[ImageJ-devel] [fiji-devel] [Bug 258] Opening multiposition LSM files by Drag&Drop throws exception (fwd)
Daniel James White
white at mpi-cbg.de
Tue Apr 5 04:32:35 CDT 2011
Hi Jason and all,
On Apr 5, 2011, at 9:58 AM, Jason Swedlow wrote:
> Hi Dan-
>
> <large scale tooting of own horn>
you should and you must!!!
>
> 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.
Exactly...
I just wonder how we are going to get imglib and these higher dimensions to play nice?
>
> In OME this is handled explicitly (http://www.openmicroscopy.org/Schemas/OME/2010-06/ome.xsd). Look under the Plane Element for details.
Good (phew!)
>
> 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?
I guess the way familiar to most imageJ users will be to have a single "hyperstack" window, which only ever shows one image at a time (or maybe 2 images in magenta / green, or 3 images as RGB or CYM) with a slider for every dimension other than x and y.
I suppose there is no need to say that x and y must be the 2 dimensions plotted to the screen.... once could choose which 2 to plot,
and relegate the others to having sliders.
In the 3D viewer.... same story, choose which 3 dimensions to render as a volume, and have sliders for the others?
As you suggest, once can also imagine a "'google maps" type viewer for large tiled image data sets, where you can see and over view of the whole structure when zoomed out, and also zoom in to see the details of one area... and of course Stephan Saalfeld already did exactly that right here:
http://fly.mpi-cbg.de/
so we have a good idea how to approach that i guess?
I think I remember that this required pre computation of the over view, zoomed out images at various scales.. and this is exactly why imaris takes forever to open large images... its calculating the down sampled representations.... so once its loaded the zooming in and out is fast...
LSM files can be 1D line scans over multiple data channels (lambda or spectral scan) over time.
We have no way of easily displaying that in imageJ right now without jumping through many hoops...
but we should aim to make a good general and trivial (for the user) solution for the 2D and 3D display of n dimensional pixels?
Whats the plan in imageJ2 for this Curtis?
Now the 1st alpha is out... its certainly the right time to get this stuff nailed down right?
Is there a design for the new "hyperstack" pixel data viewer?
I imagine a display configuration window gadget... something like the image disply properties in imaris, where you can choose which dimension to show as x and whoch as y on the 2D display, and which extra dimensions with sliders, and which as different colour channels (like composite, still with a slider?). LUTs could also be handled in there....?
This is all tied into the ongoing discussion about and OME/imglib work on n-dimensional ROIs I guess...
Right now there is the imglib1/2 stuff to sort out, so better not get too distracted from that...
but anyway, these are ideas for the future.
cheers
Dan
>
> </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
>>>
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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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>
>
>
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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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