Module batch processing: Loading results with MoBIE table fails

[jhennies]

I'm trying to load the results of the batch processing with a mobie table.

For now, I made the table manually, looking like this:

In short:

image[TAB]labels
path/to/image.tif[TAB]path/to/labels.tif

In practice:

image[TAB]labels
https://github.com/NEUBIAS/training-resources/raw/master/image_data/xy_8bit__mitocheck_incenp_t1.tif[TAB]/media/julian/Data/courses/2024_2_skimage_napari_beginners/xy_8bit__mitocheck_incenp_t1_labels.tif

Then I use MoBIE -> Open -> Open Table... and fill the dialog like so:

Then the raw image opens as normal Fiji image

The console output is:

[ERROR] Command errored: Open Table...
java.lang.RuntimeException: java.lang.NullPointerException
    at org.embl.mobie.io.imagedata.SpimDataImageData.open(SpimDataImageData.java:132)
    at org.embl.mobie.io.imagedata.SpimDataImageData.getMetadata(SpimDataImageData.java:91)
    at org.embl.mobie.lib.data.ImageGridSources.setMetadata(ImageGridSources.java:188)
    at org.embl.mobie.lib.data.ImageGridSources.<init>(ImageGridSources.java:164)
    at org.embl.mobie.lib.SourcesFromTableCreator.<init>(SourcesFromTableCreator.java:93)
    at org.embl.mobie.MoBIE.<init>(MoBIE.java:193)
    at org.embl.mobie.command.open.OpenTableCommand.run(OpenTableCommand.java:112)
    at org.embl.mobie.command.open.OpenTableCommand.run(OpenTableCommand.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: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)
Caused by: java.lang.NullPointerException
    at ch.epfl.biop.bdv.img.imageplus.ImagePlusToSpimData.getSpimData(ImagePlusToSpimData.java:62)
    at org.embl.mobie.io.imagedata.TIFFImageData$1.open(TIFFImageData.java:38)
    at org.embl.mobie.io.imagedata.SpimDataImageData.open(SpimDataImageData.java:121)
    ... 16 more

The Log output is:

# MoBIE
Opening data from table: /media/julian/Data/courses/2024_2_skimage_napari_beginners/mobie_table.csv
Fetching metadata for image, channel 0
Source: https://github.com/NEUBIAS/training-resources/raw/master/image_data/xy_8bit__mitocheck_incenp_t1.tif

[jhennies]

ping @k-dominik

[tischi]

https://github.com/NEUBIAS/training-resources/raw/master/image_data/xy_8bit__mitocheck_incenp_t1.tif

It could be that the current code in MoBIE cannot open http hosted TIFF images. Could you please try with locally stored files?

[jhennies]

Good, that works!

This is the output when adding a second image and changing "Grid" to "Transformed":

[jhennies]

If we decide to use this for the course, which of the following is easier?

• Downloading the images first to have them locally
• Changing MoBIE to be able to cope with remote locations

[k-dominik]

I think downloading (maybe a zip with a few datasets) would get you the most realistic experience. Opening URLs is convenient in the course, but my feeling is that majority of people will deal with local files in their day to day.

[tischi]

Feel free to add the ZIP of the two images here.