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

[Zara Weinberg]

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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