registration of multichannel stacks using one of the channels

[Vitha, Stanislav]

Hallo,
I have a number of  3-channel timelapse stacks of plant chloroplasts from a confocal microscope (GFP, chlorophyll fluorescence, transmitted light). I would like to perform stack registration to eliminate the movement of the chloroplast, using one channel of the stack (the red chlorophyll signal).  The ultimate goal is to measure ROI intensity in the GFP channel over time (it is a FRAP experiment), but since the GFP channel is usually fairly dim and noisy, using the red channel for registration seems like a good idea.
I have been using the StackReg plugin for single channel images (Rigid Body algorithm), but I do not see an option to either export the alignment data (to be used on another dataset or pick just one channel as a source.  I would like to avoid converting to 8-bits per pixel (currently it is 12-bit data, saved as 16 bpp tiffs)

Thanks,
Stan Vitha
 Microscopy and Imaging Center
Texas A&M University



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[Christine Labno-2]

Hello Stan,

There is a plugin called MultiStackReg by Brad Busse that does what you want.  I've used it several times with great success.  It's available for download here

http://bradbusse.net/downloads.html

Best,
Christine

Christine Labno, Ph.D.
Asst. Technical Director
Light Microscopy Core
University of Chicago
Office of Shared Research Facilities
KCBD 1250 900 E. 57th St.
[phone] (phone)
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________________________________________
From: ImageJ Interest Group [[hidden email]] on behalf of Vitha, Stanislav [[hidden email]]
Sent: Wednesday, February 06, 2013 10:29 AM
To: [hidden email]
Subject: registration of multichannel stacks using one of the channels

Hallo,
I have a number of  3-channel timelapse stacks of plant chloroplasts from a confocal microscope (GFP, chlorophyll fluorescence, transmitted light). I would like to perform stack registration to eliminate the movement of the chloroplast, using one channel of the stack (the red chlorophyll signal).  The ultimate goal is to measure ROI intensity in the GFP channel over time (it is a FRAP experiment), but since the GFP channel is usually fairly dim and noisy, using the red channel for registration seems like a good idea.
I have been using the StackReg plugin for single channel images (Rigid Body algorithm), but I do not see an option to either export the alignment data (to be used on another dataset or pick just one channel as a source.  I would like to avoid converting to 8-bits per pixel (currently it is 12-bit data, saved as 16 bpp tiffs)

Thanks,
Stan Vitha
 Microscopy and Imaging Center
Texas A&M University



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