Google Summer of Code

[Albert Cardona]

Dear all,

Fiji has been selected as a mentoring organization for the Google Summer
of Code program. The program encourages undergraduate and graduate
students to propose a software project and fulfill it with the help of a
designated mentor. The projects span exactly 3 months and provide a
stipend for the student.

We would appreciate if you can pass on this notice to any interested
students.

Fiji is Just ImageJ (batteries included):
http://pacific.mpi-cbg.de

Google Summer of Code:
http://socghop.appspot.com/

Fiji ideas page for GSoC:   (potential projects for students)
http://pacific.mpi-cbg.de/wiki/index.php/SoC2009Ideas

Please direct any questions to the Fiji mailing list:
http://groups.google.com/group/fiji-devel


We are looking forward to add yet more features to Fiji!

Albert
--
Albert Cardona
http://albert.rierol.net

[Bill Mohler]

How would FIJI-specific projects differ from general plugin development for IJ?

What are the limits for the GSoC project monitored by FIJI.

>Dear all,
>
>Fiji has been selected as a mentoring organization for the Google Summer
>of Code program. The program encourages undergraduate and graduate
>students to propose a software project and fulfill it with the help of a
>designated mentor. The projects span exactly 3 months and provide a
>stipend for the student.
>
>We would appreciate if you can pass on this notice to any interested
>students.
>
>Fiji is Just ImageJ (batteries included):
>http://pacific.mpi-cbg.de
>
>Google Summer of Code:
>http://socghop.appspot.com/
>
>Fiji ideas page for GSoC:   (potential projects for students)
>http://pacific.mpi-cbg.de/wiki/index.php/SoC2009Ideas
>
>Please direct any questions to the Fiji mailing list:
>http://groups.google.com/group/fiji-devel
>
>
>We are looking forward to add yet more features to Fiji!
>
>Albert
>--
>Albert Cardona
>http://albert.rierol.net

--
-----------------
William A. Mohler
Associate Professor
Dept. of Genetics and Developmental Biology
University of Connecticut Health Center
MC-3301
263 Farmington Ave.
Farmington, CT   06030-3301

[hidden email]
Mobile: [phone]
alt. mobile: [phone]
skype: wmohler

Office: [phone], room E2029
Lab: [phone], room E2032
Fax: [phone]

G&DB dept. ofc.: [phone]
G&DB dept. fax : [phone]
http://genetics.uchc.edu/Faculty/Mohler/Mohler.html

[dscho]

Hi,

On Sat, 28 Mar 2009, Bill Mohler wrote:

> How would FIJI-specific projects differ from general plugin development
> for IJ?

I would not lightly accept a project that runs without Fiji at all.  After
all, we put in a lot of effort into the Summer of Code (some of the
organizations that were accepted in previous years have not succeeded in
securing a place in the summer of code, but we were, in spite of being
newcomers).

We will have to put in even more effort, as mentoring is almost a
full-time job during the first weeks.

So of course, we want to have something in return: preferably long-term
contributors that add value to the parts of Fiji that do not easily run
outside of Fiji (think "plugin manager", or "scripting editor").

It is a simple matter of quid pro quo: Google provides money, we provide
extensive knowledge, experience and assistance in programming and image
processing, and the students should provide us with a project that
improves Fiji.

> What are the limits for the GSoC project monitored by FIJI.

There are no limits ;-)

Except, of course, that it must be a project that benefits Fiji in an
obvious way.

BTW if it was not clear: Google is extremely generous, paying students for
us.  And we have an obligation of spending that money wisely, fulfilling
our side of the contract: to attract more students to Open Source.

Oh, and if you have an idea for a project that is so obviously Fiji that
we cannot possibly reject it, but which is not listed on the Fiji Wiki:
the ideas we listed are only suggestions, food for thought.  Go wild.

Ciao,
Dscho

[Gabriel Landini]

On Sunday 29 March 2009, Johannes Schindelin wrote in the IJ list:
> Oh, and if you have an idea for a project that is so obviously Fiji that
> we cannot possibly reject it, but which is not listed on the Fiji Wiki:
> the ideas we listed are only suggestions, food for thought.  Go wild.

There are a number of mini-projects/ideas in the ImageJ wiki site (the
Wishlikst http://imagejdocu.tudor.lu/doku.php?id=wishlist:start) which I have
been wondering whether they would be suitable. I am adding some more here:

1) Alpha_shapes / concave_hull (could be part of item 7 below)

2) Bilateral Filtering

3) Colorizing algorithms (i.e greyscale to colour,there are several methods)

4) Retinex algorithm

5) Interactively adjustable intensity/LUT curves (not just linear controls,
but splines/etc based)

6) Support for storing ROIs in TIFF tag fields, so ROIs can be saved with the
images).

7) Graph Theory constructs (in addition to the Delaunay/Voronoi)

8) Expand the ImageFlow module base (not sure if the source is available yet).

9) Object (rather than image) selector/sorter (something like Kai's pixolu.de  
If you haven't tried it, you should) to create "objects like these"
filters/classifiers to be extracted from images and sets of images.

10) Interface between R and ImageJ/Fiji (Dimiter has done something like this,
but it would be nice to have a set of implemented procedures so IJ/Fiji can
run statistical procedures directly from Results tables, etc)

11) A set of more powerful painting brushes and image editing tools.

12) Cross platform webcam support (to produce cheap videomicroscope/telescope
units)

13) Statistical region merging segmentation:
http://www.univ-ag.fr/~rnock/Articles/Drafts/tpami04-nn.pdf

14) Fractal interpolation resizing (from the GIMP GSoC entry)

15) A unique/common segmentation interface (I have collected near 15 new
histogram segmentation methods that would be better put under a single
interface together with others already available).

16) A javascript Recorder (similar to the Macro Recorder but producing
javascript instead).

17) Virtual microscope-like image viewer.

18) HSB/Lab painting modes

Is that wild enough? :-) I am sure others will have further ideas.
Cheers,

Gabriel

[Burger Wilhelm]

To get a coarse orientation - is there is anything like a mission statement or white paper that lays out the strategic aims or near-term development goals of Fiji?
 
--Wilhelm
 
________________________________

Von: ImageJ Interest Group im Auftrag von Johannes Schindelin
Gesendet: So 29.03.2009 03:20
An: [hidden email]
Betreff: Re: Google Summer of Code



Hi,

On Sat, 28 Mar 2009, Bill Mohler wrote:

> How would FIJI-specific projects differ from general plugin development
> for IJ?

I would not lightly accept a project that runs without Fiji at all.  After
all, we put in a lot of effort into the Summer of Code (some of the
organizations that were accepted in previous years have not succeeded in
securing a place in the summer of code, but we were, in spite of being
newcomers).

We will have to put in even more effort, as mentoring is almost a
full-time job during the first weeks.

So of course, we want to have something in return: preferably long-term
contributors that add value to the parts of Fiji that do not easily run
outside of Fiji (think "plugin manager", or "scripting editor").

It is a simple matter of quid pro quo: Google provides money, we provide
extensive knowledge, experience and assistance in programming and image
processing, and the students should provide us with a project that
improves Fiji.

> What are the limits for the GSoC project monitored by FIJI.

There are no limits ;-)

Except, of course, that it must be a project that benefits Fiji in an
obvious way.

BTW if it was not clear: Google is extremely generous, paying students for
us.  And we have an obligation of spending that money wisely, fulfilling
our side of the contract: to attract more students to Open Source.

Oh, and if you have an idea for a project that is so obviously Fiji that
we cannot possibly reject it, but which is not listed on the Fiji Wiki:
the ideas we listed are only suggestions, food for thought.  Go wild.

Ciao,
Dscho

[dscho]

Hi Gabriel,

On Sun, 29 Mar 2009, Gabriel Landini wrote:

> On Sunday 29 March 2009, Johannes Schindelin wrote in the IJ list:
> > Oh, and if you have an idea for a project that is so obviously Fiji
> > that we cannot possibly reject it, but which is not listed on the Fiji
> > Wiki: the ideas we listed are only suggestions, food for thought.  Go
> > wild.
>
> There are a number of mini-projects/ideas in the ImageJ wiki site (the
> Wishlikst http://imagejdocu.tudor.lu/doku.php?id=wishlist:start) which I
> have been wondering whether they would be suitable.

Hmm. If I can choose between students that implement ImageJ plugins, and
students that work on the core infrastructure of Fiji, I will pick the
latter.

Of course, it would be nice to have all these plugins implemented, but
when do you get the chance to work on a bigger project for 3 months
straight?

> I am adding some more here:
>
> 1) Alpha_shapes / concave_hull (could be part of item 7 below)
>
> 2) Bilateral Filtering

Is in Fiji already.  That was a really small project.

> 3) Colorizing algorithms (i.e greyscale to colour,there are several
>    methods)
>
> 4) Retinex algorithm
>
> 5) Interactively adjustable intensity/LUT curves (not just linear
>    controls, but splines/etc based)
>
> 6) Support for storing ROIs in TIFF tag fields, so ROIs can be saved
>    with the images).
>
> 7) Graph Theory constructs (in addition to the Delaunay/Voronoi)
>
> 8) Expand the ImageFlow module base (not sure if the source is available
>    yet).

The source is not available yet, but I talked to Daniel about it already.  
He will be fine to have the source code in Fiji, once he released the
source to the public.

> 9) Object (rather than image) selector/sorter (something like Kai's
>    pixolu.de If you haven't tried it, you should) to create "objects
>    like these"  filters/classifiers to be extracted from images and sets
>    of images.
>
> 10) Interface between R and ImageJ/Fiji (Dimiter has done something like
>     this, but it would be nice to have a set of implemented procedures
>     so IJ/Fiji can run statistical procedures directly from Results
>     tables, etc)

R is platform specific.  As we support 7 platforms already (and somebody
is working on an 8th), that would add a tremendous maintenance burden.

I'd rather have an existing Open Source statistical package written in
Java integrated.

> 11) A set of more powerful painting brushes and image editing tools.
>
> 12) Cross platform webcam support (to produce cheap
>     videomicroscope/telescope units)

Again, this is very platform specific, what with JMF not living up to its
promises.

>
> 13) Statistical region merging segmentation:  
>     http://www.univ-ag.fr/~rnock/Articles/Drafts/tpami04-nn.pdf

I am in the middle of writing that already (would be finished if I had not
gotten side-tracked yesterday).

> 14) Fractal interpolation resizing (from the GIMP GSoC entry)
>
> 15) A unique/common segmentation interface (I have collected near 15 new
>     histogram segmentation methods that would be better put under a
>     single interface together with others already available).
>
> 16) A javascript Recorder (similar to the Macro Recorder but producing
>     javascript instead).

Why limit it to Javascript?

> 17) Virtual microscope-like image viewer.
>
> 18) HSB/Lab painting modes
>
> Is that wild enough? :-) I am sure others will have further ideas.

Heh.

Most of these ideas are too small to make even half a 3-month project,
would you not agree?

And I see only 10) 12) and 16) being Fiji-related enough for a Fiji
project, no?

Having said that, I find all of your ideas interesting!

Ciao,
Dscho

[Francesco De Comite]

hi,
Two very dummy questions (I feel a liitle bit ashamed to ask them)

I try to use the Delaunay -Voronoi plugin :
1) Where is the results window where I can output the results ?
2) If  I don't want the interactive mode, how can I tell ImageJ which
points I want to be considered ?

    I run IamgeJ under windows.

    Thanks in advance !

    F. De Comité

[dscho]

Hi,

On Sun, 29 Mar 2009, Burger Wilhelm wrote:

> To get a coarse orientation - is there is anything like a mission
> statement or white paper that lays out the strategic aims or near-term
> development goals of Fiji?

What is Fiji

In addition to an island, Fiji is an image processing package based on
ImageJ.

In case you are familiar with Linux: if ImageJ was the kernel, Fiji would
be a distribution.

Fiji enhances ImageJ by shipping with a set of plugins in a coherent menu
structure, and comprehensive documentation.

Fiji is a project aiming at simplifying

    * the installation of ImageJ
    * the usage of ImageJ
    * the usage of specific, powerful ImageJ plugins
    * the development of plugins using ImageJ

It is an Open Source project, so everybody is welcome to contribute with
plugins, patches, bug reports or "Well done" mails.

Hth,
Dscho

[dscho]

Hi,

On Sun, 29 Mar 2009, Francesco De Comité wrote:

> I try to use the Delaunay -Voronoi plugin :
> 1) Where is the results window where I can output the results ?

The results window shows up in the Window menu.

> 2) If I don't want the interactive mode, how can I tell ImageJ which
>    points I want to be considered ?

You cannot... it always considers all of them.

If you want to unconsider a point in the ROI, you have to delete it by
clicking on it with the Alt key down (on Linux, you will hold the Ctrl key
down as well, as Alt+click is reserved for, and intercepted by the Window
Manager).

If you want to have a copy of the ROI where the points are not removed,
use the ROI manager (Analyze>Tool>ROI Manager...).

Hth,
Dscho

[Prodanov Dimiter]

Hi Albert,

I am starting a project in MRI image processing with an Erasmus student but obviously more (wo)man power would be helpful.
I intend to improve the support for the Bruker format for ImageJ but am willing to collaborate with Fiji also for other things,

Best regards,

Dimiter

----------------------------
Dr. Dimiter Prodanov, MD, PhD
Biomedical Scientist
NEXT Department

E-mail: [hidden email]

aspire invent achieve

IMEC vzw  -  Register of Legal Entities Leuven VAT BE 0425.260.668    
Kapeldreef 75,  
B-3001 Leuven,
Belgium  
http://www.imec.be


<IMEC e-mail disclaimer: http://www.imec.be/wwwinter/about/email-disclaimer.shtml>
-----Original Message-----
From: Albert Cardona [mailto:[hidden email]]
Sent: Saturday 28 March 2009 15:44
Subject: Google Summer of Code

Dear all,

Fiji has been selected as a mentoring organization for the Google Summer of Code program. The program encourages undergraduate and graduate students to propose a software project and fulfill it with the help of a designated mentor. The projects span exactly 3 months and provide a stipend for the student.

We would appreciate if you can pass on this notice to any interested students.

Fiji is Just ImageJ (batteries included):
http://pacific.mpi-cbg.de

Google Summer of Code:
http://socghop.appspot.com/

Fiji ideas page for GSoC:   (potential projects for students)
http://pacific.mpi-cbg.de/wiki/index.php/SoC2009Ideas

Please direct any questions to the Fiji mailing list:
http://groups.google.com/group/fiji-devel


We are looking forward to add yet more features to Fiji!

Albert
--
Albert Cardona
http://albert.rierol.net

[Cesar Buffevant]

That's very interesting... I would like to parcipate... do yo have more information about it?

Thanks in advance.

Cesar Buffevant

--- El lun 30-mar-09, Prodanov Dimiter <[hidden email]> escribió:
De: Prodanov Dimiter <[hidden email]>
Asunto: Re: Google Summer of Code
Para: [hidden email]
Fecha: lunes, 30 de marzo de 2009, 5:55 am

Hi Albert,

I am starting a project in MRI image processing with an Erasmus student but
obviously more (wo)man power would be helpful.
I intend to improve the support for the Bruker format for ImageJ but am willing
to collaborate with Fiji also for other things,

Best regards,

Dimiter

----------------------------
Dr. Dimiter Prodanov, MD, PhD
Biomedical Scientist
NEXT Department

E-mail: [hidden email]

aspire invent achieve

IMEC vzw  -  Register of Legal Entities Leuven VAT BE 0425.260.668    
Kapeldreef 75,  
B-3001 Leuven,
Belgium  
http://www.imec.be


<IMEC e-mail disclaimer:
http://www.imec.be/wwwinter/about/email-disclaimer.shtml>
-----Original Message-----
From: Albert Cardona [mailto:[hidden email]]
Sent: Saturday 28 March 2009 15:44
Subject: Google Summer of Code

Dear all,

Fiji has been selected as a mentoring organization for the Google Summer of
Code program. The program encourages undergraduate and graduate students to
propose a software project and fulfill it with the help of a designated mentor.
The projects span exactly 3 months and provide a stipend for the student.

We would appreciate if you can pass on this notice to any interested students.

Fiji is Just ImageJ (batteries included):
http://pacific.mpi-cbg.de

Google Summer of Code:
http://socghop.appspot.com/

Fiji ideas page for GSoC:   (potential projects for students)
http://pacific.mpi-cbg.de/wiki/index.php/SoC2009Ideas

Please direct any questions to the Fiji mailing list:
http://groups.google.com/group/fiji-devel


We are looking forward to add yet more features to Fiji!

Albert
--
Albert Cardona
http://albert.rierol.net



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