3D viewing of a z stack: problem with channel colors

[emilia8]

Hello everyone,
so my problem is I'm trying to make a 3D image from images taken with a confocal microscope (.tiff images). I have all the files in the same folder, named "NAMEc1.tiff, NAMEc2.tiff etc" where c1 = blue images and c2 = red images. When I import the files (file -> import -> image sequences) all images become red (both blue c1 images and red c2 images).. why is this happening? if I separate the c1 files from c2 files the result is ok (blue is blue and red is red) but I can't do that with all my folders (some have 100+ files..).

Also another problem is it won't let me download the 3D viewer plugin..it says I don't have the permission to write to /Library/Java/Exstension .. I opened my home folder and created the Java/Extensions folder in the Library folder and changed the permission settings but it still doesn't work..
I have a macbook pro!

thank you in advance,

Emilia

[Aryeh Weiss]

On 13/07/2016 1:20 PM, emilia8 wrote:
> Hello everyone,
> so my problem is I'm trying to make a 3D image from images taken with a
> confocal microscope (.tiff images). I have all the files in the same folder,
> named "NAMEc1.tiff, NAMEc2.tiff etc" where c1 = blue images and c2 = red
> images. When I import the files (file -> import -> image sequences) all
> images become red (both blue c1 images and red c2 images).. why is this
> happening? if I separate the c1 files from c2 files the result is ok (blue
> is blue and red is red) but I can't do that with all my folders (some have
> 100+ files..).
When you import a sequence, you can specify a string that the filename
should contain. If you specify c1.tiff it will import only
the first channel, and c2.tiff will get you the second channel. Then it
will be easy to make them whatever color you want.

> Also another problem is it won't let me download the 3D viewer plugin..it
> says I don't have the permission to write to /Library/Java/Exstension .. I
> opened my home folder and created the Java/Extensions folder in the Library
> folder and changed the permission settings but it still doesn't work..
> I have a macbook pro!
I assume that it is trying to install Java 3D on you system. If you run
Fiji, then the 3D-viewer is available through the 3D update site. You
might see if that install what it needs without going to the
/Library/Java/Extensions

--aryeh

> thank you in advance,
>
> Emilia
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/3D-viewing-of-a-z-stack-problem-with-channel-colors-tp5016866.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

Ph:  972-3-5317638
FAX: [phone]

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[emilia8]

thank you for the answer. The thing is I want to merge the 2 colors..I have 80 images (NAME1c1.tiff...Name80c1.tiff) of the cells colored in blue and 80 images of the same cells colored in red (NAME1c2.tiff...Name80c2.tiff) all saved in the same folder and I want to merge them together, but when I upload all the files c1 images are not blue anymore but red (while C2 images remain red as they should be). If I only open C1 containing files (as you suggested) they will still appear red..but if I open one single C1 file (File --> open). I don't understand how this is possible! I'm a beginner so I really have no clue how to solve this problem..

[Aryeh Weiss]

I am not sure that I understand your problem,  but if you want to have
them appear as a composite image (red and blue, here are some commands
that may help you.

To change the display color:
Image>Lookup Tables...

To merge into a color or composite image:
Image>Color>Merge Channels...

To get a handle on some basic concepts (like lookup table and such)
check out the videos from the ImageJ 2015 conference.
Here is the link to mine:
http://imagej.net/Conference_2015_Program#Aryeh_Weiss1.2C2_-_An_introduction_to_digital_image_processing

Best regards
--aryeh

On 13/07/2016 2:44 PM, emilia8 wrote:

> thank you for the answer. The thing is I want to merge the 2 colors..I have
> 80 images (NAME1c1.tiff...Name80c1.tiff) of the cells colored in blue and 80
> images of the same cells colored in red (NAME1c2.tiff...Name80c2.tiff) all
> saved in the same folder and I want to merge them together, but when I
> upload all the files c1 images are not blue anymore but red (while C2 images
> remain red as they should be). If I only open C1 containing files (as you
> suggested) they will still appear red..but if I open one single C1 file
> (File --> open). I don't understand how this is possible! I'm a beginner so
> I really have no clue how to solve this problem..
>
>
>
>

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

Ph:  972-3-5317638
FAX: [phone]

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[emilia8]

thank you very much for your suggestions, they were very useful (problem solved)! and thanks for the link too