Specifying ROI based on grayscale values?

[Pang, Zhengyu (GE Global Research)]

Dear all,

Is there anyway to specify ROI based on grayscale values? I am staining
slides with 3 channels, DAPI, Cy3, and Cy5. I want to use DAPI channel
to identify the regions (ROI 1) for nucleus, Cy5 channels to indentify
membrane regions(ROI 2). Then I want to quantify my target protein
expression levels in membrane and cytoplasm (Total area -ROI1-ROI2). The
current ROI selection tool seems to use geometry only, but will be
valuable to use ROIs to compart nucleus, cytoplasm, and membrane.

All the images were captured at the same location.

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]
>
>

[Hanjun Guan]

Dear List:

Sorry I am new to ImageJ. I am wondering whether there is a way to expand selection in ImageJ like we do in the Photoshop?  Say I have a circle selection but I would like to expand 2 um more as my ROI.  Thanks in advance.

------------------
Hanjun Guan
2007-12-14

[Wayne Rasband]

The Edit>Selection>Enlarge command does this but it currently only
expands by pixels.

-wayne

On Dec 14, 2007, at 1:39 PM, Hanjun Guan wrote:

> Dear List:
>
> Sorry I am new to ImageJ. I am wondering whether there is a way to
> expand selection in ImageJ like we do in the Photoshop?  Say I have a
> circle selection but I would like to expand 2 um more as my ROI.  
> Thanks in advance.
>
> ------------------
> Hanjun Guan
> 2007-12-14
>

[Hanjun Guan]

Many thanks.

------------------
Hanjun Guan
2007-12-14

-------------------------------------------------------------
发件人：Wayne Rasband
发送日期：2007-12-14 14:00:41
收件人：[hidden email]
抄送：
主题：Re: How to expand selection?

The Edit>Selection>Enlarge command does this but it currently only
expands by pixels.

-wayne

On Dec 14, 2007, at 1:39 PM, Hanjun Guan wrote:

> Dear List:
>
> Sorry I am new to ImageJ. I am wondering whether there is a way to
> expand selection in ImageJ like we do in the Photoshop?  Say I have a
> circle selection but I would like to expand 2 um more as my ROI.  
> Thanks in advance.
>
> ------------------
> Hanjun Guan
> 2007-12-14
>

[dscho]

Hi,

On Fri, 14 Dec 2007, Pang, Zhengyu (GE, Research) wrote:

> Is there anyway to specify ROI based on grayscale values?

Just use the threshold function (Image>Adjust>Threshold...) and then turn
the selected pixels into a selection (Edit>Selection>Create Selection).

Hth,
Dscho

[Pang, Zhengyu (GE Global Research)]

Johannes,

Thanks for your help. It is very useful. Additional question, what is
the difference between create mask and create selection?  Are they same?

Thanks,

Zhengyu

-----Original Message-----
From: Johannes Schindelin [mailto:[hidden email]]
Sent: Friday, December 14, 2007 2:58 PM
To: Pang, Zhengyu (GE, Research)
Cc: [hidden email]
Subject: Re: Specifying ROI based on grayscale values?

Hi,

On Fri, 14 Dec 2007, Pang, Zhengyu (GE, Research) wrote:

> Is there anyway to specify ROI based on grayscale values?

Just use the threshold function (Image>Adjust>Threshold...) and then
turn the selected pixels into a selection (Edit>Selection>Create
Selection).

Hth,
Dscho

[dscho]

Hi,

On Sun, 16 Dec 2007, Pang, Zhengyu (GE, Research) wrote:

> Thanks for your help. It is very useful. Additional question, what is
> the difference between create mask and create selection?  Are they same?

No.  A mask is a (different) binary image, whereas the selection operates
on the current image.  Just try both to see the difference.

Ciao,
Dscho