batch processes

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batch processes

Edoardo D'Imprima
Dear all,

I am a very beginner with ImageJ and Java scripting. I would like to perform some operations in series on dm4 images like enhancing the contrast of such a percentage of saturated pixels, applying image normalisation, smoothing the result and save the image as 8 bit instead of 32. All these steps running in batch over a list of files.

Is there any template script with these or similar command which I can use to start playing with it.

Many thanks in advance,

Edoardo
---------------------------------------------------
Edoardo D'Imprima
PhD Student
Max Planck Institute of Biophysics
Structural Biology Department
Max-von-Laue Straße 3
60438 Frankfurt am Main
Germany

Tel: +49 (0) 69 6303 3015

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Re: batch processes

Ellen T Arena
Hi Edoardo…

Here are some helpful workshops/wiki-pages for getting started with Scripting in ImageJ:

* ImageJ Wiki - http://imagej.net/Welcome <http://imagej.net/Welcome> - the go-to place to search for help with ImageJ/Fiji
* Scripting overview page - http://imagej.net/Scripting <http://imagej.net/Scripting> - on the wiki
* A helpful workshop on Scripting with Fiji - https://vimeo.com/218520432 <https://vimeo.com/218520432> - the slides are here - http://imagej.github.io/presentations/fiji-scripting/#/ <http://imagej.github.io/presentations/fiji-scripting/#/>
* Introduction into Macro Programming page - http://imagej.net/Introduction_into_Macro_Programming <http://imagej.net/Introduction_into_Macro_Programming> - of the wiki
* You will want to use the Macro Recorder - http://imagej.net/Introduction_into_Macro_Programming#The_recorder <http://imagej.net/Introduction_into_Macro_Programming#The_recorder> - to start recording the code to build your scripts…
* Built-In Macro Functions list - http://imagej.net/developer/macro/functions.html <http://imagej.net/developer/macro/functions.html>

I hope this helps!  And you can always post on the ImageJ Forum as well if you want/need help with your scripts… http://forum.imagej.net/ <http://forum.imagej.net/>

Ellen


 

> On Sep 5, 2017, at 10:33 AM, Edoardo D'Imprima <[hidden email]> wrote:
>
> Dear all,
>
> I am a very beginner with ImageJ and Java scripting. I would like to perform some operations in series on dm4 images like enhancing the contrast of such a percentage of saturated pixels, applying image normalisation, smoothing the result and save the image as 8 bit instead of 32. All these steps running in batch over a list of files.
>
> Is there any template script with these or similar command which I can use to start playing with it.
>
> Many thanks in advance,
>
> Edoardo
> ---------------------------------------------------
> Edoardo D'Imprima
> PhD Student
> Max Planck Institute of Biophysics
> Structural Biology Department
> Max-von-Laue Straße 3
> 60438 Frankfurt am Main
> Germany
>
> Tel: +49 (0) 69 6303 3015
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html


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Re: batch processes

Ellen T Arena
In reply to this post by Edoardo D'Imprima
I forgot to link you to the Batch page… https://imagej.net/Batch_Processing <https://imagej.net/Batch_Processing>

So you can always batch without the need for writing your own scripts using the ‘easy’ interface… but with scripting - obviously you have more control, etc.

I hope this all helps!

Ellen


> On Sep 5, 2017, at 10:33 AM, Edoardo D'Imprima <[hidden email]> wrote:
>
> Dear all,
>
> I am a very beginner with ImageJ and Java scripting. I would like to perform some operations in series on dm4 images like enhancing the contrast of such a percentage of saturated pixels, applying image normalisation, smoothing the result and save the image as 8 bit instead of 32. All these steps running in batch over a list of files.
>
> Is there any template script with these or similar command which I can use to start playing with it.
>
> Many thanks in advance,
>
> Edoardo
> ---------------------------------------------------
> Edoardo D'Imprima
> PhD Student
> Max Planck Institute of Biophysics
> Structural Biology Department
> Max-von-Laue Straße 3
> 60438 Frankfurt am Main
> Germany
>
> Tel: +49 (0) 69 6303 3015
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html


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