Multi-D Acquisition saved image stacks are fault and refuse to open in Icy

Hey Icy crew,

I’m having some trouble with my Icy-MicroManager saved Image stacks of multiple positions. I’m having several issues so I’ll cut this post into parts:

1. Opening a file through drag and drop or the Recent Files menu gives an error:

This is making the only way for me to open image stacks through the ‘Open…’ file browser.

java.lang.IndexOutOfBoundsException: Index: 2, Size: 2
at java.util.ArrayList.rangeCheck(ArrayList.java:657)
at java.util.ArrayList.get(ArrayList.java:433)
at loci.formats.in.OMETiffReader.initFile(OMETiffReader.java:688)
at loci.formats.FormatReader.setId(FormatReader.java:1397)
at plugins.kernel.importer.LociImporterPlugin.openReader(LociImporterPlugin.java:939)
at plugins.kernel.importer.LociImporterPlugin.open(LociImporterPlugin.java:853)
at icy.file.Loader.internalLoadSingle(Loader.java:3764)
at icy.file.Loader.loadSequences(Loader.java:3237)
at icy.file.Loader$9.run(Loader.java:2663)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
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)

       2. Saved image stack from multiple-positions acquisition is a mess of what seems to be a mapping of the other positions.

I’m using multiple positions, using default position names (Pos0, Pos1, etc.). When I open the first file (Pos0) I get this odd mess of miniature versions of what seems to be the first image of all the other image stack files jumbled into small squares.

I remember that in an older version of Icy, when I dragged and dropped such a file into icy it would open a window where I could select which files from that acquisition I wanted to open (e.g. just Pos 0, Pos3 and Pos4 if I wanted). Perhaps this is an error caused by something going wrong with that function?

These files open properly in ImageJ, so there doesn’t seem to be anything wrong with the image stack itself. I’m not sure if this only happens with the first file (Pos0) or if the others are a similar mess, the reason I can’t determine this is my final point.

       3. Opening a file from such an acquisition (lets say Pos2), will automatically open Pos0 instead.

No matter which one you select you will automatically get Pos0. Again, this does not happen in ImageJ so the files can still be accessed there.

Looking at the sequence properties we find that the path points to the correct file, Pos2, yet the name and the contents of the file are Pos0:

Any idea if this could be my mistake somehow, or if it is something that has been wrong with the Icy program or MM plugin?

Let me know if you need my files. I’ll provide a MEGA link since the smallest acquisition data set is 200MB.

• This topic was modified 5 years, 5 months ago by
  MasoudR. Reason: it looked a lot better in the post-preview, I had to remove some markup