Alexa 647 channel extraction from .tif files in ImageJ

[farkasam]

Hello All,

I saved 4 channel IF (DAPI, AF488, AF568, AF647) as .tif files. In ImageJ I cannot seem to find the AF647 channel. Is there a way to do this?

Secondarily, If I rename my files as ".lsm" or some other file type will this channel be accessible?

Thank you much for your advice,
Adam

[Swayne, Theresa C.]

Dear Adam,

Did you save the files as RGB tif perhaps? RGB reduces an image to 3 color components, so it will blend your channels together depending on the pseudocolor scheme you used. Renaming will not restore the original channels.

Some software packages can export multi-channel tifs that are not RGB. Look for a "16-bit" option or something similar.

Better yet, use the Bio-Formats plugin (for ND2, LSM, CZI, etc.) or the LSM Toolbox (for LSM) to open your raw data.

Hope this helps,
Theresa

On Jul 16, 2015, at 9:58 AM, farkasam <[hidden email]<mailto:[hidden email]>> wrote:

Hello All,

I saved 4 channel IF (DAPI, AF488, AF568, AF647) as .tif files. In ImageJ I
cannot seem to find the AF647 channel. Is there a way to do this?

Secondarily, If I rename my files as ".lsm" or some other file type will
this channel be accessible?

Thank you much for your advice,
Adam

------------------------------------
Theresa Swayne, Ph.D.
Manager
Confocal and Specialized Microscopy Shared Resource<http://hiccc.columbia.edu/research/sharedresources/confocal>

Herbert Irving Comprehensive Cancer Center
Columbia University Medical Center
1130 St. Nicholas Ave., Room 222A
New York, NY 10032
Phone: [phone]
[hidden email]<mailto:[hidden email]>


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[farkasam]

Hi Theresa,

This is very helpful. Thanks for your expertise.

Best,
Adam

[Cammer, Michael]

http://microscopynotes.com/imagej/macros/color_channels_macro_v100.txt
http://microscopynotes.com/imagej/macros/composite-colors/user-selected-contrast-colors-names-save8bit.html


_________________________________________
Michael Cammer, Optical Microscopy Specialist
http://ocs.med.nyu.edu/microscopy
http://microscopynotes.com/
Cell: [phone]

________________________________________
From: ImageJ Interest Group [[hidden email]] on behalf of farkasam [[hidden email]]
Sent: Thursday, July 16, 2015 11:08 AM
To: [hidden email]
Subject: Re: Alexa 647 channel extraction from .tif files in ImageJ

Hi Theresa,

This is very helpful. Thanks for your expertise.

Best,
Adam





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