[ome-users] cannot find results for 'find and track spots'

[Jason Swedlow]

Henley--

Here are some directions.  The interface needs some cleaning up, but 
the data is really there.  try the following:

Directions for finding FindSpots results:

Remember:
-- Find Spots Analysis is actaully a "chain", that runs a series of 
analysis modules ("Nodes") against an OME Dataset (a user-defined group 
of images).

To find a set of results:

1) Click on Chain Executions (left hand menu).

2) Pick the Chain Execution you want to examine by clicking on its ID 
number.  Note you can search for these, defining them by Experimenter, 
Timestamp, ID, etc.  You'll also see that for each Chain Execution, 
there are a number of other sources of information you can see.

3) Once you choose the ID number you want to examine, you now have a 
description of the specific chain, with all the Nodes (analysis 
modules) in the Chain.  In the case of FindSpots, there are three 
nodes: Stack Statistics, FindSpots, and TrackSpots.  Clicking on any 
one of these shows the results of the execution of that Node in this 
Chain.

4) If you click on the FindSpots link, you now see all the Findspots 
executions on the Dataset in this Chain (e.g., if there were 20 images 
in the Dataset, you will have 20 FindSpots executions).  This 
particular screen is a bit confusing (we will fix this).  Note that 
each execution is linked to an Image thumbnail, and by clicking the top 
left quadrant of the thumbnail, you can see the Image info, or see the 
image itself by clicking anywhere else on the thumbnail.

5) Each execution of the Findspots module can be examined by clicking 
the ""Find spots" link next to the "module execution" label.

6) This provides a full report of all the inputs and output for this 
Image.  These can all be dumped to a text ("CSV") table. Note under the 
main table you have a link callled "View graphic overlay".  If you 
click here, this starts the SVGViewer.  To see the found objects, click 
on Overlays, and select On.  If you scroll through Z or T, you will see 
any found objects.   Note you can see all objects found through Z or T 
projected into the single image by selecting "Show all Z" or "Shoe all 
T".

Hope this helps.

Cheers,

Jason


On 18 Apr 2005, at 09:35, henley at bii-sg.org wrote:

>  Hi all,
>
>  I am a newbie to OME who has a question about using the
>  'Find and track spots' analysis function in the OME
>  Web Interface.
>
>  After running the 'Find spots' analysis, I dont seems to
>  be able to "find" the results to the analysis, using
>  the 'View Chain Results' link in the same navigation panel on
>  the left. All that was in that link is simply meta data
>  of the analysis chain that i have run previously. e.g
>  dataset,experimenter,time stamp etc which I do not think is
>  the results for the 'Find and track spots' analysis per se.
>
>  Does anyone know from which part of the web interface can
>  I retrieve my results for the 'Find and track spot' analysis ?
>
>  When i click on the 'view chain results' -> 'Find and track spot' link
>  I find that the "owner" of the AnlaysisChain is different from the
>  experimeter that is stated in 'view chain results' page.
>  Is that normal ? If not is this the cause of the problem that I have
>  described earlier ?
>
>
>  Any help here would be much appreciated even though i know
>  am asking some very basic user level questions :)
>
>  Rgds
>  Henley
>  --
>  HenLey Hor
>  Software Developer
>  Software Engineering Group
>  Bioinformatics Institute
>
>
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>

NOTE NEW EMAIL ADDRESS: jason at lifesci.dundee.ac.uk
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phone (01382) 345819
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email: jason at lifesci.dundee.ac.uk

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