[ImageJ-devel] [fiji-devel] [Bug 258] Opening multiposition LSM files by Drag&Drop throws exception (fwd)

[Jerome Mutterer]

Hi all,

Yes the positions are stuffed into the time dimension for now. I decided to
do that to keep a single image window per lsm file. However, once opened,
the image info carries the exact count of each dimension, so it's always
possible to split e.g. positions into multiple image windows.
Here's how to retrieve the number of positions and time points:

   List.setList(getMetadata('info'));

print (List.getValue('P_size'));

print (List.getValue('T_size'));

The other option would have been open each position in separate image
windows, but this would output unpredictable number of windows, possibly
breaking some workflows.

Jerome.



On Tue, Apr 5, 2011 at 9:45 AM, Daniel James White <white at mpi-cbg.de> wrote:

> Hi all .lsm sufferers,
>
>
> On Apr 4, 2011, at 11:46 PM, Johannes Schindelin wrote:
>
> > Hi Mark & other .lsm experts,
> >
> >> ---------- Forwarded message ----------
> >> [...]
> >> http://pacific.mpi-cbg.de/cgi-bin/bugzilla/show_bug.cgi?id=258
> >>
> >> [...]
> >> ------- Comment #9 from johannes.schindelin at gmx.de  2011-04-04 23:31
> -------
> >> I pushed the changes to the 'lsm-reader-4.0g' branch, and hope to merge
> >> to 'master' and to upload to the Updater soon.
> >
> > May I ask you for a quick sanity check? It's actually very small:
> >
> >
> http://pacific.mpi-cbg.de/cgi-bin/gitweb.cgi?p=fiji.git;a=commitdiff;h=7e70bc5762abf993b729910b4c3b0414e5a97ae6
>
> Hmmm, looking at the diffs... it seems that tile position is stuffed into
> the time dimension.
>
> So whats gonna happen if there is a time series tile scan?
> "There may be trouble ahead, but while there's moonlight, and music, and
> love and romance..."
>
> Do we have a strategy in imageJ2 for dealing with multi stage xy position
> data sets
> that also allows time series?
>
> Imglib is the answer guess? But hoiw?
> Does imglib have a concept for this rather strange pair of extra
> dimensions: x and y stage position?
> Some kind of x and y offset (in theory also z could be "tiled" eg. when a z
> piezo stepper has a limited range, and you do several scans in z to cover a
> larger range)
>
> ???
>
> Dan
>
>
> >
> > Ciao,
> > Dscho
> >
> > --
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>
> Dr. Daniel James White BSc. (Hons.) PhD
> Senior Microscopist / Image Visualisation, Processing and Analysis
> Light Microscopy and Image Processing Facilities
> Max Planck Institute of Molecular Cell Biology and Genetics
> Pfotenhauerstrasse 108
> 01307 DRESDEN
> Germany
>
> +49 (0)15114966933 (German Mobile)
> +49 (0)351 210 2627 (Work phone at MPI-CBG)
> +49 (0)351 210 1078 (Fax MPI-CBG LMF)
>
> http://www.bioimagexd.net       BioImageXD
> http://pacific.mpi-cbg.de               Fiji -  is just ImageJ (Batteries
> Included)
> http://www.chalkie.org.uk               Dan's Homepages
> https://ifn.mpi-cbg.de                  Dresden Imaging Facility Network
> dan (at) chalkie.org.uk
> ( white (at) mpi-cbg.de )
>
>
>
>
>
>
>
>
>
>
>
>
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