Re: split channels and all files in a directory

Posted by melkor2.0 on Apr 07, 2011; 5:46pm
URL: http://imagej.273.s1.nabble.com/split-channels-and-all-files-in-a-directory-tp3685101p3685105.html

Indeed, I think many of us, use ImageJ for the principles behind, I'm sure
many of you are in the situation that your university is paying licenses for
privative imaging software, but you still prefer to use open software, and
indeed our commentaries here help to improve things, but anyway if someone
has a problem or inconvenience is free to expose it.
let's change "hate" for frustrating
thanks again,

ramon

On 7 April 2011 19:07, Philip Ershler <[hidden email]> wrote:

> I'm sorry but I think the word "hate" is a bit strong. And for many, many
> people the macro language is perfectly acceptable. The ability to record a
> macro by saying "watch me" is a great asset. Besides, considering the price
> you paid for ImageJ makes any complaints such as this come off rather whiny.
>
> Phil
>
> On Apr 7, 2011, at 10:54 AM, Ramon Guirado wrote:
>
> > Thanks for this macro, I think many people share the hate for imageJ
> macro
> > language, indeed would be better to learn python instead.
> > Anyway I think I can find all the commands I need in your macro, just it
> > will require time to decipher what is what I need.
> > Thanks!!
> >
> > ramon
> >
> > 2011/4/7 Carnë Draug <[hidden email]>
> >
> >> On 7 April 2011 15:04, Ramon Guirado <[hidden email]> wrote:
> >>> Hi, I'm trying to write a macro able to open all the files in a
> >> directory,
> >>> split the channels of the images and analyze particles in this
> separated
> >>> channels as well as the composite between some of them (they will be
> also
> >>> binarized, etc...). I have just done small macros using the macro
> >> recorder,
> >>> so I don't know how to do it, I'm trying to get the identity of every
> >> image
> >>> in a directory and then I guess after the image calculator, I will have
> >> to
> >>> identify the new windows just created so they are processed as well,
> and
> >>> then do that recursively, but I feel a little bit lost... which would
> be
> >> the
> >>> easiest way to proceed? by know I'll try to understand the macro posted
> >>> by Carnë Draug..
> >>>
> >>> Thanks,
> >>>
> >>>
> >>> ramon
> >>
> >> I wrote a macro some time ago that does a similar thing. It opens all
> >> images, makes them composite, use one channel to find the nucleus
> >> (DAPI stained), and the two other channels to analyze particles inside
> >> the nucleus. I wrote it as macro and regret it, it's terribly
> >> confusing code. I find the ImageJ macro language terribly frustating.
> >> I should have bothered to learn Python to do it. Anyway, I pasted it
> >> into pastebin
> >>
> >> http://pastebin.com/R5dPsyqM
> >>
> >> You'll also need the other functions I posted before (I place them in
> >> macros/Library.txt so I don't have to bother copying into every
> >> macro).
> >>
> >> Carnë
> >>
>
> Philip R. Ershler Ph.D.
> University of Utah
> Cardiovascular Research and Training Institute
> 95 South 2000 East
> Salt Lake City, UT 84112-5000
>
> phone: [phone]
> alt ph: [phone]
> fax: [phone]
> e-mail: [hidden email]
>