoaderWrapper.java:79)
	at bdv.export.WriteSequenceToHdf5.writeViewToHdf5PartitionFile(WriteSequenceToHdf5.java:556)
	at bdv.export.WriteSequenceToHdf5.writeHdf5PartitionFile(WriteSequenceToHdf5.java:440)
	at bdv.export.WriteSequenceToHdf5.writeHdf5File(WriteSequenceToHdf5.java:159)
	at net.preibisch.mvrecon.fiji.plugin.resave.Generic_Resave_HDF5.writeHDF5(Generic_Resave_HDF5.java:261)
	at net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinition.createDataset(FileListDatasetDefinition.java:1280)
	at net.preibisch.mvrecon.fiji.plugin.Define_Multi_View_Dataset.defineDataset(Define_Multi_View_Dataset.java:144)
	at net.preibisch.mvrecon.fiji.plugin.queryXML.LoadParseQueryXML.queryXML(LoadParseQueryXML.java:123)
	at net.preibisch.mvrecon.fiji.plugin.queryXML.LoadParseQueryXML.queryXML(LoadParseQueryXML.java:110)
	at net.preibisch.stitcher.plugin.BigStitcher.run(BigStitcher.java:97)
	at org.scijava.command.CommandModule.run(CommandModule.java:196)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:165)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:125)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:64)
	at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:247)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:750)
java.lang.RuntimeException: Could not load '/home/mvn/Desktop/hp-276090.nd2' viewId=0, tpId=0
	at net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyFileMapImgLoaderLOCI.getImage(LegacyFileMapImgLoaderLOCI.java:156)
	at mpicbg.spim.data.legacy.LegacyImgLoaderWrapper$SetupImgLoaderWrapper.getImage(LegacyImgLoaderWrapper.java:79)
	at bdv.export.WriteSequenceToHdf5.writeViewToHdf5PartitionFile(WriteSequenceToHdf5.java:556)
	at bdv.export.WriteSequenceToHdf5.writeHdf5PartitionFile(WriteSequenceToHdf5.java:440)
	at bdv.export.WriteSequenceToHdf5.writeHdf5File(WriteSequenceToHdf5.java:159)
	at net.preibisch.mvrecon.fiji.plugin.resave.Generic_Resave_HDF5.writeHDF5(Generic_Resave_HDF5.java:261)
	at net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinition.createDataset(FileListDatasetDefinition.java:1280)
	at net.preibisch.mvrecon.fiji.plugin.Define_Multi_View_Dataset.defineDataset(Define_Multi_View_Dataset.java:144)
	at net.preibisch.mvrecon.fiji.plugin.queryXML.LoadParseQueryXML.queryXML(LoadParseQueryXML.java:123)
	at net.preibisch.mvrecon.fiji.plugin.queryXML.LoadParseQueryXML.queryXML(LoadParseQueryXML.java:110)
	at net.preibisch.stitcher.plugin.BigStitcher.run(BigStitcher.java:97)
	at org.scijava.command.CommandModule.run(CommandModule.java:196)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:165)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:125)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:64)
	at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:247)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:750)
[ERROR] Command errored: BigStitcher
java.lang.RuntimeException: Could not load /home/mvn/Desktop/hp-276090.nd2' viewId=0, tpId=0: java.lang.RuntimeException: Could not load /home/mvn/Desktop/hp-276090.nd2' viewId=0, tpId=0
	at net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyFileMapImgLoaderLOCI.getImage(LegacyFileMapImgLoaderLOCI.java:164)
	at mpicbg.spim.data.legacy.LegacyImgLoaderWrapper$SetupImgLoaderWrapper.getImage(LegacyImgLoaderWrapper.java:79)
	at bdv.export.WriteSequenceToHdf5.writeViewToHdf5PartitionFile(WriteSequenceToHdf5.java:556)
	at bdv.export.WriteSequenceToHdf5.writeHdf5PartitionFile(WriteSequenceToHdf5.java:440)
	at bdv.export.WriteSequenceToHdf5.writeHdf5File(WriteSequenceToHdf5.java:159)
	at net.preibisch.mvrecon.fiji.plugin.resave.Generic_Resave_HDF5.writeHDF5(Generic_Resave_HDF5.java:261)
	at net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinition.createDataset(FileListDatasetDefinition.java:1280)
	at net.preibisch.mvrecon.fiji.plugin.Define_Multi_View_Dataset.defineDataset(Define_Multi_View_Dataset.java:144)
	at net.preibisch.mvrecon.fiji.plugin.queryXML.LoadParseQueryXML.queryXML(LoadParseQueryXML.java:123)
	at net.preibisch.mvrecon.fiji.plugin.queryXML.LoadParseQueryXML.queryXML(LoadParseQueryXML.java:110)
	at net.preibisch.stitcher.plugin.BigStitcher.run(BigStitcher.java:97)
	at org.scijava.command.CommandModule.run(CommandModule.java:196)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:165)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:125)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:64)
	at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:247)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:750)

[melissalinkert]

Thanks for reporting this, @Eddymorphling. Probably the first thing to try is whether you are able to open every image in the .nd2 file using just the Bio-Formats plugin for ImageJ (i.e. Plugins > Bio-Formats > Bio-Formats Importer). If that works without errors, then that likely rules out a problem with Bio-Formats itself. In that case, PreibischLab/BigStitcher#107 may be related.

If you do see a problem when trying to open with just the Bio-Formats plugin, then it would be very helpful if you could upload an example file to https://zenodo.org/communities/bio-formats/ so that we can investigate.

[Eddymorphling]

Thanks @melissalinkert. The files open in Fiji without any issues. I have commented on BigStitcher post that you had shared, waiting for a response.

[melissalinkert]

Closing this based on PreibischLab/BigStitcher#107 (comment), but we can always re-open if this ends up requiring any changes in Bio-Formats itself.