Re: TrackEM alignment of .ims Imaris stack

Posted by Saalfeld, Stephan on Jul 01, 2016; 3:09pm
URL: http://imagej.273.s1.nabble.com/TrackEM-alignment-of-ims-Imaris-stack-tp5016780p5016794.html

Hi Sho,

Importing stacks as patches from stack files is a somehow ill-designed
concept in TrakEM2.  Even if it worked, you would have TrakEM2 load the
complete stack over and over again whenever it generates deformed
patches (or mouse over them), which makes bad performance across the
board.  If you have a chance to export your Imaris files into a series
of 2D tiff files, TrakEM2 will act much better.  I am not sure about
ome.tiff but generally have bad memories about Bioformats interactions
in TrakEM2.  Have you tried plain tiff in ImageJ style?

Best,
Stephan

On Thu, 2016-06-30 at 15:20 +0000, Sho Fujisawa wrote:

> Help.
>
> I'm trying to manually align slices of a stack of multi-channel
> images. The stacks are .ims Imaris files. I can load it onto FIJI/IJ
> using BioFormat Importer. But when I try to import into TrackEM, I
> get a lot of questions about the z slice value being different from
> what it's supposed to be. Then no matter what answer I choose, I
> eventually get this error.
>
> ERROR:
> java.lang.NullPointerException
>     at ini.trakem2.display.Patch.<init>(Patch.java:195)
>     at
> ini.trakem2.persistence.FSLoader.importStackAsPatches(FSLoader.java:1
> 268)
>     at ini.trakem2.persistence.Loader$9.run(Loader.java:3745)
>     at java.lang.Thread.run(Thread.java:662)
>
>
> I get the same issue even when I convert .ims to ome.tif.
> What does the error mean, and how can I go around it?
>
> Sho Fujisawa
> Molecular Cytology Core Facility
> Memorial Sloan-Kettering Cancer Center
> 415 E. 68th St. Z-1840
> New York, NY 10065
> [phone]
>
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