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saving and opening Micro-manager data

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saving and opening Micro-manager data

David Knecht
If you collect a multi-channel time lapse dataset in Micro-manager, y the standard viewer is great for manipulating channel LUTs and optimizing visualization.  What is the best way to now save the data so that the changes are retained and the file can be re-opened in FIJI retaining those changes and so one could output an RGB movie of the data?  Thanks- Dave

Dr. David Knecht
Professor of Molecular and Cell Biology
University of Connecticut
91 N. Eagleville Rd.
Storrs, CT 06269-3125
860-486-2200


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Re: saving and opening Micro-manager data

Nico Stuurman-2

On 3/9/17 6:59 AM, David Knecht wrote:
> If you collect a multi-channel time lapse dataset in Micro-manager, y
> the standard viewer is great for manipulating channel LUTs and
> optimizing visualization.  What is the best way to now save the data
> so that the changes are retained and the file can be re-opened in FIJI
> retaining those changes and so one could output an RGB movie of the data?

This is easy in 2.0: Click on the gear icon at the bottom of the viewer,
and select "Export images as displayed", then select the "ImageJ stack
window" option.  From there, choose save as AVI in ImageJ.  Export will
include things like scale bar and time stamps (if  you have those
displayed).  Also handy is the "Duplicate..." command under that same
gear icon, as it will let you crop the dataset in any dimension.

Not sure if there is an easy way in 1.4, but 2.0 will read data
generated with 1.4.

Best,

Nico

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