Time settings in metadata

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Time settings in metadata

Knecht, David
We are often collecting image sequences in Micro-Manager and then analyzing the results with the mTrackJ plugin in ImageJ.  When we open the stack of images in mTrackJ, the time interval is not automatically imported.  We normally go into Image/Properties to add the appropriate value.  Is there a way for this metadata be transferred automatically?  Dave

Dr. David Knecht    
Department of Molecular and Cell Biology
Co-head Flow Cytometry and Confocal Microscopy Facility
U-3125
91 N. Eagleville Rd.
University of Connecticut
Storrs, CT 06269
860-486-2200
860-486-4331 (fax)



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Re: Time settings in metadata

Nico Stuurman-4
Hi David,

> We are often collecting image sequences in Micro-Manager and then  
> analyzing the results with the mTrackJ plugin in ImageJ.  When we  
> open the stack of images in mTrackJ, the time interval is not  
> automatically imported.  We normally go into Image/Properties to add  
> the appropriate value.  Is there a way for this metadata be  
> transferred automatically?

Great suggestion.  Since we do that for xy coordinates, I don't see  
why that couldn't work for time stamps. We'll look into it.

Nico


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Re: Time settings in metadata

Nico Stuurman-4
>> We are often collecting image sequences in Micro-Manager and then
>> analyzing the results with the mTrackJ plugin in ImageJ.  When we
>> open the stack of images in mTrackJ, the time interval is not
>> automatically imported.  We normally go into Image/Properties to add
>> the appropriate value.  Is there a way for this metadata be
>> transferred automatically?
>
> Great suggestion.  Since we do that for xy coordinates, I don't see
> why that couldn't work for time stamps. We'll look into it.

Spoke too soon.  This is already implemented, and works well for me.  
For instance, when I do a MDA with 0.4 second interval, then use the  
Image5D->Convert to stack command, then check ImageJ menu -> Image ->  
Properties, I see a Frame Interval of 400 mseconds.

Can you describe how you acquire your image sequence and convert it to  
an ImageJ stack?

Best,

Nico


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Re: Time settings in metadata

Knecht, David
The stacks were saved as individual files to a folder and then File/Import Image Sequence was used to open them in ImageJ.  Our sequences are often too large to risk anything but Show Last Image, so we don't normally have the whole stack up at the end of an acquisition.  We run Micro-Manager and ImageJ in parallel and do Image processing in ImageJ because of the plugin headache and because we can open subsets of the data.  Your plugin set that is downloaded does not include all the plugins we use.  So each time an upgrade comes out we would have to go back and install the extra plugins on each computer.  Perhaps I should just create a folder of the extra plugins and move that to avoid the problem. There aren't many (mTrackJ is the one I know of). I thought the metadata would have the time info and be imported.  Dave

On Feb 18, 2010, at 6:22 AM, Nico Stuurman wrote:

>>> We are often collecting image sequences in Micro-Manager and then
>>> analyzing the results with the mTrackJ plugin in ImageJ.  When we
>>> open the stack of images in mTrackJ, the time interval is not
>>> automatically imported.  We normally go into Image/Properties to add
>>> the appropriate value.  Is there a way for this metadata be
>>> transferred automatically?
>>
>> Great suggestion.  Since we do that for xy coordinates, I don't see
>> why that couldn't work for time stamps. We'll look into it.
>
> Spoke too soon.  This is already implemented, and works well for me.  
> For instance, when I do a MDA with 0.4 second interval, then use the  
> Image5D->Convert to stack command, then check ImageJ menu -> Image ->  
> Properties, I see a Frame Interval of 400 mseconds.
>
> Can you describe how you acquire your image sequence and convert it to  
> an ImageJ stack?
>
> Best,
>
> Nico
>
>
> ------------------------------------------------------------------------------
> Download Intel® Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
> _______________________________________________
> micro-manager-general mailing list
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Dr. David Knecht    
Department of Molecular and Cell Biology
Co-head Flow Cytometry and Confocal Microscopy Facility
U-3125
91 N. Eagleville Rd.
University of Connecticut
Storrs, CT 06269
860-486-2200
860-486-4331 (fax)



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Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
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