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Fiji plugins for starting BigDataViewer and exporting data.

License: GNU General Public License v3.0

Java 100.00%

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nicost hkmoon arnimjenett xulman bogovicj nicokiaru theazgra cnkuyan tischi

bigdataviewer_fiji's Issues

Issue resaving data

Hi :)

I have a image volume. 32-bit.
908 x 834 x 414 (x,y,z)
1.2 GB size

I get the following error when:
Export current image as XML/HDF5

Fiji is up to date. Error occurs on RedHat linux (Rhel8).

saving h5/xml file as tif

Is it possible to save a h5/xml dataset as .tif?

Manual transformation of group not working in BDV 6.2.0

When in fused group mode, pressing T should enable one to manually transform all objects in the current group. Instead, BDV does nothing and this is printed to the console:

Exception in thread "AWT-EventQueue-0" java.lang.StackOverflowError
	at bdv.viewer.UnmodifiableViewerState.getSourcesInGroup(UnmodifiableViewerState.java:328)
	at bdv.viewer.UnmodifiableViewerState.getSourcesInGroup(UnmodifiableViewerState.java:328)
	at bdv.viewer.UnmodifiableViewerState.getSourcesInGroup(UnmodifiableViewerState.java:328)
	(...)

I use BigStitcher, which uses BDV 6.2.0, where this bug appears. A fresh Fiji installation without BigStitcher comes with BDV 6.0.0, where group transformation works as expected.
I hope this is the right place for this issue; otherwise please let me know, then I will post it to the BigStitcher repo.

Platform info:
Windows 10 Education 1803 64 bit
ImageJ 1.53a
Big_Stitcher-0.5.5
bigdataviewer_fiji-6.2.0

Cheers

"File>Import>BigDataViewer..." with resolution level > 0 gives incorrect scale

When importing an image from a BDV file using "File>Import>BigDataViewer...", the pixel size seems to be fixed at full-resolution value regardless of which resolution level is chosen for import, resulting in 2x, 4x, 8x etc. errors in scale in the output images.

Using bigdataviewer_fiji-2.0.0 plugin and ImageJ 1.50e.

Invalid byte 1 of 1-byte UTF-8 sequence error when opening hdf file

Hi there,
I am trying to open an hdf file (attached, zipped). I can open the file in HDFView, and using the "Load HDF5 File..." option in Fiji. However, if I try and open it with "Open XML/HDF5" from the BigDataViewer I get the following error. It seems it has something to do with an encoding?

(Fiji Is Just) ImageJ 2.3.0/1.53f51; Java 1.8.0_172 [64-bit]; Windows 10 10.0; 161MB of 24257MB (<1%)

java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Module threw exception

at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:307)

at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:166)

at ij.IJ.runPlugIn(IJ.java)

at ij.Executer.runCommand(Executer.java:150)

at ij.Executer.run(Executer.java:68)

at java.lang.Thread.run(Thread.java:748)

Caused by: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Module threw exception

at java.util.concurrent.FutureTask.report(FutureTask.java:122)

at java.util.concurrent.FutureTask.get(FutureTask.java:192)

at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:303)

... 5 more

Caused by: java.lang.RuntimeException: Module threw exception

at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)

at org.scijava.module.ModuleRunner.call(ModuleRunner.java:63)

at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:225)

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)

... 1 more

Caused by: java.lang.RuntimeException: mpicbg.spim.data.SpimDataIOException: org.apache.xerces.impl.io.MalformedByteSequenceException: Invalid byte 1 of 1-byte UTF-8 sequence.

at bdv.ij.BigDataViewerPlugIn.run(BigDataViewerPlugIn.java:139)

at org.scijava.command.CommandModule.run(CommandModule.java:196)

at org.scijava.module.ModuleRunner.run(ModuleRunner.java:163)

at org.scijava.module.ModuleRunner.call(ModuleRunner.java:124)

... 6 more

Caused by: mpicbg.spim.data.SpimDataIOException: org.apache.xerces.impl.io.MalformedByteSequenceException: Invalid byte 1 of 1-byte UTF-8 sequence.

at bdv.spimdata.XmlIoSpimDataMinimal.load(XmlIoSpimDataMinimal.java:75)

at bdv.BigDataViewer.open(BigDataViewer.java:505)

at bdv.ij.BigDataViewerPlugIn.run(BigDataViewerPlugIn.java:135)

... 9 more

Caused by: org.apache.xerces.impl.io.MalformedByteSequenceException: Invalid byte 1 of 1-byte UTF-8 sequence.

at org.apache.xerces.impl.io.UTF8Reader.invalidByte(Unknown Source)

at org.apache.xerces.impl.io.UTF8Reader.read(Unknown Source)

at org.apache.xerces.impl.XMLEntityScanner.load(Unknown Source)

at org.apache.xerces.impl.XMLEntityScanner.skipString(Unknown Source)

at org.apache.xerces.impl.XMLVersionDetector.determineDocVersion(Unknown Source)

at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)

at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)

at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)

at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)

at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)

at org.jdom2.input.sax.SAXBuilderEngine.build(SAXBuilderEngine.java:217)

at org.jdom2.input.sax.SAXBuilderEngine.build(SAXBuilderEngine.java:329)

at org.jdom2.input.SAXBuilder.build(SAXBuilder.java:1266)

at bdv.spimdata.XmlIoSpimDataMinimal.load(XmlIoSpimDataMinimal.java:71)

... 11 more

BG_Y0_BEFORE.zip

HDF5 saved by Fiji doesn't open in BigDataViewer

I am trying to convert a dataset to hdf5 to view it in BigDataViewer. I did the following:
-opened the stack in Fiji
-File -> Save as -> HDF5 (new or replace)

I obtained a .h5 file that I can open via File-> Import ->HDF5, but if I try to open via Plugins->BigDataViewer -> Open XML/HDF5, I get errors (below).

Why is this the case and what is the appriopritae way to convert a tif stack into multiresolution hdf5?

===
(Fiji Is Just) ImageJ 2.0.0-rc-69/1.52p; Java 1.8.0_172 [64-bit]; Windows 7 6.1; 450MB of 73552MB (<1%)

java.lang.RuntimeException:` java.util.concurrent.ExecutionException: java.lang.RuntimeException: mpicbg.spim.data.SpimDataIOException: org.apache.xerces.impl.io.MalformedByteSequenceException: Invalid byte 1 of 1-byte UTF-8 sequence.
at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:309)
at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:163)
at ij.IJ.runPlugIn(IJ.java)
at ij.Executer.runCommand(Executer.java:137)
at ij.Executer.run(Executer.java:66)
at java.lang.Thread.run(Thread.java:748)
Caused by: java.util.concurrent.ExecutionException: java.lang.RuntimeException: mpicbg.spim.data.SpimDataIOException: org.apache.xerces.impl.io.MalformedByteSequenceException: Invalid byte 1 of 1-byte UTF-8 sequence.
at java.util.concurrent.FutureTask.report(FutureTask.java:122)
at java.util.concurrent.FutureTask.get(FutureTask.java:192)
at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:305)
... 5 more
Caused by: java.lang.RuntimeException: mpicbg.spim.data.SpimDataIOException: org.apache.xerces.impl.io.MalformedByteSequenceException: Invalid byte 1 of 1-byte UTF-8 sequence.
at bdv.ij.BigDataViewerPlugIn.run(BigDataViewerPlugIn.java:118)
at org.scijava.command.CommandModule.run(CommandModule.java:199)
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66)
at org.scijava.thread.DefaultThreadService$3.call(DefaultThreadService.java:238)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
... 1 more
Caused by: mpicbg.spim.data.SpimDataIOException: org.apache.xerces.impl.io.MalformedByteSequenceException: Invalid byte 1 of 1-byte UTF-8 sequence.
at bdv.spimdata.XmlIoSpimDataMinimal.load(XmlIoSpimDataMinimal.java:76)
at bdv.BigDataViewer.open(BigDataViewer.java:487)
at bdv.ij.BigDataViewerPlugIn.run(BigDataViewerPlugIn.java:114)
... 9 more
Caused by: org.apache.xerces.impl.io.MalformedByteSequenceException: Invalid byte 1 of 1-byte UTF-8 sequence.
at org.apache.xerces.impl.io.UTF8Reader.invalidByte(Unknown Source)
at org.apache.xerces.impl.io.UTF8Reader.read(Unknown Source)
at org.apache.xerces.impl.XMLEntityScanner.load(Unknown Source)
at org.apache.xerces.impl.XMLEntityScanner.skipString(Unknown Source)
at org.apache.xerces.impl.XMLVersionDetector.determineDocVersion(Unknown Source)
at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
at org.jdom2.input.sax.SAXBuilderEngine.build(SAXBuilderEngine.java:217)
at org.jdom2.input.sax.SAXBuilderEngine.build(SAXBuilderEngine.java:329)
at org.jdom2.input.SAXBuilder.build(SAXBuilder.java:1266)
at bdv.spimdata.XmlIoSpimDataMinimal.load(XmlIoSpimDataMinimal.java:72)
... 11 more

Brightness and Color dialog min/max sliders not updating values

I came across this issue while using BDV from within BigStitcher. I'm working with a simple set of overlapping tiles (one timepoint and channel). When I wish to adjust individually a tile's brighness, I open the aforementioned dialog. When I move adjust min/max values using the sliders the numeric values shown in the dialog don't change. However, typing in new values or clicking the two up-down arrows works fine.

Please also note that the sliders don't seem to interact with the min/max value range limiters (those that appear when clicking the >>).

Using Fiji/ImageJ 1.53b, Java 1.8.0_202 and the latest plugins on Macos Mojave.

Customization of brightness and LUT

Thanks for making the tool available!
Some of my data has weird dynamic range and I really struggle to see the images. It would be great to implement LUTs as well as an auto adjust button.

Apple Silicon Support for N5 Viewer

Hello,

I've been trying to open a .zarr file using the N5 Viewer included with the plugin. When I try to do so I get the stack trace below (omitted parts due to maximum message length), indicating a native library is missing. Is there any chance that a native library is available for Apple Silicon?

        file:/Applications/Fiji.app/plugins/Volume_Viewer-2.01.3.jar, file:/Applications/Fiji.app/plugins/Sync_Win-1.7-fiji4.jar])
	at com.sun.jna.NativeLibrary.loadLibrary(NativeLibrary.java:307)
	at com.sun.jna.NativeLibrary.getInstance(NativeLibrary.java:467)
	at com.sun.jna.Native.register(Native.java:1774)
	at com.sun.jna.Native.register(Native.java:1493)
	at org.blosc.IBloscDll.<clinit>(IBloscDll.java:15)
	at org.blosc.JBlosc.init(JBlosc.java:30)
	at org.blosc.JBlosc.<init>(JBlosc.java:24)
	at org.janelia.saalfeldlab.n5.blosc.BloscCompression.<clinit>(BloscCompression.java:70)
	at java.base/java.lang.Class.forName0(Native Method)
	at java.base/java.lang.Class.forName(Class.java:315)
	at org.janelia.saalfeldlab.n5.CompressionAdapter.update(CompressionAdapter.java:84)
	at org.janelia.saalfeldlab.n5.CompressionAdapter.update(CompressionAdapter.java:111)
	at org.janelia.saalfeldlab.n5.CompressionAdapter.getJsonAdapter(CompressionAdapter.java:175)
	at org.janelia.saalfeldlab.n5.AbstractGsonReader.<init>(AbstractGsonReader.java:58)
	at org.janelia.saalfeldlab.n5.N5FSReader.<init>(N5FSReader.java:116)
	at org.janelia.saalfeldlab.n5.zarr.N5ZarrReader.<init>(N5ZarrReader.java:103)
	at org.janelia.saalfeldlab.n5.ij.N5Factory.openZarrReader(N5Factory.java:214)
	at org.janelia.saalfeldlab.n5.ij.N5Factory.openReader(N5Factory.java:383)
	at org.janelia.saalfeldlab.n5.ij.N5Importer$N5ViewerReaderFun.apply(N5Importer.java:710)
	at org.janelia.saalfeldlab.n5.ij.N5Importer$N5ViewerReaderFun.apply(N5Importer.java:691)
	at org.janelia.saalfeldlab.n5.ui.DatasetSelectorDialog.openContainer(DatasetSelectorDialog.java:555)
	at org.janelia.saalfeldlab.n5.ui.DatasetSelectorDialog.openContainer(DatasetSelectorDialog.java:531)
	at org.janelia.saalfeldlab.n5.ui.DatasetSelectorDialog.lambda$run$2(DatasetSelectorDialog.java:315)
	at java.desktop/javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1967)
	at java.desktop/javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2308)
	at java.desktop/javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:405)
	at java.desktop/javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:262)
	at java.desktop/javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:279)
	at java.desktop/java.awt.Component.processMouseEvent(Component.java:6635)
	at java.desktop/javax.swing.JComponent.processMouseEvent(JComponent.java:3342)
	at java.desktop/java.awt.Component.processEvent(Component.java:6400)
	at java.desktop/java.awt.Container.processEvent(Container.java:2263)
	at java.desktop/java.awt.Component.dispatchEventImpl(Component.java:5011)
	at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2321)
	at java.desktop/java.awt.Component.dispatchEvent(Component.java:4843)
	at java.desktop/java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4918)
	at java.desktop/java.awt.LightweightDispatcher.processMouseEvent(Container.java:4547)
	at java.desktop/java.awt.LightweightDispatcher.dispatchEvent(Container.java:4488)
	at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2307)
	at java.desktop/java.awt.Window.dispatchEventImpl(Window.java:2772)
	at java.desktop/java.awt.Component.dispatchEvent(Component.java:4843)
	at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:772)
	at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:721)
	at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:715)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85)
	at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:95)
	at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:745)
	at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:743)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85)
	at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:742)
	at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203)
	at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
	at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
	at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
	at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
	at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)
	Suppressed: java.lang.UnsatisfiedLinkError: dlopen(libblosc.dylib, 0x0009): tried: 'libblosc.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OSlibblosc.dylib' (no such file), '/opt/homebrew/Cellar/openjdk@11/11.0.16.1_1/libexec/openjdk.jdk/Contents/Home/bin/server/libblosc.dylib' (no such file), '/opt/homebrew/Cellar/openjdk@11/11.0.16.1_1/libexec/openjdk.jdk/Contents/Home/bin/../lib/jli/libblosc.dylib' (no such file), '/usr/lib/libblosc.dylib' (no such file, not in dyld cache), 'libblosc.dylib' (no such file), '/usr/local/lib/libblosc.dylib' (no such file), '/usr/lib/libblosc.dylib' (no such file, not in dyld cache)
		at com.sun.jna.Native.open(Native Method)
		at com.sun.jna.NativeLibrary.loadLibrary(NativeLibrary.java:197)
		... 57 more
	Suppressed: java.lang.UnsatisfiedLinkError: dlopen(libblosc.dylib, 0x0009): tried: 'libblosc.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OSlibblosc.dylib' (no such file), '/opt/homebrew/Cellar/openjdk@11/11.0.16.1_1/libexec/openjdk.jdk/Contents/Home/bin/server/libblosc.dylib' (no such file), '/opt/homebrew/Cellar/openjdk@11/11.0.16.1_1/libexec/openjdk.jdk/Contents/Home/bin/../lib/jli/libblosc.dylib' (no such file), '/usr/lib/libblosc.dylib' (no such file, not in dyld cache), 'libblosc.dylib' (no such file), '/usr/local/lib/libblosc.dylib' (no such file), '/usr/lib/libblosc.dylib' (no such file, not in dyld cache)
		at com.sun.jna.Native.open(Native Method)
		at com.sun.jna.NativeLibrary.loadLibrary(NativeLibrary.java:210)
		... 57 more
	Suppressed: java.lang.UnsatisfiedLinkError: dlopen(/Users/frans/Library/Frameworks/blosc.framework/blosc, 0x0009): tried: '/Users/frans/Library/Frameworks/blosc.framework/blosc' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/frans/Library/Frameworks/blosc.framework/blosc' (no such file), '/Users/frans/Library/Frameworks/blosc.framework/blosc' (no such file), '/Library/Frameworks/blosc.framework/blosc' (no such file), '/System/Library/Frameworks/blosc.framework/blosc' (no such file, not in dyld cache)
		at com.sun.jna.Native.open(Native Method)
		at com.sun.jna.NativeLibrary.loadLibrary(NativeLibrary.java:254)
		... 57 more
	Suppressed: java.lang.UnsatisfiedLinkError: dlopen(/Library/Frameworks/blosc.framework/blosc, 0x0009): tried: '/Library/Frameworks/blosc.framework/blosc' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Library/Frameworks/blosc.framework/blosc' (no such file), '/Library/Frameworks/blosc.framework/blosc' (no such file), '/System/Library/Frameworks/blosc.framework/blosc' (no such file, not in dyld cache)
		at com.sun.jna.Native.open(Native Method)
		at com.sun.jna.NativeLibrary.loadLibrary(NativeLibrary.java:254)
		... 57 more
	Suppressed: java.lang.UnsatisfiedLinkError: dlopen(/System/Library/Frameworks/blosc.framework/blosc, 0x0009): tried: '/System/Library/Frameworks/blosc.framework/blosc' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/System/Library/Frameworks/blosc.framework/blosc' (no such file), '/System/Library/Frameworks/blosc.framework/blosc' (no such file, not in dyld cache), '/Library/Frameworks/blosc.framework/blosc' (no such file)
		at com.sun.jna.Native.open(Native Method)
		at com.sun.jna.NativeLibrary.loadLibrary(NativeLibrary.java:254)
		... 57 more
	Suppressed: java.io.IOException: Native library (darwin-aarch64/libblosc.dylib) not found in resource path

Support more datatypes for HDF5 export

bigdataviewer-core has for a while (since bigdataviewer-core-10.4.7) supported exporting datasets to HDF5 with data types besides UnsignedShortType. However, this is not yet accessible through the Fiji UI.

'Open KLB' triggers exception

Hi,

I currently try to use the TGMM algorithms to my own data set (time series of single fluorescence channel volumes (X, Y, Z) ) following the "Software_Guide_Compact".

In the instructions, there is a part when the TGMM results are exported to xml/ hdf5 by the Fiji bigdataviewer plugin:

Import TGMM objects using MaMuT importer in Fiji. As image data location use
the .xml file generated from the .klb image files, as described in the first section
“Setting up the software environment”

According to the chapter Setting up the software environment I have to use the plugin function Open KLB:

[...] to generate a new .xml file from a .klb image series in Fiji, follow
these steps:
 - Go to “Plugins”, “BigDataViewer”, and select “Open KLB”.

As soon as I press the button a Exception Window appears:

Exception Window Message:

(Fiji Is Just) ImageJ 2.0.0-rc-69/1.52p; Java 1.8.0_172 [64-bit]; Windows 10 10.0; 364MB of 24450MB (1%)
 
java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.NoClassDefFoundError: net/preibisch/mvrecon/fiji/spimdata/SpimData2
	at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:309)
	at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:163)
	at ij.IJ.runPlugIn(IJ.java)
	at ij.Executer.runCommand(Executer.java:137)
	at ij.Executer.run(Executer.java:66)
	at java.lang.Thread.run(Thread.java:748)
Caused by: java.util.concurrent.ExecutionException: java.lang.NoClassDefFoundError: net/preibisch/mvrecon/fiji/spimdata/SpimData2
	at java.util.concurrent.FutureTask.report(FutureTask.java:122)
	at java.util.concurrent.FutureTask.get(FutureTask.java:192)
	at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:305)
	... 5 more
Caused by: java.lang.NoClassDefFoundError: net/preibisch/mvrecon/fiji/spimdata/SpimData2
	at org.janelia.simview.klb.bdv.ui.KlbIjPlugin.run(KlbIjPlugin.java:25)
	at org.scijava.command.CommandModule.run(CommandModule.java:199)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66)
	at org.scijava.thread.DefaultThreadService$3.call(DefaultThreadService.java:238)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	... 1 more
Caused by: java.lang.ClassNotFoundException: net.preibisch.mvrecon.fiji.spimdata.SpimData2
	at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:349)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
	... 10 more

Console Window Message:

[ERROR] Module threw error
java.lang.NoClassDefFoundError: net/preibisch/mvrecon/fiji/spimdata/SpimData2
	at org.janelia.simview.klb.bdv.ui.KlbIjPlugin.run(KlbIjPlugin.java:25)
	at org.scijava.command.CommandModule.run(CommandModule.java:199)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66)
	at org.scijava.thread.DefaultThreadService$3.call(DefaultThreadService.java:238)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.ClassNotFoundException: net.preibisch.mvrecon.fiji.spimdata.SpimData2
	at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:349)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
	... 10 more

Save current view with meaningful pixel size

I would like to save a currently viewed projection in the BDV with the meaningful pixel size - ideally the same as my resolution of the 0-set in h5 file.

Record a movie doesn't work for me as it requires me to specify the size of the image, which is exactly the opposite of what I want. Because I want to know the physical size of the pixel in microns at the resulting image. Ideally, it should be the same as for the sharpest 0-set of the original h5, where pixel size was specified.

I would not have this problem with orthogonal views as I would section the sample easily in python or elsewhere, but BDV viewer seems to be handy solution for making nice diagonal views and there I want to know what I am looking at.

Could you please advise me a solution.

Best,
Maxim

Brightness and color dialog not spawning separate sections for multiple sources

I came across this issue while using BDV from within BigStitcher. I may be missing something, but I just can't obtain a behavior of the Brightness and Color dialog box as described in the online documentation at https://imagej.net/BigDataViewer

I'm working with a simple set of overlapping tiles (one timepoint and channel). When I wish to adjust individually a tile's brighness, I open the aforementioned dialog and deselect the corresponding source, expecting that the dialog will spawn a separate control section. This behavior is described in the documentation as follows:

If you uncheck one of the sources, it will move to its own new min-max-group. Now you can adjust the values for each source individually. The sliders of new group are initialized as a copy of the old group.

However, this does not occur. In fact, I never managed to obtain more than one control section in that dialog.

Using Fiji/ImageJ 1.53b, Java 1.8.0_202 and the latest plugins on Macos Mojave.

Enable OpenImagePlusPlugin to open several images

Quite often, I find myself wanting to open multiple images (ImagePlus's) together with the bdv plugin. They are sometimes different sizes / data types and so combining into a single multi-channel image is not so straightforward.

One downside would that this will add an extra click in the case that one wants to simply open the current image... I'm imagining a dialog in which one chooses among the available images to open with bdv.

If we agree that this is useful, I'm happy to implement it and file a PR.

2D image defaults for ExportImagePlusAsN5Plugin

For some 2D images, the default subsampling factors / chunk sizes are not optimal. e.g. for an 8-bit image of 8704 x 9044 pixels, with dimensions of 10.0320 x 10.0320 x 1 nanometer.
The calculated downsampling factors are:
[[1,1,1],[1,1,2],[1,1,4],[1,1,8],[2,2,16],[4,4,32],[8,8,64],[16,16,128],[32,32,256],[64,64,512]]
and the block size of the first layer is [32, 32, 256]

Would it be possible to keep the z downsampling/chunk size at 1 for 2D images?
Thanks!