TrakEM2 released

[Albert Cardona]

Dear all,

TrakEM2 0.2 beta plugin released at
http://www.ini.unizh.ch/~acardona/trakem2.html

See some *snapshots*
http://www.ini.unizh.ch/~acardona/snapshots.html

This plugin has been designed for morphological data mining, and I will give a
presentation on it at the ImageJ conference in about a week.

So what can you do with it?

- Extract the object hierarchy from your data
- Model and export 3D.
- Work from your laptop on your huge, remote image storage.
- Work with an endless number of images, limited only by the hard drive
capacity. Dozens of formats supported thanks to ImageJ.
- Import stacks and even entire grids (montages) of images.
- Add layers conveniently. Each layer has its own Z coordinate and thickness,
and contains images, labels, profiles...
- Insert layer sets into layers: so your electron microscopy serial sections can
live inside your optical microscopy sections.
- Run any ImageJ plugin on any image.
- Measure everything: areas, volumes, pixel intensities, etc. using standard
ImageJ ROIs.
- Visualize RGB color channels changing the opacity of each on the fly,
non-destructively.
- Annotate images non-destructively with floating text labels.
- Montage images manually using transparencies, by dragging the images one onto
another.
- Undo: revert to your original images with one click. The original images
remain intact always as a backup copy.

And well, eventually many tasks will get automated, such as image montaging and
outlining. A 3D previewer is comming in soon.

Enjoy!

Albert Cardona

Molecular Cell Developmental Biology
University of California Los Angeles
Tel [phone]
Programming: http://www.pensament.net/java/
Research: http://www.mcdb.ucla.edu/Research/Hartenstein/
Web design: http://www.pixelets.com


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[DeBarr, Gabriel]

Your project looks interesting, and - potentially - useful.

A question:  on the project's page, mention is made that "Currently, a modified ij137f.jar file is necessary as the 'ij.jar'."  What modifications are we talking about (e.g. is it likely to 'break' any of my other plugins, or did you just patch in an interface to the SQL class[es]])?

        -Gabriel

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]]On Behalf Of
Albert Cardona
Sent: Thursday, May 11, 2006 9:58 PM
To: [hidden email]
Subject: TrakEM2 released


Dear all,

TrakEM2 0.2 beta plugin released at
http://www.ini.unizh.ch/~acardona/trakem2.html

See some *snapshots*
http://www.ini.unizh.ch/~acardona/snapshots.html

This plugin has been designed for morphological data mining, and I will give a
presentation on it at the ImageJ conference in about a week.

So what can you do with it?

- Extract the object hierarchy from your data
- Model and export 3D.
- Work from your laptop on your huge, remote image storage.
- Work with an endless number of images, limited only by the hard drive
capacity. Dozens of formats supported thanks to ImageJ.
- Import stacks and even entire grids (montages) of images.
- Add layers conveniently. Each layer has its own Z coordinate and thickness,
and contains images, labels, profiles...
- Insert layer sets into layers: so your electron microscopy serial sections can
live inside your optical microscopy sections.
- Run any ImageJ plugin on any image.
- Measure everything: areas, volumes, pixel intensities, etc. using standard
ImageJ ROIs.
- Visualize RGB color channels changing the opacity of each on the fly,
non-destructively.
- Annotate images non-destructively with floating text labels.
- Montage images manually using transparencies, by dragging the images one onto
another.
- Undo: revert to your original images with one click. The original images
remain intact always as a backup copy.

And well, eventually many tasks will get automated, such as image montaging and
outlining. A 3D previewer is comming in soon.

Enjoy!

Albert Cardona

Molecular Cell Developmental Biology
University of California Los Angeles
Tel [phone]
Programming: http://www.pensament.net/java/
Research: http://www.mcdb.ucla.edu/Research/Hartenstein/
Web design: http://www.pixelets.com


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[Dimiter Prodanov]

Hi Albert,

This is great. There is another program doing similar things it's called
Reconstruct. Perharps you could find it useful.

best regards

Dimiter Prodanov

[Albert Cardona]

Gabriel,

TrakEM2 runs now with ImageJ 1.37g without any modifications.

The webpage is updated:
http://www.ini.unizh.ch/~acardona/trakem2.html

The only two modifications were: fields 'roi' and 'currentSlice' where protected
instead of private in class ImagePlus. Modifications where listed in the README
inside the source zip (but you're right, they should have been listed more
visibily).

It is very unlikely that these modifications would have ever broken a single
plugin, and now they are integrated into ImageJ.

We are using TrakEM2 since day one, and all the public release wants to
accomplish is to save other's people time if they are to design a similar
plugin. It would be interesting to know how you find it useful for your own
purposes.

And a note: TrakeM2 0.2 is beta quality. There are a few know issues, for
instance pasting into an image results in disaster, unlinking pipes and ball
objects generates incorrect relinks, and deleting a layer will break the
linking chain. Work in progress.

Albert

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[Albert Cardona]

Dimiter,

Yes we are aware of Reconstruct and INI has been using it for a while already.
Eventually TrakEM2 has to replace it in full and add all that we are missing on
it!

> This is great. There is another program doing similar things it's called
> Reconstruct. Perharps you could find it useful.


Albert

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[Vladimir Hegyi]

Dear Albert,
I would like to ryn TrakEM2 0.2 beta on my system (ImageJ ver. 137g, Win XP)
but I do not know how to update my ImageJ.cfg file.
It says as follows:
.
jre\bin\javaw.exe
-Xmx700m -cp ij.jar ij.ImageJ

Would you be so kind to help me how to add to the cfg file
postgresql-8.1-405.jdbc3.jar, please.
Regards
Vladimir Hegyi

Assoc.Prof.Vladimir Hegyi,MD,PhD.
Dept. of Pediatric Dermatovenerology
School of Medicine
Comenius University
Limbova 1
833 40 Bratislava
Slovak Republic
e-mail: [hidden email]
www.dermatology.sk

----- Original Message -----
From: "Albert Cardona" <[hidden email]>
To: <[hidden email]>
Sent: Friday, May 12, 2006 3:57 AM
Subject: TrakEM2 released

> Dear all,
>
> TrakEM2 0.2 beta plugin released at
> http://www.ini.unizh.ch/~acardona/trakem2.html
>
> See some *snapshots*
> http://www.ini.unizh.ch/~acardona/snapshots.html
>
> This plugin has been designed for morphological data mining, and I will
> give a
> presentation on it at the ImageJ conference in about a week.
>
> So what can you do with it?
>
> - Extract the object hierarchy from your data
> - Model and export 3D.
> - Work from your laptop on your huge, remote image storage.
> - Work with an endless number of images, limited only by the hard drive
> capacity. Dozens of formats supported thanks to ImageJ.
> - Import stacks and even entire grids (montages) of images.
> - Add layers conveniently. Each layer has its own Z coordinate and
> thickness,
> and contains images, labels, profiles...
> - Insert layer sets into layers: so your electron microscopy serial
> sections can
> live inside your optical microscopy sections.
> - Run any ImageJ plugin on any image.
> - Measure everything: areas, volumes, pixel intensities, etc. using
> standard
> ImageJ ROIs.
> - Visualize RGB color channels changing the opacity of each on the fly,
> non-destructively.
> - Annotate images non-destructively with floating text labels.
> - Montage images manually using transparencies, by dragging the images one
> onto
> another.
> - Undo: revert to your original images with one click. The original images
> remain intact always as a backup copy.
>
> And well, eventually many tasks will get automated, such as image
> montaging and
> outlining. A 3D previewer is comming in soon.
>
> Enjoy!
>
> Albert Cardona
>
> Molecular Cell Developmental Biology
> University of California Los Angeles
> Tel [phone]
> Programming: http://www.pensament.net/java/
> Research: http://www.mcdb.ucla.edu/Research/Hartenstein/
> Web design: http://www.pixelets.com
>
>
> --------------------------------------------------------------------
> This message was sent using Webmail@INI: https://webmail.ini.ethz.ch
>
>

[Albert Cardona]

Dear Vladimir,

I have updated the setup instructions for windows:
http://www.ini.unizh.ch/~acardona/trakem2_manual.html#imagej_setup

In your particular case, drop the postgresql jar in the ImageJ directory and
then edit the ImageJ.cfg so that it reads:

.
jre\bin\javaw.exe
-Xmx700m -cp ij.jar;postgresql-8.1-405.jdbc3.jar ij.ImageJ

Then restart ImageJ.

I have done very few tests in Windows (noone uses it here) so I would appreciate
if you can share your experiences with TrakEM2 (thanks!)


Albert

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[Vladimir Hegyi]

Dear Albert,
Thank you very much for your help.
But, when the plugin is started, there is a dialog box, which I do not know
how to fill.
Question are as follows:
host:
port:
database name:
user name:
password:
What to do, please.
Vladimir

----- Original Message -----
From: "Albert Cardona" <[hidden email]>
To: <[hidden email]>
Sent: Sunday, May 14, 2006 7:51 PM
Subject: Re: TrakEM2 released

> Dear Vladimir,
>
> I have updated the setup instructions for windows:
> http://www.ini.unizh.ch/~acardona/trakem2_manual.html#imagej_setup
>
> In your particular case, drop the postgresql jar in the ImageJ directory
> and
> then edit the ImageJ.cfg so that it reads:
>
> .
> jre\bin\javaw.exe
> -Xmx700m -cp ij.jar;postgresql-8.1-405.jdbc3.jar ij.ImageJ
>
> Then restart ImageJ.
>
> I have done very few tests in Windows (noone uses it here) so I would
> appreciate
> if you can share your experiences with TrakEM2 (thanks!)
>
>
> Albert
>
> --------------------------------------------------------------------
> This message was sent using Webmail@INI: https://webmail.ini.ethz.ch
>
>

[Albert Cardona]

Dear Vladimir,

First:

http://www.ini.unizh.ch/~acardona/trakem2_manual.html#create_database

Then:

http://www.ini.unizh.ch/~acardona/trakem2_manual.html#template

Finally:

http://www.ini.unizh.ch/~acardona/trakem2_manual.html#start_project

while doing that, record a macro to automate the process for the next time:

http://www.ini.unizh.ch/~acardona/trakem2_manual.html#record_macro


Albert

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[Volker Baecker]

Hello,
I tried to run the trakem2 plugin. I successfully created a project and
the project window opens.
The project window look like this:

Template   Project Objects     Layers
* mouse    *Project[project]   *Top Level[Layer Set]

Is this normal? I thought the objects defined in the xml would show up?
Maybe there is an error in my xml file?
Does anyone have a working example?

Now, whatever I do, right-click, left-click, ... - nothing happens.

Can someone give me a hint?

The xml file looks like this:
<mouse id="1" title="mouse">
   <jaw id="10" title="jaw">
       <profile_list>
                       <profile id="11" index="1" />
                       <profile id="12" index="2" />
                       <profile id="13" index="3" />
              </profile_list>
   </jaw>
</mouse>

Thank you,
Volker Baecker

Albert Cardona a écrit :

> Dear Vladimir,
>
> First:
>
> http://www.ini.unizh.ch/~acardona/trakem2_manual.html#create_database
>
> Then:
>
> http://www.ini.unizh.ch/~acardona/trakem2_manual.html#template
>
> Finally:
>
> http://www.ini.unizh.ch/~acardona/trakem2_manual.html#start_project
>
> while doing that, record a macro to automate the process for the next time:
>
> http://www.ini.unizh.ch/~acardona/trakem2_manual.html#record_macro
>
>
> Albert
>
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>
>  

--
passerelle antivirus du campus CNRS de Montpellier
--

[Vladimir Hegyi]

Dear Albert,
Thank you very much for you marvelous help. I will try to do all necessary
steps as you advice.
It seems to me that I could run the plug-in if connected to Internet only.
Am I right, please?
Regards
Vladimir

----- Original Message -----
From: "Albert Cardona" <[hidden email]>
To: <[hidden email]>
Sent: Monday, May 15, 2006 7:33 AM
Subject: Re: TrakEM2 released

> Dear Vladimir,
>
> First:
>
> http://www.ini.unizh.ch/~acardona/trakem2_manual.html#create_database
>
> Then:
>
> http://www.ini.unizh.ch/~acardona/trakem2_manual.html#template
>
> Finally:
>
> http://www.ini.unizh.ch/~acardona/trakem2_manual.html#start_project
>
> while doing that, record a macro to automate the process for the next
> time:
>
> http://www.ini.unizh.ch/~acardona/trakem2_manual.html#record_macro
>
>
> Albert
>
> --------------------------------------------------------------------
> This message was sent using Webmail@INI: https://webmail.ini.ethz.ch
>
>

[Albert Cardona]

Dear Volker Baecker,

The XML file needs a reference header, so that it would look like below.
Eventually I write an editor that will automate all these XML details.

Albert


<?xml version="1.0" encoding="ISO-8859-1"?>
<!DOCTYPE Mouse_jaw [
        <!ELEMENT mouse (jaw)>
        <!ATTLIST mouse id NMTOKEN #REQUIRED>
        <!ATTLIST mouse title NMTOKEN #REQUIRED>
        <!ELEMENT jaw (profile_list)>
        <!ATTLIST jaw id NMTOKEN #REQUIRED>
        <!ATTLIST jaw title NMTOKEN #REQUIRED>
        <!ELEMENT profile_list (profile+)>
        <!ELEMENT profile EMPTY>
        <!ATTLIST profile id NMTOKEN #REQUIRED>
        <!ATTLIST profile index NMTOKEN #REQUIRED>
]>

<mouse id="1" title="mouse">
   <jaw id="10" title="jaw">
       <profile_list>
           <profile id="11" index="1" />
           <!-- many more profiles -->
       </profile_list>
   </jaw>
</mouse>

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[Albert Cardona]

Dear Vladimir,

The database can exist in your local computer (thus you don't need internet) or
remotely on any computer on the internet (best case, a server in your local
LAN).

Albert

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