Contributions to the ImageJ User Guide

[Tiago Ferreira-2]

Hi,

There has long been a need for a printable ImageJ users manual. In addition,
ImageJ has evolved so fast that updated documentation is also needed.

I've started assembling an User Guide, and to make a really long story short, I
think this document has now the potential to be the most complete IJ manual
written to date.

Although the bulk of the sections is done, it is yet to be finished, and I'am
afraid I won't be able to commit to it as much as I would like to from now on.

Apart from the command descriptions that are missing (highlighted with a
'To be completed' label),I think the guide still misses:

- More Tips and Tricks on ImageJ usage
- Descriptions of less known aspects of ImageJ or its internal Plugins
- Added information on FFT
- Added information on Segmentation
- Added information on Processing Filters
- Rules of thumb concerning image processing
- Corrections, suggestions, imprecisions, etc..

I was wondering: Do you think you can contribute with any of the above?

Wayne is hosting the preliminary draft at:
    <http://rsbweb.nih.gov/ij/docs/user-guide.pdf>

I would ask you to have a look at it, see how it looks, and If you think you can
help I would be delighted to collect your input.

Thanks in advance,

\Tiago

[Francis Burton]

A heroic effort, Tiago. Your 'preliminary draft' is already comprehensive
and, at first glance, attractive and readable. When complete, it will be a
definitive ImageJ reference, I'm sure.

I would be happy to provide casual proofreading feedback, if that would be
useful. To whom should corrections be sent?

Francis  
 
At 14:14 15/02/2010, Tiago Ferreira <[hidden email]> wrote:

>Hi,
>
>There has long been a need for a printable ImageJ users manual. In addition,
>ImageJ has evolved so fast that updated documentation is also needed.
>
>I've started assembling an User Guide, and to make a really long story short, I
>think this document has now the potential to be the most complete IJ manual
>written to date.
>
>Although the bulk of the sections is done, it is yet to be finished, and I'am
>afraid I won't be able to commit to it as much as I would like to from now on.
>
>Apart from the command descriptions that are missing (highlighted with a
>'To be completed' label),I think the guide still misses:
>
>- More Tips and Tricks on ImageJ usage
>- Descriptions of less known aspects of ImageJ or its internal Plugins
>- Added information on FFT
>- Added information on Segmentation
>- Added information on Processing Filters
>- Rules of thumb concerning image processing
>- Corrections, suggestions, imprecisions, etc..
>
>I was wondering: Do you think you can contribute with any of the above?
>
>Wayne is hosting the preliminary draft at:
>    <http://rsbweb.nih.gov/ij/docs/user-guide.pdf>
>
>I would ask you to have a look at it, see how it looks, and If you think you can
>help I would be delighted to collect your input.
>
>Thanks in advance,
>
>\Tiago

[Francis Burton]

To answer my own question - the document requests comments and corrections
be sent to the author (Tiago Ferreira) at the address below.

Francis

At 14:55 15/02/2010, I wrote:

>A heroic effort, Tiago. Your 'preliminary draft' is already comprehensive
>and, at first glance, attractive and readable. When complete, it will be a
>definitive ImageJ reference, I'm sure.
>
>I would be happy to provide casual proofreading feedback, if that would be
>useful. To whom should corrections be sent?
>
>Francis  
>
>At 14:14 15/02/2010, Tiago Ferreira <[hidden email]> wrote:
>>Hi,
>>
>>There has long been a need for a printable ImageJ users manual. In addition,
>>ImageJ has evolved so fast that updated documentation is also needed.
>>
>>I've started assembling an User Guide, and to make a really long story short, I
>>think this document has now the potential to be the most complete IJ manual
>>written to date.
>>
>>Although the bulk of the sections is done, it is yet to be finished, and I'am
>>afraid I won't be able to commit to it as much as I would like to from now on.
>>[...]

[migue]

Hi

Thanks Tiago, it looks fine!. Can I suggest a reference to jython and jedit
bridge when speaking about extending IJ?

I repeat thank you for this very nice effort.

Miguel

[dscho]

Hi,

On Tue, 16 Feb 2010, Miguel Peinado wrote:

> Thanks Tiago, it looks fine!. Can I suggest a reference to jython and
> jedit bridge when speaking about extending IJ?

There is a reference to Jython in the part about Fiji.

Regarding the JEdit bridge: would this not be something for a developers'
guide? Otherwise we'd have to include a reference to Fiji's "Script"
Editor, to the many tutorials how to compile and run with Eclipse,
NetBeans, etc, and of course Benjamin Schmid's vi bridge.

Ciao,
Dscho

[migue]

You're absolutetly right and all of these must be also referenced. what I
mean is a brief reference about life beyond macros and IJ editor.

Best

[Prodanov Dimiter]

Hi I am happy to contribute.
I welcome your use of LaTeX :)
How would you structure the writing process?

Best regards,

Dimiter

-----Original Message-----
From: Tiago Ferreira [mailto:[hidden email]]
Sent: Monday 15 February 2010 15:14
Subject: Contributions to the ImageJ User Guide

Hi,

There has long been a need for a printable ImageJ users manual. In addition,
ImageJ has evolved so fast that updated documentation is also needed.

I've started assembling an User Guide, and to make a really long story short, I
think this document has now the potential to be the most complete IJ manual
written to date.

Although the bulk of the sections is done, it is yet to be finished, and I'am
afraid I won't be able to commit to it as much as I would like to from now on.

Apart from the command descriptions that are missing (highlighted with a
'To be completed' label),I think the guide still misses:

- More Tips and Tricks on ImageJ usage
- Descriptions of less known aspects of ImageJ or its internal Plugins
- Added information on FFT
- Added information on Segmentation
- Added information on Processing Filters
- Rules of thumb concerning image processing
- Corrections, suggestions, imprecisions, etc..

I was wondering: Do you think you can contribute with any of the above?

Wayne is hosting the preliminary draft at:
    <http://rsbweb.nih.gov/ij/docs/user-guide.pdf>

I would ask you to have a look at it, see how it looks, and If you think you can
help I would be delighted to collect your input.

Thanks in advance,

\Tiago

[Gabriel Landini]

The guide looks very nice, and I it shows that a lot of effort has been gone
into making it. That is great.

On the practical side, I think that adding corrections by emailing without
access to editing the source itself is both inconvenient and duplicating a lot
of effort unnecessarily. For example one cannot correct small details on the
spot and it will put off some people from contributing.

Why not opening the text in the wiki at Tudor? (which, by the way, was one of
its purposes).
That way one does not have to compile corrections, mail them, wait for the
corrections to be made, convert to pdf, etc. Progress would be much quicker.

Also, there is nothing stopping us having the latest nicely-formatted version
and an online "working" version of the text from which the former feeds.
The wiki ability to look through the history of the document is very useful
for both the final compilation and to keep track of what has been added
recently.

Cheers,

G.

[Daniel James White]

Hi Tiago,

i think the user manual is a great idea, and i applaud your efforts  
here.

I wonder if this effort could be made less painless by using some web2  
ideas.

For instance instead of maintaining a text document, and trying to  
keep up with changes in imageJ
a more dynamic way it to put it in a wiki pr similar,
where its much easier to edit, and allow others to also contribute.

in the pipes is imageJ2 and the manual will need to keep up with  
developments there i guess....
even though backwards compatability will be a priority.

As you point out, you might not have much time in the future to keep  
it up to date...
so letting the community do that is a smart choice... IMHO

cheers

Dan



Begin forwarded message:

>
> Date:    Mon, 15 Feb 2010 17:25:29 +0000
> From:    Francis Burton <[hidden email]>
> Subject: Re: Contributions to the ImageJ User Guide
>
> To answer my own question - the document requests comments and  
> corrections
> be sent to the author (Tiago Ferreira) at the address below.
>
> Francis
>
> At 14:55 15/02/2010, I wrote:
>> A heroic effort, Tiago. Your 'preliminary draft' is already  
>> comprehensive
>> and, at first glance, attractive and readable. When complete, it  
>> will be a
>> definitive ImageJ reference, I'm sure.
>>
>> I would be happy to provide casual proofreading feedback, if that  
>> would be
>> useful. To whom should corrections be sent?
>>
>> Francis
>>
>> At 14:14 15/02/2010, Tiago Ferreira <[hidden email]>  
>> wrote:
>>> Hi,
>>>
>>> There has long been a need for a printable ImageJ users manual. In  
>>> addition,
>>> ImageJ has evolved so fast that updated documentation is also  
>>> needed.
>>>
>>> I've started assembling an User Guide, and to make a really long  
>>> story short, I
>>> think this document has now the potential to be the most complete  
>>> IJ manual
>>> written to date.
>>>
>>> Although the bulk of the sections is done, it is yet to be  
>>> finished, and I'am
>>> afraid I won't be able to commit to it as much as I would like to  
>>> from now on.
>>> [...]

Dr. Daniel James White BSc. (Hons.) PhD
Senior Microscopist / Image Visualisation, Processing and Analysis
Light Microscopy and Image Processing Facilities
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 DRESDEN
Germany

[phone] (German Mobile)
[phone] (Work phone at MPI-CBG)
[phone] (Fax MPI-CBG LMF)

http://www.bioimagexd.net  BioImageXD
http://pacific.mpi-cbg.de                Fiji -  is just ImageJ (Batteries Included)
http://www.chalkie.org.uk                Dan's Homepages
https://ifn.mpi-cbg.de  Dresden Imaging Facility Network
dan (at) chalkie.org.uk
( white (at) mpi-cbg.de )

[Tiago Ferreira-2]

First of all thank you all for your comments.

I will try to answer to all of you, so forgive me for not doing it individually.

I am really sorry if my call sounded dubious:
- I do not expect any monetary profit from this
- I do want this to be open, to be a community effort. Thats the only reason,
  why this was announced here in first place.

Johannes has offered to host the pdf source on a Git repository. I think that
would be the way to go.

The reason I involuntary "forked" the documentation is just casual. I had to
assemble some pages for a small group of people and the thing just grew out
of control. :)

I'm extremely found of the IJ wiki. I was thrilled when Christian announced the
new version, with the neat pdf converter.

But for understandable reasons I did not start this document there (neither any
of several others who have started similar documents). If I had predicted the
evolution of the guide, then I would have though in much detail about the
writing process...

So this is how I 'envision' the future of the ImageJ manual (please bear with my
personal opinion), even if I did not think how to implement it:
    - I'll populate the IJ wiki with my notes
      (any thoughts on how to do that programmatically?)
    - We all mature the wiki pages.
    - In parallel,  the same process happens with the LaTeX source (which I
      predict will have less participants).
    - At whatever periodicity, we feedback both, and hopefully, lets say once a
      year, a new document can be compiled and the HTML version could be sent to
      Wayne.
    - I also think an overloaded guide won't be useful to the average user, so
      if the documentation starts to grow I would append it to a second
      manual, "The Advanced User guide" or something like that.

But honestly in the immediate run I would like to just finish what I have. In my
naive perception of things, if you identify yourself with this right away and
want to contribute, you could:
    - Annotate the draft (Jarnal, Skim, Xournal, Foxit, Acrobat, etc.) and send
      me your comments.
    - Create or edit a "GUI Command" entry on the wiki, that I could then use
     <http://imagejdocu.tudor.lu/doku.php?id=gui:start>
    - Just email me your notes in whatever format you prefer.    
   
Otherwise, if you need the files I can upload them somewhere or we could start
the repository right away. Or I can create an account on ScribTeX or MonkeyTeX,
(use dropbox?) and would make it collaborative that way.

Let me know what you think,

Tiago

[ctrueden]

Hi Tiago,

Thanks for your hard work on this excellent manual!

I agree with others that an online resource, able to be edited
collaboratively, would help everyone. Using the ImageJ Documentation Wiki
makes a lot of sense. My main concern with your proposal is keeping two
parallel sources. Would it be easier to autogenerate the print version from
the online one (perhaps using the "Export PDF" function you mentioned), to
avoid duplication of effort?

   - I'll populate the IJ wiki with my notes
>      (any thoughts on how to do that programmatically?)
>

Transferring the text wholesale probably wouldn't be too difficult, but the
figures will be trickier.

For some of the more troublesome stuff you could perhaps use the
dokuwiki_latex plugin (though I haven't tried it):
  http://boyle.black-holes.org/dokuwiki_latex

Regards,
Curtis

On Tue, Feb 16, 2010 at 11:32 AM, Tiago Ferreira <
[hidden email]> wrote:

> First of all thank you all for your comments.
>
> I will try to answer to all of you, so forgive me for not doing it
> individually.
>
> I am really sorry if my call sounded dubious:
> - I do not expect any monetary profit from this
> - I do want this to be open, to be a community effort. Thats the only
> reason,
>  why this was announced here in first place.
>
> Johannes has offered to host the pdf source on a Git repository. I think
> that
> would be the way to go.
>
> The reason I involuntary "forked" the documentation is just casual. I had
> to
> assemble some pages for a small group of people and the thing just grew out
> of control. :)
>
> I'm extremely found of the IJ wiki. I was thrilled when Christian announced
> the
> new version, with the neat pdf converter.
>
> But for understandable reasons I did not start this document there (neither
> any
> of several others who have started similar documents). If I had predicted
> the
> evolution of the guide, then I would have though in much detail about the
> writing process...
>
> So this is how I 'envision' the future of the ImageJ manual (please bear
> with my
> personal opinion), even if I did not think how to implement it:
>    - I'll populate the IJ wiki with my notes
>      (any thoughts on how to do that programmatically?)
>    - We all mature the wiki pages.
>    - In parallel,  the same process happens with the LaTeX source (which I
>      predict will have less participants).
>    - At whatever periodicity, we feedback both, and hopefully, lets say
> once a
>      year, a new document can be compiled and the HTML version could be
> sent to
>      Wayne.
>    - I also think an overloaded guide won't be useful to the average user,
> so
>      if the documentation starts to grow I would append it to a second
>      manual, "The Advanced User guide" or something like that.
>
> But honestly in the immediate run I would like to just finish what I have.
> In my
> naive perception of things, if you identify yourself with this right away
> and
> want to contribute, you could:
>    - Annotate the draft (Jarnal, Skim, Xournal, Foxit, Acrobat, etc.) and
> send
>      me your comments.
>    - Create or edit a "GUI Command" entry on the wiki, that I could then
> use
>     <http://imagejdocu.tudor.lu/doku.php?id=gui:start>
>    - Just email me your notes in whatever format you prefer.
>
> Otherwise, if you need the files I can upload them somewhere or we could
> start
> the repository right away. Or I can create an account on ScribTeX or
> MonkeyTeX,
> (use dropbox?) and would make it collaborative that way.
>
> Let me know what you think,
>
> Tiago
>

[Christian Moll]

Hello Tiago,

very nice approach.  Due to I am today a little bit limited in time. I
will keep it short.

>I'm extremely found of the IJ wiki. I was thrilled when Christian
announced the
new version, with the neat pdf converter.

We also thought about doing a printable version of the wiki. That's why be
implemented the pdf option.

>- I'll populate the IJ wiki with my notes
      (any thoughts on how to do that programmatically?)

That's not clear for me. What do you mean with programmatically? Do you
want to change the content of various pages by a script or something
similar? Then I have to say no, that's not possible. But as  I see you are
already registered in the wiki. So you are free to edit the pages and
mature them.

There is also a possibility to create an "editor page", where all single
pages can be collected and sorted. This page could then be used to
generate a pdf of the complete collection.
We also tested an other pdf export for the wiki, which directly generates
LaTex. But therefore the pages have to be very precisely written. You have
to choose the Heading-Level correctly and some other issues. So we do not
use this plugin in a public wiki, because you have to invest very much
time in correcting page, so that they can be compiled in LaTex.

>- Create or edit a "GUI Command" entry on the wiki, that I could then use
     <http://imagejdocu.tudor.lu/doku.php?id=gui:start>

You need something like that:
http://imagejdocu.tudor.lu/doku.php?id=gui:start2 
Right? If it is laike that we can easily setup an area for different
editions of printable versions of the wiki.

For any further questions, feel free to mail me.

Best regards,

Christian and the ImageJdocu team


-----------------------------------------------------------------
Christian Moll  -  Ingenieur de Recherche
[hidden email]
-----------------------------------------------------------------
CRP Henri Tudor  -  http://santec.tudor.lu
2A, rue Kalchesbrück
L-1852 Luxembourg
-----------------------------------------------------------------



Tiago Ferreira <[hidden email]>
Sent by: ImageJ Interest Group <[hidden email]>
02/16/2010 06:37 PM
Please respond to
ImageJ Interest Group <[hidden email]>


To
[hidden email]
cc

Subject
Re: Contributions to the ImageJ User Guide






First of all thank you all for your comments.

I will try to answer to all of you, so forgive me for not doing it
individually.

I am really sorry if my call sounded dubious:
- I do not expect any monetary profit from this
- I do want this to be open, to be a community effort. Thats the only
reason,
  why this was announced here in first place.

Johannes has offered to host the pdf source on a Git repository. I think
that
would be the way to go.

The reason I involuntary "forked" the documentation is just casual. I had
to
assemble some pages for a small group of people and the thing just grew
out
of control. :)

I'm extremely found of the IJ wiki. I was thrilled when Christian
announced the
new version, with the neat pdf converter.

But for understandable reasons I did not start this document there
(neither any
of several others who have started similar documents). If I had predicted
the
evolution of the guide, then I would have though in much detail about the
writing process...

So this is how I 'envision' the future of the ImageJ manual (please bear
with my
personal opinion), even if I did not think how to implement it:
    - I'll populate the IJ wiki with my notes
      (any thoughts on how to do that programmatically?)
    - We all mature the wiki pages.
    - In parallel,  the same process happens with the LaTeX source (which
I
      predict will have less participants).
    - At whatever periodicity, we feedback both, and hopefully, lets say
once a
      year, a new document can be compiled and the HTML version could be
sent to
      Wayne.
    - I also think an overloaded guide won't be useful to the average
user, so
      if the documentation starts to grow I would append it to a second
      manual, "The Advanced User guide" or something like that.

But honestly in the immediate run I would like to just finish what I have.
In my
naive perception of things, if you identify yourself with this right away
and
want to contribute, you could:
    - Annotate the draft (Jarnal, Skim, Xournal, Foxit, Acrobat, etc.) and
send
      me your comments.
    - Create or edit a "GUI Command" entry on the wiki, that I could then
use
     <http://imagejdocu.tudor.lu/doku.php?id=gui:start>
    - Just email me your notes in whatever format you prefer.
 
Otherwise, if you need the files I can upload them somewhere or we could
start
the repository right away. Or I can create an account on ScribTeX or
MonkeyTeX,
(use dropbox?) and would make it collaborative that way.

Let me know what you think,

Tiago