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

Tue Apr 5 02:58:20 CDT 2011

Hi Dan-

<large scale tooting of own horn>

In fact, this type of data collection is not strange at all-- we, and  
many others do it alot.  It's really very helpful for gathering many  
examples in timelapse, and also for tiling.  Another example is the  
concept of a WellSample in HCS-- multiple images in different  
locations of the same Well.

In OME this is handled explicitly (http://www.openmicroscopy.org/Schemas/OME/2010-06/ome.xsd 
).  Look under the Plane Element for details.

I understand this approach is somewhat at odds with imglib. As we move  
forward towards a similar concept (http://trac.openmicroscopy.org.uk/ome/ticket/3678 
), we'll definitely keep an eye on what the Fiji/Imagejdev team is  
doing there.

Obviously, implementing this in software is technically not  
challenging, but it's not always clear how user wants data displayed.   
View 10 20 GB images at once?  Toggle them?  Montage? Tile?

</large scale tooting of own horn>

Cheers,

jason

On 5 Apr 2011, at 08:45, Daniel James White 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
>>
>> -- 
>> You received this message because you are subscribed to the Google  
>> Groups "Fiji-devel" group.
>> To post to this group, send email to fiji-devel at googlegroups.com.
>> To unsubscribe from this group, send email to fiji-devel+unsubscribe at googlegroups.com 
>> .
>> For more options, visit this group at http://groups.google.com/group/fiji-devel?hl=en 
>> .
>>
>
> 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 )
>
>
>
>
>
>
>
>
>
>
>
>
> _______________________________________________
> ImageJ-devel mailing list
> ImageJ-devel at imagejdev.org
> http://imagejdev.org/mailman/listinfo/imagej-devel

**************************
Wellcome Trust Centre for Gene Regulation & Expression
College of Life Sciences
MSI/WTB/JBC Complex
University of Dundee
Dow Street
Dundee  DD1 5EH
United Kingdom

phone (01382) 385819
Intl phone:  44 1382 385819
FAX   (01382) 388072
email: jason at lifesci.dundee.ac.uk

Lab Page: http://gre.lifesci.dundee.ac.uk/staff/jason_swedlow.html
Open Microscopy Environment: http://openmicroscopy.org
**************************

The University of Dundee is a Scottish Registered Charity, No. SC015096.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://imagej.net/pipermail/imagej-devel/attachments/20110405/eff0eaa2/attachment.html>