4 channel .nd2 file into photoshop

[egrevstad]

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Does anyone have experience transferring 4 channel fluorescent images out of NIS-Elements
and into photoshop as a single file that retains the channel separations?  We have tried saving
as a TIFF, but when opened in either FIJI or Photoshop only three channels appear (with the
fourth blending into 2 of the channels), similarly to if one would save it as an RBG file.

Thanks in advance for any help,

Elle Grevstad

Elle Kielar Grevstad, Ph.D
Director of the Biochemistry Optical Core
Department of Biochemistry
University of Wisconsin-Madison

[Aryeh Weiss]

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On 4/2/15 8:35 PM, Elle Grevstad wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> Does anyone have experience transferring 4 channel fluorescent images out of NIS-Elements
> and into photoshop as a single file that retains the channel separations?  We have tried saving
> as a TIFF, but when opened in either FIJI or Photoshop only three channels appear (with the
> fourth blending into 2 of the channels),
>   similarly to if one would save it as a RBG file.
>
> Thanks in advance for any help,
>
> Elle Grevstad
>
> Elle Kielar Grevstad, Ph.D
> Director of the Biochemistry Optical Core
> Department of Biochemistry
> University of Wisconsin-Madison
>

I dont know about photoshop, but you can read th nd2 files directly in
Fiji, and the should open up with all 4 channels.
That should be easier than exporting from NIS Elements.
If you have trouble doing that, send me an example and I will try in on
my computer.

--aryeh

--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]

[DamirSudar]

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Hi Elle,

You can read the original ND2 into Fiji using Bio-Formats and it will
show up as a 4-channel dataset. Then when you Save that as a TIFF, it
will generate a single TIFF file with all 4 channels as separate
channels (i.e. not assembled into an RGB). How Photoshop would handle
such a multi-channel file, I don't know. I don't have that program.

Cheers,
- Damir

On 4/2/2015 10:35 AM, Elle Grevstad wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> Does anyone have experience transferring 4 channel fluorescent images out of NIS-Elements
> and into photoshop as a single file that retains the channel separations?  We have tried saving
> as a TIFF, but when opened in either FIJI or Photoshop only three channels appear (with the
> fourth blending into 2 of the channels), similarly to if one would save it as an RBG file.
>
> Thanks in advance for any help,
>
> Elle Grevstad
>
> Elle Kielar Grevstad, Ph.D
> Director of the Biochemistry Optical Core
> Department of Biochemistry
> University of Wisconsin-Madison

--
Damir Sudar - Staff Scientist
Lawrence Berkeley Laboratory / Life Sciences Division
One Cyclotron Road, MS 977, Berkeley, CA 94720, USA
T: 510/486-5346 - F: 510/486-5586 - E: [hidden email]
WWW: http://www.lbl.gov/lifesciences/labs/sudar_lab.html

[Linda Barthel]

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Elle,
Export all 4 channels as a separate tiff.  Open each in Photoshop.  Select
and copy one image.  Make a new image file, then "paste special", "paste in
place" the first tiff.  Do the same for the other 3 channels.  "Paste in
Place" is important to ensure correct registration  Each channel should now
be a layer in the new file.  Highlight the top layer, go to the layers tab
where it says "normal", at the pulldown arrow select "lighten".  Do this
for the next two layers.  This adds a transparency to the layers allowing
the others below to show through.  The "screen" function does the same but
I find "lighten" to retain more of the image qualities.   Each layer can be
enhanced and adjusted to optimize your final image.
Regards,
Linda Barthel

Linda Barthel, M.S.
*Research Laboratory Specialist Lead*

*Department of Molecular, Cellular, and Developmental Biology*
                      3010 Natural Sciences Building (Kraus)
                                    830 N. University
                             Ann Arbor, MI  48109-1048

fax: [phone]
http://sites.lsa.umich.edu/raymond-lab/
<http://www-personal.umich.edu/~praymond/>

      *  Microscopy & Image-analysis Laboratory-North *
            Biomedical Research Core Facilities
              2800 Plymouth Rd, Rm 53S, Bdg 20
                 Ann Arbor, MI  48109-2800

office: [phone]
fax:    [phone]
http://www.umncrc.org


On Thu, Apr 2, 2015 at 1:35 PM, Elle Grevstad <[hidden email]> wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> Does anyone have experience transferring 4 channel fluorescent images out
> of NIS-Elements
> and into photoshop as a single file that retains the channel separations?
> We have tried saving
> as a TIFF, but when opened in either FIJI or Photoshop only three channels
> appear (with the
> fourth blending into 2 of the channels), similarly to if one would save it
> as an RBG file.
>
> Thanks in advance for any help,
>
> Elle Grevstad
>
> Elle Kielar Grevstad, Ph.D
> Director of the Biochemistry Optical Core
> Department of Biochemistry
> University of Wisconsin-Madison
>

--
Linda Barthel, M.S.
*Research Laboratory Specialist Lead*

*Department of Molecular, Cellular, and Developmental Biology*
                      3010 Natural Sciences Building (Kraus)
                                    830 N. University
                             Ann Arbor, MI  48109-1048

fax: [phone]
http://sites.lsa.umich.edu/raymond-lab/
<http://www-personal.umich.edu/~praymond/>

      *  Microscopy & Image-analysis Laboratory-North *
            Biomedical Research Core Facilities
              2800 Plymouth Rd, Rm 53S, Bdg 20
                 Ann Arbor, MI  48109-2800

office: [phone]
fax:    [phone]
http://www.umncrc.org

[kspencer007]

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Hi Elle;
        In Elements, if you hold the Control key, you can select the red, green, and blue tabs to save as a tiff. Then click on the tab for your 4th color, save that as a separate tiff. Open the two images in Photoshop. Add one image to the other as a new layer. You can independently modify the layers, then flatten for your final image.
        Tiff images only deal with 3 color channels; everything else is a blend of those colors.
        Kathy
       
The Scripps Research Institute
Dept of Molecular and Cellular Neuroscience
10550 N. Torrey Pines Road
DNC 210
La Jolla, Ca 92037



-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Elle Grevstad
Sent: Thursday, April 02, 2015 10:35 AM
To: [hidden email]
Subject: 4 channel .nd2 file into photoshop

*****
To join, leave or search the confocal microscopy listserv, go to:
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Post images on http://www.imgur.com and include the link in your posting.
*****

Does anyone have experience transferring 4 channel fluorescent images out of NIS-Elements and into photoshop as a single file that retains the channel separations?  We have tried saving as a TIFF, but when opened in either FIJI or Photoshop only three channels appear (with the fourth blending into 2 of the channels), similarly to if one would save it as an RBG file.

Thanks in advance for any help,

Elle Grevstad

Elle Kielar Grevstad, Ph.D
Director of the Biochemistry Optical Core Department of Biochemistry University of Wisconsin-Madison