Bioformats no longer used for opening files from drag and drop


#1

MacOS Sierra 10.12.5
FIJI/Image 1.51n, Java 1.8.0_66

Previously: Drag and drop .nd2 file onto FIJI app in Mac dock, opens FIJI, loads file using bioformats import options window.

Now: If I drag and drop .nd2 (nikon) files to the FIJI app icon in my dock, it no longer opens those files with the bioformats import options window. This action loads FIJI but then nothing happens (toolbar goes through update check). Same thing happens for .avi file (opens FIJI but file is not loaded, wouldn’t expect bio-formats here).

If I open FIJI and drag and drop to the toolbar, the .nd2 file opens but without bioformats import window (it also doesn’t seem to be loading metadata other than channel colors).

Going to plugins>bioformats>importer and then opening an .nd2 works as expected (importer window with options, reads metadata, etc).

Drag and dropping .avi onto opened FIJI toolbar works but also gives the following (but may be unrelated to bioformats problem):

[INFO] Verifying AVI format
[INFO] Searching for image data
java.io.IOException: io.scif.img.ImgIOException: java.io.IOException: io.scif.UnsupportedCompressionException: 543649392 not supported
	at io.scif.services.DefaultDatasetIOService.open(DefaultDatasetIOService.java:136)
	at io.scif.services.DefaultDatasetIOService.open(DefaultDatasetIOService.java:111)
	at io.scif.io.DatasetIOPlugin.open(DatasetIOPlugin.java:75)
	at io.scif.io.DatasetIOPlugin.open(DatasetIOPlugin.java:50)
	at net.imagej.legacy.plugin.DefaultLegacyOpener.open(DefaultLegacyOpener.java:136)
	at net.imagej.legacy.DefaultLegacyHooks.interceptDragAndDropFile(DefaultLegacyHooks.java:363)
	at ij.plugin.DragAndDrop.openFile(DragAndDrop.java)
	at ij.plugin.DragAndDrop.run(DragAndDrop.java:159)
	at java.lang.Thread.run(Thread.java:745)
Caused by: io.scif.img.ImgIOException: java.io.IOException: io.scif.UnsupportedCompressionException: 543649392 not supported
	at io.scif.img.ImgOpener.createReader(ImgOpener.java:570)
	at io.scif.img.ImgOpener.openImgs(ImgOpener.java:144)
	at io.scif.services.DefaultDatasetIOService.open(DefaultDatasetIOService.java:126)
	... 8 more
Caused by: java.io.IOException: io.scif.UnsupportedCompressionException: 543649392 not supported
	at io.scif.AbstractReader.setSource(AbstractReader.java:274)
	at io.scif.services.DefaultInitializeService.initializeReader(DefaultInitializeService.java:90)
	at io.scif.img.ImgOpener.createReader(ImgOpener.java:561)
	... 10 more
Caused by: io.scif.UnsupportedCompressionException: 543649392 not supported
	at io.scif.formats.AVIFormat$Parser.readChunk(AVIFormat.java:680)
	at io.scif.formats.AVIFormat$Parser.typedParse(AVIFormat.java:481)
	at io.scif.formats.AVIFormat$Parser.typedParse(AVIFormat.java:453)
	at io.scif.AbstractParser.parse(AbstractParser.java:253)
	at io.scif.AbstractParser.parse(AbstractParser.java:336)
	at io.scif.AbstractParser.parse(AbstractParser.java:52)
	at io.scif.AbstractReader.setSource(AbstractReader.java:270)
	... 12 more

#2

Dear @Jordan_Becker,

Drag&drop onto the dock icon is currently not supported (Java 8 issue). This might change with future versions of Java, but no promises. See Can't Drag/Drop files to Fiji for more details.

Could you check if you have somehow enabled the windowless import for ND2 files? Also, do you have the ND2 Reader plugin from Nikon installed?

That’s actually not a Bio-Formats problem. Could you check if you have SCIFIO enabled under Edit > Options > ImageJ? If so, try deactivating and opening an AVI after restarting ImageJ/Fiji.

Best,
Stefan


#3

Thanks Stefan.

Bummer on the Java 8 drag and drop problem but not a huge deal.

Windowless was not checked in the Bio-formats Plugins Configuration for Nikon ND2. Toggling on, opening an ND2 (of course no bio-formats import options window), toggling back off windowless, opening an ND2 = still no bio-formats even closing and re-opening FIJI. I am only getting the import options window if I call files using the Bio-formats Importer, not so bad but drag and drop to toolbar was my workflow, I’ll adapt and try some other solutions.

I do not have the ND2 reader plugin installed, as it didn’t seem to be necessary. Looking at the link you provided, perhaps it is now. I’ll install that and check it out. (edit: ND2 reader is Windows only…)

RE: AVI. Of course, I was just also testing opening different files and noticed the avi problem. I deactivated the SCIFIO, did not receive an error upon opening an AVI. I reactivated it and I did not receive an error. Not too worried about this one though.


#4

Could you deactivate it and try to drag&drop an ND2 onto Fiji? This has solved the issue on my macOS machine…