[ome-users] Request Format Addition: Andor Dragonfly IMS

[David Gault (Staff)]

Hi Zara,

Thank you for uploading the sample file. I tried loading the file with BigStitcher and although I can see the “[ERROR] bad version 72 at filePos 94692298” message I was not able to reproduce the exception you are seeing.
Can you provide further step by step instructions on the workflow you used to reproduce the issue?

With Thanks,
David Gault

On 28 Mar 2019, at 20:38, Zara Weinberg <weinberz at umich.edu<mailto:weinberz at umich.edu>> wrote:

Hello,

Andor Technology maintains a software package Fusion that is used to control their Dragonfly microscopy unit. Fusion outputs acquired images in an Imaris-compatible .ims format, but as noted elsewhere (https://forum.image.sc/t/andor-dragonfly-ims-files-with-z-stack-failing-to-open-with-bioformats-5-9-2/21768) this format is not identical to Imaris's format. As such this can cause issues when using third party plugins (such as BigStitcher) in FIJI to process Fusion IMS files.

I have updated an example file at https://www.openmicroscopy.org/qa2/qa/feedback/27456/?token=8a29b3c3c9c5596f1402ef4693e45252. This is properly loaded by Fiji (although the console reports '[ERROR] bad version 72 at filePos 94692298'). However, when attempting to load individual frames (as with BigStitcher's method of loading multiple timepoints from the same file), those file loads with the follow error and stack trace:

java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
at java.util.ArrayList.rangeCheck(ArrayList.java:653)
at java.util.ArrayList.get(ArrayList.java:429)
at ome.xml.model.Pixels.getPlane(Pixels.java:738)
at ome.xml.meta.OMEXMLMetadataImpl.getPlanePositionX(OMEXMLMetadataImpl.java:3773)
at net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyStackImgLoaderLOCI.loadTileLocation(LegacyStackImgLoaderLOCI.java:527)
at net.preibisch.mvrecon.fiji.datasetmanager.StackListLOCI.loadTileLocationFromMetaData(StackListLOCI.java:95)
at net.preibisch.mvrecon.fiji.datasetmanager.StackList.loadAllTileLocations(StackList.java:188)
at net.preibisch.mvrecon.fiji.datasetmanager.StackList.createDataset(StackList.java:308)
at net.preibisch.mvrecon.fiji.plugin.Define_Multi_View_Dataset.defineDataset(Define_Multi_View_Dataset.java:134)
at net.preibisch.mvrecon.fiji.plugin.Define_Multi_View_Dataset.run(Define_Multi_View_Dataset.java:78)
at ij.IJ.runUserPlugIn(IJ.java:229)
at ij.IJ.runPlugIn(IJ.java:193)
at ij.Executer.runCommand(Executer.java:137)
at ij.Executer.run(Executer.java:66)
at java.lang.Thread.run(Thread.java:745)

It'd be awesome if these could be natively supported in Bio-Formats!

Let me know if you need anything else from me! I have also cc'ed Andor's support alias , in case they might be able to provide more info about how these files differ from Imaris's implementation.

Cheers,

Zara Weinberg, Ph.D
Postdoctoral Scholar
Puthenveedu Lab
University of Michigan
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