Re: Creating Pseudocolor Images with more than 3 channels

Posted by Pang, Zhengyu (GE Global Research) on Jun 06, 2008; 7:57pm
URL: http://imagej.273.s1.nabble.com/Creating-Pseudocolor-Images-with-more-than-3-channels-tp3696013p3696015.html

Wayne,

Thanks for your guidance. I followed your instruction and get my
composite images right.

I plan to make a macro to batch process about 200 images. I don't like
to use the function Image>Stack>"Images to Stack"  to create my stack.
It seems to me that I have no control of channel order. For instance, I
would like to put the image ending with DAPI.tif as my first channel,
and image ending with Alexa488 as my second channel. How do I realize
this in macro language?

Thanks,

Zhengyu

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
Wayne Rasband
Sent: Friday, June 06, 2008 1:23 PM
To: [hidden email]
Subject: Re: Creating Pseudocolor Images with more than 3 channels

> How do I create a pseudo-color images with more than 3 colors. I have
> a set of images with 5 channels with different bio-markers, and would
> like to specify the color for each marker. For example, blue color for

> DAPI, green color for cytoplamic marker, orange color for target
> protein.

    1. Create a stack containing the 5 images
    2. Use Image>Color>Make Composite to create a 5 channel composite
image
    3. Press shift-z (Image>Hyperstack>Channels) to open the Channels
window
    4. Select "Color" in the Channels window
    5. Use the slider under the composite image to select the DAPI
channel
    6. Select Image>Lookup Tables>Blue
    7. Select the cytoplamic marker channel
    8. Select Image>Lookup Tables>Green
    9. Select the target protein channel
    10. Open the LUT Editor (Image>Color>Edit LUT)
    11. Create an orange LUT (drag across all 256 entries then set
red=255, green=~160, blue=0)
    12. Add LUTs to the other 2 channels
    13. Select "Composite" in the Channels window
    14. Use the B&C tool (press shift-c to open) to adjust each of the
channels
    15. Use the Channels tool to enable/disable channels

For practice, open the 5 channel File>Open Samples>Neuron image, which
was added in v1.41d.

> In addition, is there any automated registration plugin or tools for
> the alignment for these images? Any suggestion for registration of
> images is highly appreciated.

There is the StackReg plugin at
<http://bigwww.epfl.ch/thevenaz/stackreg/>.

-wayne

>
> Thanks,
>
> Zhengyu
>
>> g Global Research Center
>>
>> _____________________________________________________________________
>> _
>>
>>           Zhengyu Pang, Ph.D.
> Bioanalytics and Protein Science Laboratory
> Biosciences Global Technology Organization
>> One Research Circle, K1 5B37A
>> Niskayuna, NY12309
>> * [hidden email]
>> *[phone]
>>
>>
>