image calculator batch macro help required

[mfbx9nn4]

Hi,

First time macro user on ImageJ so very much learning as I go.
I'd like to process a series of images where i stack pairs, run functions such as smoothen etc, stack>images then divide one by the other. Each image ends with w3YFP_t1 or w2CFPexYFPem_t1.

I've tried browsing online to find a solution to this with no success. Essentially the issue is in the image calculator function, where I can't define images with a variable prefix for the image calculator. Below is what I have so far.


name = getTitle();
prefix = substring (name, 0, lastIndexOf(name, " "));
run("Images to Stack", "name=Stack title=[] use");
run("Smooth", "stack");
run("Subtract Background...", "rolling=125 stack");
run("32-bit");
run("16 colors");
run("Stack to Images");
imageCalculator("Divide create", "+prefix+" w3YFP_t1, "+prefix+" w2CFPexYFPem_t1);
selectWindow("Result of DPI 002 18hpa x4obj Eve Dead_w3YFP_t1");

Any advice on how to resolve this would be massively appreciated. Thanks!

[Aryeh Weiss]

Hi,

I put a correction interleaved in your code below.

On 25/08/2016 3:34 AM, mfbx9nn4 wrote:

> Hi,
>
> First time macro user on ImageJ so very much learning as I go.
> I'd like to process a series of images where i stack pairs, run functions
> such as smoothen etc, stack>images then divide one by the other. Each image
> ends with w3YFP_t1 or w2CFPexYFPem_t1.
>
> I've tried browsing online to find a solution to this with no success.
> Essentially the issue is in the image calculator function, where I can't
> define images with a variable prefix for the image calculator. Below is what
> I have so far.
>
>
> name = getTitle();
> prefix = substring (name, 0, lastIndexOf(name, " "));
> run("Images to Stack", "name=Stack title=[] use");
> run("Smooth", "stack");
> run("Subtract Background...", "rolling=125 stack");
> run("32-bit");
> run("16 colors");

Why do you change to 16 colors? You should leave it as 32 bit, or even
just create a 32-bit result with the imageCalculator
as in
imageCaculator(Divide create 32-bit stack", ...
in which case you may not need to run("32-bit")
> run("Stack to Images");
Why are you converting to images? Why not divide the entire stack at
once? imageCalculator can do that is you at the stack keyword in the
command. For example:
imageCaculator(Divide create stack", ...
> imageCalculator("Divide create", "+prefix+" w3YFP_t1, "+prefix+"
> w2CFPexYFPem_t1);

Try:
imageCalculator("Divide create", prefix + "w3YFP_t1", prefix +
"w2CFPexYFPem_t1");

or

imageCalculator("Divide create 32-bit stack", prefix + "w3YFP_t1",
prefix + "w2CFPexYFPem_t1");


you quoted your variable and left the string unquoted. This is backwards
of what you intended.

--aryeh

> selectWindow("Result of DPI 002 18hpa x4obj Eve Dead_w3YFP_t1");
>
> Any advice on how to resolve this would be massively appreciated. Thanks!
>
>
>
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> Sent from the ImageJ mailing list archive at Nabble.com.
>
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>

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

Ph:  972-3-5317638
FAX: [phone]

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