Hi all,<div><br></div><div>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. </div>
<div>Here's how to retrieve the number of positions and time points:</div><div><br></div><div><meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
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<p class="p1">List.setList(getMetadata('info'));</p>
<p class="p1"><meta charset="utf-8"><span class="Apple-style-span" style="font-family: arial; font-size: small; "></span></p><p class="p1" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal 'Lucida Grande'; ">
print (List.getValue('P_size'));</p><div><meta charset="utf-8"><p class="p1" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 14px/normal 'Lucida Grande'; ">
print (List.getValue('T_size'));</p></div><div><br></div><p></p></div><div>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.</div>
<div><br></div><div>Jerome.</div><div><br></div><div><br><br><div class="gmail_quote">On Tue, Apr 5, 2011 at 9:45 AM, Daniel James White <span dir="ltr"><<a href="mailto:white@mpi-cbg.de">white@mpi-cbg.de</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Hi all .lsm sufferers,<br>
<br>
<br>
On Apr 4, 2011, at 11:46 PM, Johannes Schindelin wrote:<br>
<br>
> Hi Mark & other .lsm experts,<br>
><br>
>> ---------- Forwarded message ----------<br>
>> [...]<br>
>> <a href="http://pacific.mpi-cbg.de/cgi-bin/bugzilla/show_bug.cgi?id=258" target="_blank">http://pacific.mpi-cbg.de/cgi-bin/bugzilla/show_bug.cgi?id=258</a><br>
>><br>
>> [...]<br>
>> ------- Comment #9 from <a href="mailto:johannes.schindelin@gmx.de">johannes.schindelin@gmx.de</a> 2011-04-04 23:31 -------<br>
>> I pushed the changes to the 'lsm-reader-4.0g' branch, and hope to merge<br>
>> to 'master' and to upload to the Updater soon.<br>
><br>
> May I ask you for a quick sanity check? It's actually very small:<br>
><br>
> <a href="http://pacific.mpi-cbg.de/cgi-bin/gitweb.cgi?p=fiji.git;a=commitdiff;h=7e70bc5762abf993b729910b4c3b0414e5a97ae6" target="_blank">http://pacific.mpi-cbg.de/cgi-bin/gitweb.cgi?p=fiji.git;a=commitdiff;h=7e70bc5762abf993b729910b4c3b0414e5a97ae6</a><br>
<br>
Hmmm, looking at the diffs... it seems that tile position is stuffed into the time dimension.<br>
<br>
So whats gonna happen if there is a time series tile scan?<br>
"There may be trouble ahead, but while there's moonlight, and music, and love and romance..."<br>
<br>
Do we have a strategy in imageJ2 for dealing with multi stage xy position data sets<br>
that also allows time series?<br>
<br>
Imglib is the answer guess? But hoiw?<br>
Does imglib have a concept for this rather strange pair of extra dimensions: x and y stage position?<br>
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)<br>
<br>
???<br>
<br>
Dan<br>
<br>
<br>
><br>
> Ciao,<br>
> Dscho<br>
><br>
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><br>
<br>
Dr. Daniel James White BSc. (Hons.) PhD<br>
Senior Microscopist / Image Visualisation, Processing and Analysis<br>
Light Microscopy and Image Processing Facilities<br>
Max Planck Institute of Molecular Cell Biology and Genetics<br>
Pfotenhauerstrasse 108<br>
01307 DRESDEN<br>
Germany<br>
<br>
+49 (0)15114966933 (German Mobile)<br>
<a href="tel:%2B49%20%280%29351%20210%202627">+49 (0)351 210 2627</a> (Work phone at MPI-CBG)<br>
<a href="tel:%2B49%20%280%29351%20210%201078">+49 (0)351 210 1078</a> (Fax MPI-CBG LMF)<br>
<br>
<a href="http://www.bioimagexd.net" target="_blank">http://www.bioimagexd.net</a> BioImageXD<br>
<a href="http://pacific.mpi-cbg.de" target="_blank">http://pacific.mpi-cbg.de</a> Fiji - is just ImageJ (Batteries Included)<br>
<a href="http://www.chalkie.org.uk" target="_blank">http://www.chalkie.org.uk</a> Dan's Homepages<br>
<a href="https://ifn.mpi-cbg.de" target="_blank">https://ifn.mpi-cbg.de</a> Dresden Imaging Facility Network<br>
dan (at) <a href="http://chalkie.org.uk" target="_blank">chalkie.org.uk</a><br>
( white (at) <a href="http://mpi-cbg.de" target="_blank">mpi-cbg.de</a> )<br>
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</blockquote></div><br></div>