Help with stacks and 4 channel files

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Help with stacks and 4 channel files

Paletzki, Ron (NIH/NIMH) [C]
I hope someone can help me figure this out with ImageJ/fiji.  I have a folder of tiff files containing a series of coronal brain slices.  Each tiff file has 4 channels, red, green, blue and yellow.   I would like to open them as a single stack so that I can scroll threw the slices while being able to hide or show some or all of the colored channels.  I need to do this as a virtual stack since the files are large almost 900 MB each with > 90 files.  I have tried Image//Image Sequence to load the files as a virtual stack but that only works if I have 3 channel RGB tiff files not on my 4 channel files.  I believe the plugin Image5D should be able to do what I want but I have not gotten it to work.  When I try the Imge5D//Virtual Image5D Opener and the Imge5D//Open Series As Imge5D I can never get more then the first image open.
If I decrease each file size to 20% I can open all of my files and then use  Image//Stacks//Tools//Concatenate to produce what I want but then I have lost most of my resolution by decreasing the file size.

Any help would be greatly appreciated Thanks
 Ron

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Re: Help with stacks and 4 channel files

Christian Goosmann-2
Hi Ron,
here is what I do with multipage tiffs containing channels: Load the
files with 'file>import>image sequence...' The stack then shows all the
single channel images in sequence (number of tiffs x channels = length
of stack). Then use 'image>hyperstacks>stack to hyperstack...' and
specify the number of channels and number of slices. Use the channels
tool (shift+ctrl+z) to view in composite mode. You can also change the
LUT of each channel individually.
hth
Christian

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Christian Goosmann
Mikroskopie
Max-Planck-Institut für Infektionsbiologie
Campus Charité Mitte
Charitéplatz 1
10117 Berlin
Tel.: +49 30 28460 388

Paletzki, Ron (NIH/NIMH) [C] wrote:
> I hope someone can help me figure this out with ImageJ/fiji.  I have a folder of tiff files containing a series of coronal brain slices.  Each tiff file has 4 channels, red, green, blue and yellow.   I would like to open them as a single stack so that I can scroll threw the slices while being able to hide or show some or all of the colored channels.  I need to do this as a virtual stack since the files are large almost 900 MB each with > 90 files.  I have tried Image//Image Sequence to load the files as a virtual stack but that only works if I have 3 channel RGB tiff files not on my 4 channel files.  I believe the plugin Image5D should be able to do what I want but I have not gotten it to work.  When I try the Imge5D//Virtual Image5D Opener and the Imge5D//Open Series As Imge5D I can never get more then the first image open.
> If I decrease each file size to 20% I can open all of my files and then use  Image//Stacks//Tools//Concatenate to produce what I want but then I have lost most of my resolution by decreasing the file size.
>
> Any help would be greatly appreciated Thanks
>   Ron
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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Re: Help with stacks and 4 channel files

Ron Paletzki
In reply to this post by Paletzki, Ron (NIH/NIMH) [C]
Thanks Christian,  
It works for small images but not my larger files since the computer runs out of memory even with 32GB and 28GB assigned to Fiji.  Some of my image folders have files totaling 75GB so I really need to do this with virtual stacks and it appears that file>import>image sequence does not work with tiff files containing 4 channels each.

Anyone have an idea how to open virtual stacks of large tiff files, each with 4 channels.  Thanks
Ron

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Re: Help with stacks and 4 channel files

Rasband, Wayne (NIH/NIMH) [E]
> On Apr 24, 2015, at 9:50 AM, Paletzki, Ron (NIH/NIMH) [C] <[hidden email]> wrote:
>
> Thanks Christian,  
> It works for small images but not my larger files since the computer runs out of memory even with 32GB and 28GB assigned to Fiji.  Some of my image folders have files totaling 75GB so I really need to do this with virtual stacks and it appears that file>import>image sequence does not work with tiff files containing 4 channels each.

In the latest ImageJ daily build (1.49s8), the File>Import>Image Sequence command will open a folder of multi-image tiff files as a virtual stack.

-wayne

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