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side-by-side merge

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Michal Opas

side-by-side merge

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Dear Listers,

This harks back to prhistory:
on Bio-Rad MRC 600 and Confocal Assistant by Todd Brelje one could merge
dual wavelength images taken simultaneously using split screen ("split
box") feature of the scope.
This "side-by-side merge" feature was very convenient for the dual
excitation, split image frames as one could quickly merge left with
right and see how good the merged image is.
Sadly, the Confocal Assistant will not work under 64-bit OS.
I look for a functionality allowing for "side-by-side merge" in ImageJ
and Fiji but failed to find it.
I am discombobulated: is such a useful feature gone forever (past Win
XP) or my ineptitude is gross?

Thank you very much for advice.

Michal

--

* Dr. Michal Opas
Professor
Department of Laboratory Medicine and Pathobiology
University of Toronto
1 King's College Circle
Medical Sciences Building, room 6326
Toronto, Ontario, M5S 1A8 Canada

**°°°°°°°°°°°°°**
phone: (416) 978-8947 (laboratory)
(416) 971-2140 (office)
fax: (416) 978-5959
e*-*mail: **[hidden email] <mailto:[hidden email]>***

*WWW**:** **http://www.utoronto.ca/mocell
*

simon walker (BI)-2

Re: side-by-side merge

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

Hi Michal,
You could try using the Cairn Optosplit plugin for ImageJ.
You can download it here: http://www.cairn-research.co.uk/support/software
Simon

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Michal Opas
Sent: 12 March 2013 13:35
To: [hidden email]
Subject: side-by-side merge

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

Dear Listers,

This harks back to prhistory:
on Bio-Rad MRC 600 and Confocal Assistant by Todd Brelje one could merge dual wavelength images taken simultaneously using split screen ("split
box") feature of the scope.
This "side-by-side merge" feature was very convenient for the dual excitation, split image frames as one could quickly merge left with right and see how good the merged image is.
Sadly, the Confocal Assistant will not work under 64-bit OS.
I look for a functionality allowing for "side-by-side merge" in ImageJ and Fiji but failed to find it.
I am discombobulated: is such a useful feature gone forever (past Win
XP) or my ineptitude is gross?

Thank you very much for advice.

Michal

--

* Dr. Michal Opas
Professor
Department of Laboratory Medicine and Pathobiology
University of Toronto
1 King's College Circle
Medical Sciences Building, room 6326
Toronto, Ontario, M5S 1A8 Canada

**°°°°°°°°°°°°°**
phone: (416) 978-8947 (laboratory)
(416) 971-2140 (office)
fax: (416) 978-5959
e*-*mail: **[hidden email] <mailto:[hidden email]>***

*WWW**:** **http://www.utoronto.ca/mocell
*
The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT Registered Charity No. 1053902.
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Unruh, Jay

Re: side-by-side merge

In reply to this post by Michal Opas

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

There are a couple of ways to do this in ImageJ. First you need to split the colors with Image>Color>Split Channels. If you want to merge them side by side permanently, convert to RGB (Image>Type>RGB Color) use Image>Stacks>Tools>Combine. If you just want to browse them together, use Analyze>Tools>Sync Windows.

Jay

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Michal Opas
Sent: Tuesday, March 12, 2013 8:35 AM
To: [hidden email]
Subject: side-by-side merge

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

Dear Listers,

This harks back to prhistory:
on Bio-Rad MRC 600 and Confocal Assistant by Todd Brelje one could merge dual wavelength images taken simultaneously using split screen ("split
box") feature of the scope.
This "side-by-side merge" feature was very convenient for the dual excitation, split image frames as one could quickly merge left with right and see how good the merged image is.
Sadly, the Confocal Assistant will not work under 64-bit OS.
I look for a functionality allowing for "side-by-side merge" in ImageJ and Fiji but failed to find it.
I am discombobulated: is such a useful feature gone forever (past Win
XP) or my ineptitude is gross?

Thank you very much for advice.

Michal

--

* Dr. Michal Opas
Professor
Department of Laboratory Medicine and Pathobiology
University of Toronto
1 King's College Circle
Medical Sciences Building, room 6326
Toronto, Ontario, M5S 1A8 Canada

**°°°°°°°°°°°°°**
phone: (416) 978-8947 (laboratory)
(416) 971-2140 (office)
fax: (416) 978-5959
e*-*mail: **[hidden email] <mailto:[hidden email]>***

*WWW**:** **http://www.utoronto.ca/mocell
*

Neil Kad

Re: side-by-side merge

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

You can also use micromanager for this. Also, I have written macro scripts for ImageJ for dual and triple colour combinations. The triple is available on my website and the dual I can send offline if you would like, just try the tiple first and see if its what you need:

http://www.essex.ac.uk/bs/motor_protein/downloads.html

Cheers

Neil

> Date: Tue, 12 Mar 2013 14:40:43 +0000
> From: [hidden email]
> Subject: Re: side-by-side merge
> To: [hidden email]
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> There are a couple of ways to do this in ImageJ. First you need to split the colors with Image>Color>Split Channels. If you want to merge them side by side permanently, convert to RGB (Image>Type>RGB Color) use Image>Stacks>Tools>Combine. If you just want to browse them together, use Analyze>Tools>Sync Windows.
>
> Jay
>
> -----Original Message-----
> From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Michal Opas
> Sent: Tuesday, March 12, 2013 8:35 AM
> To: [hidden email]
> Subject: side-by-side merge
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Dear Listers,
>
> This harks back to prhistory:
> on Bio-Rad MRC 600 and Confocal Assistant by Todd Brelje one could merge dual wavelength images taken simultaneously using split screen ("split
> box") feature of the scope.
> This "side-by-side merge" feature was very convenient for the dual excitation, split image frames as one could quickly merge left with right and see how good the merged image is.
> Sadly, the Confocal Assistant will not work under 64-bit OS.
> I look for a functionality allowing for "side-by-side merge" in ImageJ and Fiji but failed to find it.
> I am discombobulated: is such a useful feature gone forever (past Win
> XP) or my ineptitude is gross?
>
> Thank you very much for advice.
>
> Michal
>
>
> --
>
> * Dr. Michal Opas
> Professor
> Department of Laboratory Medicine and Pathobiology
> University of Toronto
> 1 King's College Circle
> Medical Sciences Building, room 6326
> Toronto, Ontario, M5S 1A8 Canada
>
> **°°°°°°°°°°°°°**
> phone: (416) 978-8947 (laboratory)
> (416) 971-2140 (office)
> fax: (416) 978-5959
> e*-*mail: **[hidden email] <mailto:[hidden email]>***
>
> *WWW**:** **http://www.utoronto.ca/mocell
> *

mcammer

Re: side-by-side merge

In reply to this post by Unruh, Jay

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

But the original BioRad merge feature made each channel only 4 bits and scrambled the LUT in an odd way, so don't rue too much...

If anyone has an importer, converter etc to open these old .pic merged images, please let me know!

Regards,

Michael C.

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Unruh, Jay
Sent: Tuesday, March 12, 2013 10:41 AM
To: [hidden email]
Subject: Re: side-by-side merge

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

There are a couple of ways to do this in ImageJ. First you need to split the colors with Image>Color>Split Channels. If you want to merge them side by side permanently, convert to RGB (Image>Type>RGB Color) use Image>Stacks>Tools>Combine. If you just want to browse them together, use Analyze>Tools>Sync Windows.

Jay

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Michal Opas
Sent: Tuesday, March 12, 2013 8:35 AM
To: [hidden email]
Subject: side-by-side merge

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

Dear Listers,

This harks back to prhistory:
on Bio-Rad MRC 600 and Confocal Assistant by Todd Brelje one could merge dual wavelength images taken simultaneously using split screen ("split
box") feature of the scope.
This "side-by-side merge" feature was very convenient for the dual excitation, split image frames as one could quickly merge left with right and see how good the merged image is.
Sadly, the Confocal Assistant will not work under 64-bit OS.
I look for a functionality allowing for "side-by-side merge" in ImageJ and Fiji but failed to find it.
I am discombobulated: is such a useful feature gone forever (past Win
XP) or my ineptitude is gross?

Thank you very much for advice.

Michal

--

* Dr. Michal Opas
Professor
Department of Laboratory Medicine and Pathobiology
University of Toronto
1 King's College Circle
Medical Sciences Building, room 6326
Toronto, Ontario, M5S 1A8 Canada

**°°°°°°°°°°°°°**
phone: (416) 978-8947 (laboratory)
(416) 971-2140 (office)
fax: (416) 978-5959
e*-*mail: **[hidden email] <mailto:[hidden email]>***

*WWW**:** **http://www.utoronto.ca/mocell
*

Johannes Schindelin

Re: side-by-side merge

In reply to this post by Michal Opas

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

Dear Michal,

On Tue, 12 Mar 2013, Michal Opas wrote:

> on Bio-Rad MRC 600 and Confocal Assistant by Todd Brelje one could merge
> dual wavelength images taken simultaneously using split screen ("split
> box") feature of the scope.
>
> This "side-by-side merge" feature was very convenient for the dual
> excitation, split image frames as one could quickly merge left with
> right and see how good the merged image is.
>
> [...]
>
> I am discombobulated: is such a useful feature gone forever (past Win
> XP) or my ineptitude is gross?

I am not quite certain about what you want, exactly, but if you describe
the desired functionality precisely (i.e. are the channels shown
side by side, or is the image cut in half and you can switch on/off
channels in the left and right half separately?), it should not be too
difficult to implement.

Note that in ImageJ (and therefore also in the ImageJ distribution called
Fiji), there is a Channels Tool in Image>Hyperstacks which allows you to
switch on/off channels easily (you need to be in "Composite" mode to see
merges, though).

Ciao,
Johannes

mcammer

Re: side-by-side merge

In reply to this post by Unruh, Jay

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

Try this. Works for me on old BioRad 600 pics. But colors might be reversed.

// Michael Cammer 20120312
// Macro to split grayscale image and merge.
// Works on stacks.

macro "Split and Merge" {
right = getTitle;
width = getWidth;
height = getHeight;
if ((width/2) != floor(width/2)) exit("Image not even # pixels wide.");
makeRectangle(0, 0, width/2, height);
slices = nSlices;
run("Duplicate...", "title=LEFT duplicate range=1-"+slices);
left = getTitle;
selectWindow(right);
makeRectangle(width/2, 0, width/2, height);
run("Crop");
run("Merge Channels...", "c1=LEFT c2="+right);
rename("merged_"+right);
} // end

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Unruh, Jay
Sent: Tuesday, March 12, 2013 10:41 AM
To: [hidden email]
Subject: Re: side-by-side merge

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

There are a couple of ways to do this in ImageJ. First you need to split the colors with Image>Color>Split Channels. If you want to merge them side by side permanently, convert to RGB (Image>Type>RGB Color) use Image>Stacks>Tools>Combine. If you just want to browse them together, use Analyze>Tools>Sync Windows.

Jay

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Michal Opas
Sent: Tuesday, March 12, 2013 8:35 AM
To: [hidden email]
Subject: side-by-side merge

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

Dear Listers,

This harks back to prhistory:
on Bio-Rad MRC 600 and Confocal Assistant by Todd Brelje one could merge dual wavelength images taken simultaneously using split screen ("split
box") feature of the scope.
This "side-by-side merge" feature was very convenient for the dual excitation, split image frames as one could quickly merge left with right and see how good the merged image is.
Sadly, the Confocal Assistant will not work under 64-bit OS.
I look for a functionality allowing for "side-by-side merge" in ImageJ and Fiji but failed to find it.
I am discombobulated: is such a useful feature gone forever (past Win
XP) or my ineptitude is gross?

Thank you very much for advice.

Michal

--

* Dr. Michal Opas
Professor
Department of Laboratory Medicine and Pathobiology
University of Toronto
1 King's College Circle
Medical Sciences Building, room 6326
Toronto, Ontario, M5S 1A8 Canada

**°°°°°°°°°°°°°**
phone: (416) 978-8947 (laboratory)
(416) 971-2140 (office)
fax: (416) 978-5959
e*-*mail: **[hidden email] <mailto:[hidden email]>***

*WWW**:** **http://www.utoronto.ca/mocell
*

split and merge macro v100.txt (810 bytes) Download Attachment

Guy Cox-2

Re: side-by-side merge

In reply to this post by mcammer

*****
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http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

Sure, the Bio-Rad merged image put each channel into 4 bits. But the side - by- side image contained each channel at full 8 bit resolution, 384 * 512, in greyscale. I keep an old (but powerful) computer running XP just so that I can use the old utilities such as Confocal Assistant. But with any imaging program you can cut the picture in two - just make sure you get it exact - and then combine the two 384 * 512 greyscale images into an RGB image.

As to the 4-bit merged images, I did write a program to uncombine them. Whether it will run under XP I'm not sure (it is a DOS program). Of course you still only have 4 bits of data, but once they are each in an 8-bit image you can at least open them! If you have precious data saved in this format, send me a sample image and I'll try, but please not until after Easter since I'm away at the moment (snowed up in England on the way to FOM in Maastricht).

Guy

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Cammer, Michael
Sent: Wednesday, 13 March 2013 1:50 AM
To: [hidden email]
Subject: Re: side-by-side merge

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

But the original BioRad merge feature made each channel only 4 bits and scrambled the LUT in an odd way, so don't rue too much...

If anyone has an importer, converter etc to open these old .pic merged images, please let me know!

Regards,

Michael C.

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Unruh, Jay
Sent: Tuesday, March 12, 2013 10:41 AM
To: [hidden email]
Subject: Re: side-by-side merge

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

There are a couple of ways to do this in ImageJ. First you need to split the colors with Image>Color>Split Channels. If you want to merge them side by side permanently, convert to RGB (Image>Type>RGB Color) use Image>Stacks>Tools>Combine. If you just want to browse them together, use Analyze>Tools>Sync Windows.

Jay

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Michal Opas
Sent: Tuesday, March 12, 2013 8:35 AM
To: [hidden email]
Subject: side-by-side merge

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

Dear Listers,

This harks back to prhistory:
on Bio-Rad MRC 600 and Confocal Assistant by Todd Brelje one could merge dual wavelength images taken simultaneously using split screen ("split
box") feature of the scope.
This "side-by-side merge" feature was very convenient for the dual excitation, split image frames as one could quickly merge left with right and see how good the merged image is.
Sadly, the Confocal Assistant will not work under 64-bit OS.
I look for a functionality allowing for "side-by-side merge" in ImageJ and Fiji but failed to find it.
I am discombobulated: is such a useful feature gone forever (past Win
XP) or my ineptitude is gross?

Thank you very much for advice.

Michal

--

* Dr. Michal Opas
Professor
Department of Laboratory Medicine and Pathobiology
University of Toronto
1 King's College Circle
Medical Sciences Building, room 6326
Toronto, Ontario, M5S 1A8 Canada

**°°°°°°°°°°°°°**
phone: (416) 978-8947 (laboratory)
(416) 971-2140 (office)
fax: (416) 978-5959
e*-*mail: **[hidden email] <mailto:[hidden email]>***

*WWW**:** **http://www.utoronto.ca/mocell
*

Jim Haley

Re: side-by-side merge

In reply to this post by mcammer

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

Michael,

If you would email me one of the PIC files, I will test it and see if I
have a solution for you. I have gotten these to open/convert in the
past, but there were different versions of the PIC format, so I would
like to test and experiment before I can give you a definitive solution.

Thanks And Have a Great Day!

Jim Haley

******************************
Jim Haley
Applications Engineer
MVIA, Inc.
P.O. Box 161
Monaca, PA 15061
voice: (724) 728-7493
fax: (412) 291-1709
e-mail:[hidden email]
MVIA Website <http://www.mvia.com/>
Digital Microscope Cameras from MVIA <http://www.mvia.com/Digcams/dig_cameras.html>
Image Analysis Software from MVIA <http://www.mvia.com/IASoftware/ia_software.html>
******************************

On 3/12/2013 10:50 AM, Cammer, Michael wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> But the original BioRad merge feature made each channel only 4 bits and scrambled the LUT in an odd way, so don't rue too much...
>
> If anyone has an importer, converter etc to open these old .pic merged images, please let me know!
>
> Regards,
>
> Michael C.
>
> -----Original Message-----
> From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Unruh, Jay
> Sent: Tuesday, March 12, 2013 10:41 AM
> To: [hidden email]
> Subject: Re: side-by-side merge
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> There are a couple of ways to do this in ImageJ. First you need to split the colors with Image>Color>Split Channels. If you want to merge them side by side permanently, convert to RGB (Image>Type>RGB Color) use Image>Stacks>Tools>Combine. If you just want to browse them together, use Analyze>Tools>Sync Windows.
>
> Jay
>
> -----Original Message-----
> From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Michal Opas
> Sent: Tuesday, March 12, 2013 8:35 AM
> To: [hidden email]
> Subject: side-by-side merge
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Dear Listers,
>
> This harks back to prhistory:
> on Bio-Rad MRC 600 and Confocal Assistant by Todd Brelje one could merge dual wavelength images taken simultaneously using split screen ("split
> box") feature of the scope.
> This "side-by-side merge" feature was very convenient for the dual excitation, split image frames as one could quickly merge left with right and see how good the merged image is.
> Sadly, the Confocal Assistant will not work under 64-bit OS.
> I look for a functionality allowing for "side-by-side merge" in ImageJ and Fiji but failed to find it.
> I am discombobulated: is such a useful feature gone forever (past Win
> XP) or my ineptitude is gross?
>
> Thank you very much for advice.
>
> Michal
>
>