Closed kmdouglass closed 7 years ago
sbesson
commented
7 years ago Hi @kmdouglass, the debug level output above should be harmless with regard to the OME-TIFF writing functionality. They indeed indicate that the dependencies for various services are missing but these libraries are largely required for reading proprietary file formats. I suspect the issue lies elsewhere in the writing stack. Do you have more details on the OME-XML corruption preventing the OME-TIFF to be read in Fiji?
kmdouglass
commented
7 years ago Hi @sbesson,
Thanks for the response. I agree with your assessment of the output and that it looks like it is mostly related to missing libraries for "3rd-party" formats.
Concerning the FIJI import, there are three notable behaviors:
File > Open... produces an error message dialog that I alluded to.I am not in the lab today, so I will post the bug report from Fiji tomorrow when I can reproduce it. It looks like the problem may very likely lie with Fiji.
Cheers, Kyle
kmdouglass
commented
7 years ago Hello @sbesson ,
Here is the bug report that Fiji returns when I try to use File > Open... to open one of the images from Micro-Manager:
(Fiji Is Just) ImageJ 2.0.0-rc-8/1.49c; Java 1.6.0_24 [64-bit]; Windows 7 6.1; 21MB of 147418MB (<1%)
java.lang.IllegalArgumentException: Not a linear axis: null
at io.scif.util.FormatTools.calibrate(FormatTools.java:257)
at io.scif.ome.formats.OMETIFFFormat$Metadata.populateImageMetadata(OMETIFFFormat.java:385)
at io.scif.AbstractParser.parse(AbstractParser.java:254)
at io.scif.ome.formats.OMETIFFFormat$Parser.parse(OMETIFFFormat.java:603)
at io.scif.ome.formats.OMETIFFFormat$Parser.parse(OMETIFFFormat.java:546)
at io.scif.AbstractParser.parse(AbstractParser.java:335)
at io.scif.AbstractParser.parse(AbstractParser.java:52)
at io.scif.AbstractReader.setSource(AbstractReader.java:270)
at io.scif.services.DefaultInitializeService.initializeReader(DefaultInitializeService.java:90)
at io.scif.img.ImgOpener.createReader(ImgOpener.java:542)
at io.scif.img.ImgOpener.openImgs(ImgOpener.java:144)
at net.imagej.DefaultDatasetService.open(DefaultDatasetService.java:266)
at net.imagej.DefaultDatasetService.open(DefaultDatasetService.java:250)
at net.imagej.io.DatasetIOPlugin.open(DatasetIOPlugin.java:78)
at net.imagej.io.DatasetIOPlugin.open(DatasetIOPlugin.java:50)
at net.imagej.legacy.plugin.DefaultLegacyOpener.open(DefaultLegacyOpener.java:135)
at net.imagej.legacy.DefaultLegacyHooks.interceptFileOpen(DefaultLegacyHooks.java:420)
at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:153)
at ij.IJ.runPlugIn(IJ.java)
at ij.Executer.runCommand(Executer.java:131)
at ij.Executer.run(Executer.java:64)
at java.lang.Thread.run(Thread.java:662)I actually just discovered that I can reproduce the three behaviors noted in my post above when generating OME.TIFF files in plain Micro-Manager, i.e. Micro-Manager run as an ImageJ plugin, not inside MATLAB.
Perhaps the problem then is really with Fiji and not Micro-Manager.
sbesson
commented
7 years ago Hi Kyle,
given the stack trace, the error you are receiving seems to be at the SCIFIO level. Does it still happen if you disable SCIFIO and use only Bio-Formats ?
kmdouglass
commented
7 years ago Hello @sbesson , That did the trick. I updated Fiji and disabled SCIFIO and everything is working now.
Thanks for the feedback. I should have been able to solve this but I was erroneously thinking it was a Micro-Manager problem, when in reality it was simply that Fiji was out of date.
Thanks again! Kyle
Currently I am receiving the error below at the first time I try to write a single image or image stack to disk in a MM session in MATLAB. The resulting files will not open in FIJI because the OME-XML is corrupted; they will however open in ImageJ.
I suspect that some of the LOCI libraries need to be added to the javaclasspath.
Error report
javaclasspath