Saving, Accessing the data from BoneJ table

Usage & Issues
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#1

Hi there,

I have created a macro that implement the Thickness function of BoneJ to measure the mean thickness of blood vessels in multiple stacks. At the end, I am left with the BoneJ results table holding many measurements. I feel a bit stupid but is it not possible to save the BoneJ results table as a text or csv file? I can’t figure out how to do it. There are no menus in the table itself. Saving as txt from the main fiji window doesn’t work…
Or does it have to be done programmatically? and if so, how?

I have a windows 10 machine, and I am running the latest Fiji (imageJ 1.52s, Java 1.8.0_121). BoneJ is updated via its update site.

Thanks in advance,

David

#2

Hi David,

See this issue #129:


and this comment:

You can copy (click in the table, then ctrl + a and ctrl + c) and paste it to other softwares like Microsoft Excel, etc.

#3

I have the same problem; I try to export a table from BoneJ anisotropy measurements.
Selecting the line in the table and use copy-paste in Excel gives me the numbers, but does not copy the headers.

The solution suggested in the other thread, to use File → Export → Table does not work, it throws a Java exception:

(Fiji Is Just) ImageJ 2.1.0/1.53c; Java 1.8.0_172 [64-bit]; Windows 10 10.0; 237MB of 48997MB (<1%)
 
java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.UnsupportedOperationException: No compatible saver found.
	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:65)
	at java.lang.Thread.run(Thread.java:748)
Caused by: java.util.concurrent.ExecutionException: java.lang.UnsupportedOperationException: No compatible saver found.
	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.UnsupportedOperationException: No compatible saver found.
	at org.scijava.table.io.DefaultTableIOService.save(DefaultTableIOService.java:102)
	at org.scijava.table.io.ExportTableCommand.run(ExportTableCommand.java:84)
	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:124)
	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

I have scijava-table-0.6.1.jar installed with Fiji latest update.

Suggestions?
I need to be able to save the table programmatically for this to be useful in a workflow.