overlay/merge TIFF images

[Sylvie Le Guyader-2]

Hi everyone

 

Does anyone know of a simple freeware to overlay/merge Tiff images of
identical size but eg different channels?

 

I searched the ImageJ wiki for new plugins but have only found the good old
RGB gray merge which is fine when one has only a few images to overlay (too
many clicks required!) and doesn't need to adjust the levels for each
channel. I also had a quick look at BioimageXD but it seems that I cannot
open TIFF images that are not stacks.

 

Any advice?

 

Med vänlig hälsning / Best regards

 

Sylvie

 

@@@@@@@@@@@@@@@@@@@@@@@@

Sylvie Le Guyader

Dept of Biosciences and Nutrition

Karolinska Institutet

Novum

14157 Huddinge

Sweden

[phone]

 

[Edwin Bennink]

- Commercial interest -


Dear Sylvie,

The freeware capabilities of our Huygens Professional software allow you
to do this. The Tcl scripting shell can be used to e.g. apply basic
arithmetic operations on images. If you would like to join the channels
of images a and b in image c, the command would be "a join b -> c".

More information can be found on our wiki:
 - http://support.svi.nl/HuCoreMan/Arithmetic_operations.html
 - http://support.svi.nl/HuCoreMan/Image_manipulation_operatio.html
Note that note all commands are available in freeware mode.

You can download the freeware Huygens version from our website:
 - www.svi.nl


Best,

Edwin Bennink
Developer for Scientific Volume Imaging
www.svi.nl



Sylvie Le Guyader wrote:

> Hi everyone
>
>  
>
> Does anyone know of a simple freeware to overlay/merge Tiff images of
> identical size but eg different channels?
>
>  
>
> I searched the ImageJ wiki for new plugins but have only found the good old
> RGB gray merge which is fine when one has only a few images to overlay (too
> many clicks required!) and doesn't need to adjust the levels for each
> channel. I also had a quick look at BioimageXD but it seems that I cannot
> open TIFF images that are not stacks.
>
>  
>
> Any advice?
>
>  
>
> Med vänlig hälsning / Best regards
>
>  
>
> Sylvie
>
>  
>
> @@@@@@@@@@@@@@@@@@@@@@@@
>
> Sylvie Le Guyader
>
> Dept of Biosciences and Nutrition
>
> Karolinska Institutet
>
> Novum
>
> 14157 Huddinge
>
> Sweden
>
> [phone]
>
>  
>
>  

[Peter Humphreys]

You might try the Image5D plugin for image J.
Peter

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On
Behalf Of Sylvie Le Guyader
Sent: 27 May 2009 14:01
To: [hidden email]
Subject: overlay/merge TIFF images

Hi everyone

 

Does anyone know of a simple freeware to overlay/merge Tiff images of
identical size but eg different channels?

 

I searched the ImageJ wiki for new plugins but have only found the good old
RGB gray merge which is fine when one has only a few images to overlay (too
many clicks required!) and doesn't need to adjust the levels for each
channel. I also had a quick look at BioimageXD but it seems that I cannot
open TIFF images that are not stacks.

 

Any advice?

 

Med vänlig hälsning / Best regards

 

Sylvie

 

@@@@@@@@@@@@@@@@@@@@@@@@

Sylvie Le Guyader

Dept of Biosciences and Nutrition

Karolinska Institutet

Novum

14157 Huddinge

Sweden

[phone]

 

[Dale Callaham]

Hi Sylvie,

ImageJ can do this easily. I assume that you have 8-bit tiffs
(monochrome, even if it has a color palette assigned. ou may need to
change to grayscale and change bit depth to 8-bits. Those are also easy
operations. Then, in ImageJ (use a current version, I have ver 1.42 and
it works), just open the images (they must be open), and use "Image |
Color | Merge Channels" and it allows you to assign the open images to
the R, G, B, and grayscale channels so you can merge red, green, and
blue + DIC images for example.

Dale

Sylvie Le Guyader wrote:

> Hi everyone
>
>  
>
> Does anyone know of a simple freeware to overlay/merge Tiff images of
> identical size but eg different channels?
>
>  
>
> I searched the ImageJ wiki for new plugins but have only found the good old
> RGB gray merge which is fine when one has only a few images to overlay (too
> many clicks required!) and doesn't need to adjust the levels for each
> channel. I also had a quick look at BioimageXD but it seems that I cannot
> open TIFF images that are not stacks.
>
>  
>
> Any advice?
>
>  
>
> Med vänlig hälsning / Best regards
>
>  
>
> Sylvie
>
>  
>
> @@@@@@@@@@@@@@@@@@@@@@@@
>
> Sylvie Le Guyader
>
> Dept of Biosciences and Nutrition
>
> Karolinska Institutet
>
> Novum
>
> 14157 Huddinge
>
> Sweden
>
> [phone]
>
>  

[Sylvie Le Guyader-2]

Hi everyone

Thanks for your answers! The ImageJ image5D plugin worked very well. I could
open 20 double channel acquisitions at once, adjust the display for each
channel and save the overlay!

Since it took me a little while to figure out, for the sake of those who
need this feature, here is what I did:
Download the Image5D plugin
Click plugin/Image5D/open series as image5D
Select first image in folder (I had 20 images for 10 cells imaged in 2
channels) and click open then OK
3rd dimension was channel and its size was 2
4th dimension was t and its size was 10.
Underneath the color button I selected 'color' and adjusted the contrast for
each cell in each channel then I checked the overlay by selecting 'ovl'
instead of 'color'.
I selected plugin/Image5D/make montage then ticked in 'display channels
only' + 'all time frames' + 'copy contrast and brightness'. I could then
save my stack of overlays or split them into individual overlays.


Thanks list! :)

Med vänlig hälsning / Best regards
 
Sylvie
 
@@@@@@@@@@@@@@@@@@@@@@@@
Sylvie Le Guyader
Dept of Biosciences and Nutrition
Karolinska Institutet
Novum
14157 Huddinge
Sweden
[phone]

> -----Original Message-----
> From: Confocal Microscopy List
> [mailto:[hidden email]] On Behalf Of Dale
> Callaham
> Sent: 27 May 2009 17:34
> To: [hidden email]
> Subject: Re: overlay/merge TIFF images
>
> Hi Sylvie,
>
> ImageJ can do this easily. I assume that you have 8-bit tiffs
> (monochrome, even if it has a color palette assigned. ou may need to
> change to grayscale and change bit depth to 8-bits. Those are also easy
> operations. Then, in ImageJ (use a current version, I have ver 1.42 and
> it works), just open the images (they must be open), and use "Image |
> Color | Merge Channels" and it allows you to assign the open images to
> the R, G, B, and grayscale channels so you can merge red, green, and
> blue + DIC images for example.
>
> Dale
>
> Sylvie Le Guyader wrote:
> > Hi everyone
> >
> >
> >
> > Does anyone know of a simple freeware to overlay/merge Tiff images of
> > identical size but eg different channels?
> >
> >
> >
> > I searched the ImageJ wiki for new plugins but have only found the good

old
> > RGB gray merge which is fine when one has only a few images to overlay
(too
> > many clicks required!) and doesn't need to adjust the levels for each
> > channel. I also had a quick look at BioimageXD but it seems that I
cannot

> > open TIFF images that are not stacks.
> >
> >
> >
> > Any advice?
> >
> >
> >
> > Med vänlig hälsning / Best regards
> >
> >
> >
> > Sylvie
> >
> >
> >
> > @@@@@@@@@@@@@@@@@@@@@@@@
> >
> > Sylvie Le Guyader
> >
> > Dept of Biosciences and Nutrition
> >
> > Karolinska Institutet
> >
> > Novum
> >
> > 14157 Huddinge
> >
> > Sweden
> >
> > [phone]
> >
> >

[Andreas Bruckbauer]

Hi,
i think yo can now select image5D as an option in the bioformats plugin from loci  (when installed) . This allows to open all kinds of formats very flexible and usually selects the right options for the different channels

best wishes

Andreas

-----Original Message-----
From: Sylvie Le Guyader <[hidden email]>
To: [hidden email]
Sent: Thu, 28 May 2009 9:28
Subject: Re: overlay/merge TIFF images

Hi everyone



Thanks for your answers! The ImageJ image5D plugin worked very well. I could

open 20 double channel acquisitions at once, adjust the display for each

channel and save the overlay!



Since it took me a little while to figure out, for the sake of those who

need this feature, here is what I did:

Download the Image5D plugin

Click plugin/Image5D/open series as image5D

Select first image in folder (I had 20 images for 10 cells imaged in 2

channels) and click open then OK

3rd dimension was channel and its size was 2

4th dimension was t and its size was 10.

Underneath the color button I selected 'color' and adjusted the contrast for

each cell in each channel then I check
ed the overlay by selecting 'ovl'

instead of 'color'.

I selected plugin/Image5D/make montage then ticked in 'display channels

only' + 'all time frames' + 'copy contrast and brightness'. I could then

save my stack of overlays or split them into individual overlays.





Thanks list! :)



Med vänlig hälsning / Best regards

 

Sylvie

 

@@@@@@@@@@@@@@@@@@@@@@@@

Sylvie Le Guyader

Dept of Biosciences and Nutrition

Karolinska Institutet

Novum

14157 Huddinge

Sweden

[phone]



> -----Original Message-----

> From: Confocal Microscopy List

> [mailto:[hidden email]] On Behalf Of Dale

> Callaham

> Sent: 27 May 2009 17:34

> To: [hidden email]

> Subject: Re: overlay/merge TIFF images

> 

> Hi Sylvie,

> 

> ImageJ can do this easily. I assume that you have 8-bit tiffs

> (monochrome, even if it has a color palette assigned. ou may need to

> change to grayscale and change bit depth to 8-bits. Those are also easy

> operations. Then, in ImageJ (use a current version, I have ver 1.42 and

> it works), just open the images (they must be open), and use "Image |

> Color | Merge Channels" and it allows you to assign the open images to

> the R, G, B, and grayscale channels so you can merge red, green, an
d

> blue + DIC images for example.

> 

> Dale

> 

> Sylvie Le Guyader wrote:

> > Hi everyone

> >

> >

> >

> > Does anyone know of a simple freeware to overlay/merge Tiff images of

> > identical size but eg different channels?

> >

> >

> >

> > I searched the ImageJ wiki for new plugins but have only found the good

old

> > RGB gray merge which is fine when one has only a few images to overlay

(too

> > many clicks required!) and doesn't need to adjust the levels for each

> > channel. I also had a quick look at BioimageXD but it seems that I

cannot

> > open TIFF images that are not stacks.

> >

> >

> >

> > Any advice?

> >

> >

> >

> > Med vänlig hälsning / Best regards

> >

> >

> >

> > Sylvie

> >

> >

> >

> > @@@@@@@@@@@@@@@@@@@@@@@@

> >

> > Sylvie Le Guyader

> >

> > Dept of Biosciences and Nutrition

> >

> > Karolinska Institutet

> >

> > Novum

> >

> > 14157 Huddinge

> >

> > Sweden

> >

> > [phone]

> >

> >