Re: TrackEM alignment of .ims Imaris stack

Posted by Saalfeld, Stephan on Jul 01, 2016; 3:26pm
URL: http://imagej.273.s1.nabble.com/TrackEM-alignment-of-ims-Imaris-stack-tp5016780p5016796.html

TrakEM2 does not work well with multi-channel images.  You can, though
export all channels independently, import them as individual patches
(from import txt files that can be easily generated with scripts or
e.g. Excel), and display them with additive composite mode and color
filters (play with 'adjust image filters' and 'properties' > 'overlay
mode' on selections of patches).  Transformations applied to a layer
(section) would then affect all patches in the layer, and you can use a
subset of the patches for alignment by making others invisible.

So, the answer has layers ;): Yes, there is a way to get it to work,
but it is different from what one would intuitively expect to do.

Best,
Stephan

On Fri, 2016-07-01 at 15:30 +0000, Sho Fujisawa wrote:

> No I haven't tried. Had hoped there might be a different way, but
> alas.
>
> Does TrakEM2 work ok with multi-channel images? I havn't really
> started working with the plugin, so I'm not sure of the details yet.
> I have a 5-channel images that need to be aligned. I'd like to align
> with just one of the 5 channels, and apply the same alignment to all
> other channels.
>
> Sho Fujisawa
> Sr. Digital Microscopist
> Molecular Cytology Core Facility
> Memorial Sloan-Kettering Cancer Center
> 417 E. 68th St.
> Zuckerman Room 1834
> New York NY 10065
> [phone]
> [phone]
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Saalfeld, Stephan
> Sent: Friday, July 01, 2016 11:23 AM
> To: [hidden email]
> Subject: Re: TrackEM alignment of .ims Imaris stack
>
> 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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