[ome-users] Find Spots trouble

[Ilya Goldberg]

Hi Gloria
I'm sorry that you're having trouble.
Let's start with cb_1.r3d since its an image we both have access to.   
I'm also using 2.6.1 so we have the same interface.

Make a dataset called "FindSpots test" containing only cb_1.r3d
Click on Find Spots under Analysis.
Make sure these important settings are correct in this web UI:
Selected dataset: FindSpots test
Channel: 500 *** Not the 568 selected "by default".  500 is the GFP  
channel with the "spots".  568 is the channel with nucleus.
The rest should be the default settings:
Beginning/end
Threshold Type: Relative to Geometric Mean
Threshold Value: 1.5
Min spot volume: 10
Define spots only at time: All Ts
Run the tracking algorithm should also be checked

Click on the Execute button.
When the page reloads, you will have:
1x Find spots
1x Track spots
1x Stack statistics (image server)

Click on the blue "Find spots"
This takes you directly to the module execution view for the spot- 
finding algorithm.  It should be full of output.
Click on the "View graphic overlay" link right above the "Outputs"  
heading.
The yellow box at the top of the viewer will have an "Overlays" label  
as the last item in the second row.  Click on it.
A semi-transparent window will appear called "Overlay Manager".  You  
can move it out of the way by dragging the title bar.
The first line of the Overlay Manager will say "Layer Spots Off".   
Click the "Off" to turn it on.
Click the circle to the right of "Show all Z", turning it white  
("on"). This turns the overlays on for all Zs - not just the spot's Z- 
centroids.
You will see blue circles overlayed on the image.  You can turn them  
on for all timepoints as well by clicking the "Show all Ts" circle.

If this does not work, please let me know.
-Ilya



On Nov 20, 2007, at 9:20 AM, Gloria Torralba wrote:

> Hello,
>
> Sorry if that is documented elsewhere but I did not find anything
> related in the mailing list.
> We want to use OME as a secure and available system to store and share
> image data. But we would like also to do analysis.
>
> We have currently installed version 2.6.1. With both, web interface
> client (Win and IE) and java client (Shoola ver. 2.2) is possible to
> access the data server, create datasets, projects, annotate, importing
> images. Exporting and importing from/to ImageJ and VisBio seems  
> also to
> be okay. Exported ome-xml format is readable in ImageJ and so on. We
> have the SVG viewer installed and we can also visualize image (z>1,
> t>1).
>
> But running Find Spots never worked, neither when we had an older
> version (2.4.0) one year ago.  I read carefully the tutorial about,  
> and
> I run FindSpots over some images test with the correct threshold  
> values
> calculated as the document suggests. "View Chain Results" reports  
> about
> an "Analysis chain Find and Track Spots" executed, but any information
> about the spots is displayed ( "View graphic overlays" shows the same
> original image, and neither the popup "overlays"  or "overlay manager"
> are present in the viewer). The tabular interface for displaying the
> output of analysis modules is also empty?
>
> Last, I run findspots over  the same image example (cb_1.r3d) as in
> http://www.openmicroscopy.org/getting-started/analysis.html, using  
> this
> time the same values for threshold as in the web-example (may be the
> threshold before was wrong calculated and nothing was "found"), but
> again I got the same results. What I am doing wrong? Error logs are  
> not
> also found.
>
> I would appreciate very much your help. GetGraphics.pm at
> /usr/local/share/perl/5.8.8/OME/Web is the one without the bug.
>
> Many thanks in advance, Gloria
>
>
>
>
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