Opening output in MoBIE does not work

[tischi]

Following on the plugin use, I couldn’t make the Mobie explorer work like you do in the documentation: the table does not open (headers are for some reason not recognized). Could you confirm that it works for you? The interface seems to be slightly different now than the one you show on the screenshot, so I’m thinking maybe something else could have changed.

https://forum.image.sc/t/microglia-morphometry-fiji-plugin-parameters-cell-size-not-working/95045/4

[tischi]

I ran the segmentation and morphometry on a small crop of your data, which resulted in this folder with files: test.zip

Then in MoBIE, I could open them with

Java Code

OpenTableCommand command = new OpenTableCommand();
command.root = new File("/Users/tischer/Desktop/microglia-data/test");
command.table = new File("/Users/tischer/Desktop/microglia-data/test/test-crop-8bit-ds2.csv");
command.images = "Path_Intensities=Signal";
command.labels = "Path_LabelMasks=Segmentation";
command.removeSpatialCalibration = true;
command.run();

ImageJ GUI Screenshot

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Can you reproduce this?

[mambroset]

No it does not work with the data you provided either: In the Log I get

MoBIE

Opening data from table: C:\Users\mambroset\Desktop\test\test-crop-8bit-ds2.csv [WARNING] Found duplicate column names, e.g.: 9.219544457292887 [WARNING] Trying now to open the table assuming that there are two header rows...

And in the Console: [ERROR] Command errored: Open Table... java.lang.ArrayIndexOutOfBoundsException: 1 at org.embl.mobie.lib.table.saw.TableOpener.dealWithTwoHeaderRowsIfNeeded(TableOpener.java:250) at org.embl.mobie.lib.table.saw.TableOpener.openDelimitedTextFile(TableOpener.java:220) at org.embl.mobie.lib.table.saw.TableOpener.openDelimitedTextFile(TableOpener.java:274) at org.embl.mobie.lib.SourcesFromTableCreator.(SourcesFromTableCreator.java:60) at org.embl.mobie.MoBIE.(MoBIE.java:182) at org.embl.mobie.command.open.OpenTableCommand.run(OpenTableCommand.java:105) at org.embl.mobie.command.open.OpenTableCommand.run(OpenTableCommand.java:78) 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:748)

I'm wondering if it has to do with the way it recognizes the headers in a csv table but I have no clue where to look to fix it! Is it possible that it's a weird difference between OSs?

[tischi]

Yes, it is possible that the OS plays a role, in which case this is also difficult to debug for me, because I do not have access to a Windows computer.

Could you do me a favour and try whether it also does not work with the MoBIE-beta update site? This update site contains a newer version of MoBIE....

However, it indeed feels more like an OS issue, it seems like your computer does not recognise the line breaks in the CSV, that's why it considers 9.219544457292887 a column header even though that is already part of the normal table rows; super weird though...sorry, also a bit speechless right now...

[mambroset]

Same behavior with MoBIE-beta! I have no clue what could be wrong...

[tischi]

I am using the Java tablesaw library to open the tables. Seems like other people had similar issues before.

[tischi]

I asked also for us: https://github.com/jtablesaw/tablesaw/issues/1255

[mambroset]

Thanks for the dedication! I confirm that a simple workaround for now is to open and save the csv tables before opening them with MoBIE! Doing so in Fiji works perfectly fine so it's easily scriptable :).

[tischi]

Thanks for finding this out! This is so weird 🤯

[tischi]

@mambroset could you please share here with me the table after re-saving from Fiji?

[mambroset]

iMGL_AAV2MOI105_6h_DAPI_IBA1_well6_image2_C2.csv