Becoming an expert at writing ImageJ plugins

[Aaron Hendrickson]

Hello,

I have been using ImageJ to process large ammounts of images so I can
test the electro-optical performance of high-speed cameras (dynamic
range, quantum efficiency, etc.).  My probelm is that virtually none
of the processes I perform for each test are automated.  This means I
spend vast ammounts of time repeating the same process over and over
(its getting old).  My goal is to be able to write my own ImageJ
plugins that will automate my data reduction procedures and output the
measurements I am looking for.  Unfortuneatley I have very little
programming experiance and do not have any direction to get started.
Any input would be much appreciated.

Thanks in advance,
-Aaron.

[Rainer M. Engel]

Unfortuneatley I have very little programming experiance and do not have
any direction to get started.

Hey Aaron,

I don't know on what kind of plugins you already depend, but why not
starting with ImageJ's Macro Language. Most plugins are supported well
and you could learn about basic automation concepts.

http://rsbweb.nih.gov/ij/developer/macro/macros.html

Example-Macros
http://rsbweb.nih.gov/ij/developer/index.html

good luck.. and don't forget to record your own repetitive tasks
(Plugins>Macros>Record). By that you could prototype your workflow.

Regards,
Rainer


--
Rainer M. Engel, Dipl. Digital Artist
scientific|Media GbR
Pichelsdorferstr. 143
D-13595 Berlin

[BenTupper]

Hi,

I highly recommend this book:  http://www.imagingbook.com/

I found it to be the perfect guide for moving beyond macro programming to plugin development.  The authors responded to questions I directed to them about methodology.  It's very much worth acquiring and actually a bargain as these kinds of books go.

Cheers,
Ben


On Jan 19, 2012, at 11:08 AM, Aaron Hendrickson wrote:

> Hello,
>
> I have been using ImageJ to process large ammounts of images so I can
> test the electro-optical performance of high-speed cameras (dynamic
> range, quantum efficiency, etc.).  My probelm is that virtually none
> of the processes I perform for each test are automated.  This means I
> spend vast ammounts of time repeating the same process over and over
> (its getting old).  My goal is to be able to write my own ImageJ
> plugins that will automate my data reduction procedures and output the
> measurements I am looking for.  Unfortuneatley I have very little
> programming experiance and do not have any direction to get started.
> Any input would be much appreciated.
>
> Thanks in advance,
> -Aaron.

[wirthvolker]

2012/1/19 Ben Tupper <[hidden email]>:
> I highly recommend this book:  http://www.imagingbook.com/
>
> I found it to be the perfect guide for moving beyond macro programming to plugin development.  The authors responded to questions I directed to them about methodology.  It's very much worth acquiring and actually a bargain as these kinds of books go.


... and if your institution has access to SpringerLink, you can find
it also here:
http://www.springerlink.com/content/978-1-84628-379-6/contents/

Best,
Volker

[Cammer, Michael]

I second the suggestions about macros.  The macro language is much easier to deal with than Java, especially if you're not used to object oriented programming.  As long as you don't have to do a lot of pixel operations and can be patient to wait a few seconds or minutes for results from large datasets, the macro language is the way to go.
________________________________________________________
Michael Cammer, Assistant Research Scientist
Skirball Institute of Biomolecular Medicine
Lab: [phone]  Cell: [phone]



-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Rainer M. Engel
Sent: Thursday, January 19, 2012 11:31 AM
To: [hidden email]
Subject: Re: Becoming an expert at writing ImageJ plugins

Unfortuneatley I have very little programming experiance and do not have
any direction to get started.

Hey Aaron,

I don't know on what kind of plugins you already depend, but why not
starting with ImageJ's Macro Language. Most plugins are supported well
and you could learn about basic automation concepts.

http://rsbweb.nih.gov/ij/developer/macro/macros.html

Example-Macros
http://rsbweb.nih.gov/ij/developer/index.html

good luck.. and don't forget to record your own repetitive tasks
(Plugins>Macros>Record). By that you could prototype your workflow.

Regards,
Rainer


--
Rainer M. Engel, Dipl. Digital Artist
scientific|Media GbR
Pichelsdorferstr. 143
D-13595 Berlin

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=================================

[David Webster]

Also, you can use the macro recorder to record your steps then
automatiucaly convert to an ImageJ macro, JavaScript or a pllugin.

David Webster

On Thu, Jan 19, 2012 at 9:03 AM, Cammer, Michael <[hidden email]
> wrote:

> I second the suggestions about macros.  The macro language is much easier
> to deal with than Java, especially if you're not used to object oriented
> programming.  As long as you don't have to do a lot of pixel operations and
> can be patient to wait a few seconds or minutes for results from large
> datasets, the macro language is the way to go.
> ________________________________________________________
> Michael Cammer, Assistant Research Scientist
> Skirball Institute of Biomolecular Medicine
> Lab: [phone]  Cell: [phone]
>
>
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Rainer M. Engel
> Sent: Thursday, January 19, 2012 11:31 AM
> To: [hidden email]
> Subject: Re: Becoming an expert at writing ImageJ plugins
>
> Unfortuneatley I have very little programming experiance and do not have
> any direction to get started.
>
> Hey Aaron,
>
> I don't know on what kind of plugins you already depend, but why not
> starting with ImageJ's Macro Language. Most plugins are supported well
> and you could learn about basic automation concepts.
>
> http://rsbweb.nih.gov/ij/developer/macro/macros.html
>
> Example-Macros
> http://rsbweb.nih.gov/ij/developer/index.html
>
> good luck.. and don't forget to record your own repetitive tasks
> (Plugins>Macros>Record). By that you could prototype your workflow.
>
> Regards,
> Rainer
>
>
> --
> Rainer M. Engel, Dipl. Digital Artist
> scientific|Media GbR
> Pichelsdorferstr. 143
> D-13595 Berlin
>
> ------------------------------------------------------------
> This email message, including any attachments, is for the sole use of the
> intended recipient(s) and may contain information that is proprietary,
> confidential, and exempt from disclosure under applicable law. Any
> unauthorized review, use, disclosure, or distribution is prohibited. If you
> have received this email in error please notify the sender by return email
> and delete the original message. Please note, the recipient should check
> this email and any attachments for the presence of viruses. The
> organization accepts no liability for any damage caused by any virus
> transmitted by this email.
> =================================
>

[dscho]

Hi,

On Thu, 19 Jan 2012, Aaron Hendrickson wrote:

> My goal is to be able to write my own ImageJ plugins that will automate
> my data reduction procedures and output the measurements I am looking
> for.

As mentioned by others, probably you need to get into programming in the
first place, and thanks to the macro recorder, macro programming is a very
good place to start.

There are also tutorials how to modify the recorded macro so that you can
use it on multiple images, e.g. (shameless plug):
http://fiji.sc/How_to_apply_a_common_operation_to_a_complete_directory

Once you are proficient in easy macro programming, you might want to go to
full-blown Java plugins. A very good introduction IMHO is Werner Bailer's:
http://www.gm.fh-koeln.de/~konen/WPF-BV/tutorial-ImageJ_V1.71.pdf

A lot of the tedious steps are unnecessary, of course, if you use Fiji's
Script Editor which allows you not only to write Java plugins but also run
them from within Fiji/ImageJ. It also has a Templates menu in which you
will find examples that you only need to modify instead of writing
everything from scratch.

Ciao,
Johannes

[Aaron Hendrickson]

Thank you for all your suggestions this should definently help get me going.

On 1/19/12, Johannes Schindelin <[hidden email]> wrote:

> Hi,
>
> On Thu, 19 Jan 2012, Aaron Hendrickson wrote:
>
>> My goal is to be able to write my own ImageJ plugins that will automate
>> my data reduction procedures and output the measurements I am looking
>> for.
>
> As mentioned by others, probably you need to get into programming in the
> first place, and thanks to the macro recorder, macro programming is a very
> good place to start.
>
> There are also tutorials how to modify the recorded macro so that you can
> use it on multiple images, e.g. (shameless plug):
> http://fiji.sc/How_to_apply_a_common_operation_to_a_complete_directory
>
> Once you are proficient in easy macro programming, you might want to go to
> full-blown Java plugins. A very good introduction IMHO is Werner Bailer's:
> http://www.gm.fh-koeln.de/~konen/WPF-BV/tutorial-ImageJ_V1.71.pdf
>
> A lot of the tedious steps are unnecessary, of course, if you use Fiji's
> Script Editor which allows you not only to write Java plugins but also run
> them from within Fiji/ImageJ. It also has a Templates menu in which you
> will find examples that you only need to modify instead of writing
> everything from scratch.
>
> Ciao,
> Johannes
>