Funded ImageJ development effort: Imagejdev.org

[ctrueden]

Hi everyone,

Most of you know me, but for those who don't, my name is Curtis Rueden of
the Laboratory for Optical and Computational Instrumentation (LOCI) at the
University of Wisconsin-Madison. Together with Glencoe Software and the Open
Microscopy Environment (OME) consortium, LOCI releases the Bio-Formats
library for reading microscopy file formats. Many of you know this software
as a suite of ImageJ plugins which allow you to import pixels and metadata
in more than 70 formats into ImageJ.

Recently, together with the Marine Biological Laboratory (MBL) at Woods Hole
and the Broad Institute of MIT and Harvard, LOCI submitted a successful
proposal to NIH to fund ImageJ development (for details, see
http://imagejdev.org/funding). We also have letters of support from both
Wayne Rasband and the Fiji development group (http://pacific.mpi-cbg.de/) at
the Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG).
The project is still in the early planning stage, but we have launched a
website (http://imagejdev.org/) describing the project aims, with we will
heavily expand upon in coming weeks.

As of now, the actively involved people include: Wayne Rasband of NIH;
Curtis Rueden of LOCI and Grant Harris of MBL as technical project leads;
Lee Kamentsky and Adam Fraser of Broad's CellProfiler project; an additional
3-4 LOCI full-time staff programmers being brought on board within the next
month; Fiji developers Albert Cardona, Johannes Schindelin and Stephan
Preibisch; and principal investigators Kevin Eliceiri (LOCI), Anne Carpenter
(Broad) and Rudolf Oldenbourg (MBL).

There has been a recent surge of interest in ImageJ and related projects:
ImageJ itself, Fiji/ImageJA, ImageJX, VisBio, TrakEM2, Endrov, and now of
course Imagejdev.org. There are also many other projects with at least some
interest in ImageJ as it evolves into the future: BioImageXD, CellProfiler,
FARSIGHT, Micro-Manager, OME, and many more. As such, I have CCed
participants in all of these projects, in the hope of maintaining an open
dialogue as the project moves forward. Please forward on to anyone else who
might be interested.

The mission of imagejdev.org is:
  * To lead ImageJ development with a clear vision.
  * To continue developing one official version of ImageJ to keep the user
community unified and happy.
  * To collaborate with other interested parties and institutions wherever
useful.
  * To ensure ImageJ remains useful and relevant to the broadest possible
community.
  * To maintain backwards compatibility with the current ImageJ as close to
100% as possible.
  * To avoid duplication of effort and instead leverage each others' work
wherever practical.
  * To provide a central online resource for ImageJ: program downloads, a
plugin repository, developer resources and more.

These goals will require careful planning and hard work to deliver, but will
be well worth the effort. There is great potential to use ImageJ as a
library, provide interoperability, or otherwise share code and ideas between
these efforts. Now is the time to guide ImageJ's future development.

For those interested in the technical goals, they are:

Aim I – Improve the ImageJ core architecture
   a. Separate the data model from the user interface
      * Interface-driven, MVC design. Support AWT, Swing, headless/console,
etc. [see: http://imagejdev.org/plan]
      * Grant Harris has successfully refactored ImageJ's GUI into an
interface-centric design and replaced the AWT interface with Swing. [see:
http://imagejdev.org/files/imagejdev.org/ImageJX_Mar09.pdf]
      * Raymond Martin is also actively researching this issue. [see:
http://n2.nabble.com/ImageJ-development-involvement-contributions-td4102492.html
]
   b. Introduce an extensions framework for algorithms
      * Dimiter Prodanov proposed a revised PluginPlus interface on the
ImageJX mailing list that would serve as a reasonable starting point for
this aim, though there are many other questions and issues surrounding the
architecture of such an extensions framework. [see:
http://groups.google.com/group/imagejx/browse_thread/thread/3ac4cd10a7f1ec3c
]
   c. Broaden the image data model
      * Stephan Preibisch of Fiji has developed a Generic Image Processing
Library that could serve as a foundation for the broadened image data model.

Aim II – Expand functionality by interfacing ImageJ with existing
open-source programs

Aim III – Grow community-driven development while maintaining compatibility

For more details, you can read about the aims at: http://imagejdev.org/aims.
Soon, we will also post the accepted grant proposal in its entirety.

Over the next few days, Grant Harris and I will be responding to a number of
technical discussions that have cropped up on the ImageJ and ImageJX
development lists, as well as replying to a few private emails from some of
you as well. We apologize for the delay on these replies, but it has been a
very hectic time. Moving forward, you can expect many additions to the
imagejdev.org website and associated tools, and a solidifying development
plan as we meet with colleagues and discussion the best way forward for
these efforts.

In the meantime, please let us know if you have any questions or ideas for
collaboration!

Regards,
Curtis

[Michael Schell]

Curtis, I don't have any immediate ideas or questions.  However, as (mainly) an ImageJ end user, I just want to celebrate your success on funding.  The NIH has chosen to support something truly worthy.   The money they have chosen to invest will pay back many-fold, both to the scientific community and to society as a whole.   We are witnessing the best fruits of the open source concept, and I salute you and your many excellent collaborators for making it happen.  I sort of feel sorry for the vendors of commercial software.  But not so much.

Michael

Michael J. Schell, Ph.D., CIV, USUHS
Assist. Professor
Dept. of Pharmacology
Uniformed Services University
4301 Jones Bridge Rd.
Bethesda, MD  20814-3220
tel:  [phone]
[hidden email]
Classification:  UNCLASSIFIED
Caveats: FOUO

[lechristophe]

Curtis,

These are great news. As a rather average user I'm looking forward to see
ImageJ grow and strengthen, keeping the openness and flexibility that have
always been keys to its success. I also want to add that you and LOCI have
done an incredible job with Bio-Formats. It is one of the best exemple of
what open source can bring to the scientific community. I remember a few
years ago when you were strictly tied to specific vendor software because of
proprietary formats, these days are gone thanks to Bio-Formats.
I wish you great success in refactoring ImageJ and hope I will be able to
help in some way.

Christophe

On Wed, Dec 9, 2009 at 1:16 AM, Curtis Rueden <[hidden email]> wrote:

> Hi everyone,
>
> Most of you know me, but for those who don't, my name is Curtis Rueden of
> the Laboratory for Optical and Computational Instrumentation (LOCI) at the
> University of Wisconsin-Madison. Together with Glencoe Software and the
> Open
> Microscopy Environment (OME) consortium, LOCI releases the Bio-Formats
> library for reading microscopy file formats. Many of you know this software
> as a suite of ImageJ plugins which allow you to import pixels and metadata
> in more than 70 formats into ImageJ.
>
> Recently, together with the Marine Biological Laboratory (MBL) at Woods
> Hole
> and the Broad Institute of MIT and Harvard, LOCI submitted a successful
> proposal to NIH to fund ImageJ development (for details, see
> http://imagejdev.org/funding). We also have letters of support from both
> Wayne Rasband and the Fiji development group (http://pacific.mpi-cbg.de/)
> at
> the Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG).
> The project is still in the early planning stage, but we have launched a
> website (http://imagejdev.org/) describing the project aims, with we will
> heavily expand upon in coming weeks.
>
> As of now, the actively involved people include: Wayne Rasband of NIH;
> Curtis Rueden of LOCI and Grant Harris of MBL as technical project leads;
> Lee Kamentsky and Adam Fraser of Broad's CellProfiler project; an
> additional
> 3-4 LOCI full-time staff programmers being brought on board within the next
> month; Fiji developers Albert Cardona, Johannes Schindelin and Stephan
> Preibisch; and principal investigators Kevin Eliceiri (LOCI), Anne
> Carpenter
> (Broad) and Rudolf Oldenbourg (MBL).
>
> There has been a recent surge of interest in ImageJ and related projects:
> ImageJ itself, Fiji/ImageJA, ImageJX, VisBio, TrakEM2, Endrov, and now of
> course Imagejdev.org. There are also many other projects with at least some
> interest in ImageJ as it evolves into the future: BioImageXD, CellProfiler,
> FARSIGHT, Micro-Manager, OME, and many more. As such, I have CCed
> participants in all of these projects, in the hope of maintaining an open
> dialogue as the project moves forward. Please forward on to anyone else who
> might be interested.
>
> The mission of imagejdev.org is:
>  * To lead ImageJ development with a clear vision.
>  * To continue developing one official version of ImageJ to keep the user
> community unified and happy.
>  * To collaborate with other interested parties and institutions wherever
> useful.
>  * To ensure ImageJ remains useful and relevant to the broadest possible
> community.
>  * To maintain backwards compatibility with the current ImageJ as close to
> 100% as possible.
>  * To avoid duplication of effort and instead leverage each others' work
> wherever practical.
>  * To provide a central online resource for ImageJ: program downloads, a
> plugin repository, developer resources and more.
>
> These goals will require careful planning and hard work to deliver, but
> will
> be well worth the effort. There is great potential to use ImageJ as a
> library, provide interoperability, or otherwise share code and ideas
> between
> these efforts. Now is the time to guide ImageJ's future development.
>
> For those interested in the technical goals, they are:
>
> Aim I – Improve the ImageJ core architecture
>   a. Separate the data model from the user interface
>      * Interface-driven, MVC design. Support AWT, Swing, headless/console,
> etc. [see: http://imagejdev.org/plan]
>      * Grant Harris has successfully refactored ImageJ's GUI into an
> interface-centric design and replaced the AWT interface with Swing. [see:
> http://imagejdev.org/files/imagejdev.org/ImageJX_Mar09.pdf]
>      * Raymond Martin is also actively researching this issue. [see:
>
> http://n2.nabble.com/ImageJ-development-involvement-contributions-td4102492.html
> ]
>   b. Introduce an extensions framework for algorithms
>      * Dimiter Prodanov proposed a revised PluginPlus interface on the
> ImageJX mailing list that would serve as a reasonable starting point for
> this aim, though there are many other questions and issues surrounding the
> architecture of such an extensions framework. [see:
>
> http://groups.google.com/group/imagejx/browse_thread/thread/3ac4cd10a7f1ec3c
> ]
>   c. Broaden the image data model
>      * Stephan Preibisch of Fiji has developed a Generic Image Processing
> Library that could serve as a foundation for the broadened image data
> model.
>
> Aim II – Expand functionality by interfacing ImageJ with existing
> open-source programs
>
> Aim III – Grow community-driven development while maintaining compatibility
>
> For more details, you can read about the aims at:
> http://imagejdev.org/aims.
> Soon, we will also post the accepted grant proposal in its entirety.
>
> Over the next few days, Grant Harris and I will be responding to a number
> of
> technical discussions that have cropped up on the ImageJ and ImageJX
> development lists, as well as replying to a few private emails from some of
> you as well. We apologize for the delay on these replies, but it has been a
> very hectic time. Moving forward, you can expect many additions to the
> imagejdev.org website and associated tools, and a solidifying development
> plan as we meet with colleagues and discussion the best way forward for
> these efforts.
>
> In the meantime, please let us know if you have any questions or ideas for
> collaboration!
>
> Regards,
> Curtis
>

[PabloSAguilar]

these are great news! congratulations to all!

On Dec 8, 2009, at 10:16 PM, Curtis Rueden wrote:

> Hi everyone,
>
> Most of you know me, but for those who don't, my name is Curtis  
> Rueden of
> the Laboratory for Optical and Computational Instrumentation (LOCI)  
> at the
> University of Wisconsin-Madison. Together with Glencoe Software and  
> the Open
> Microscopy Environment (OME) consortium, LOCI releases the Bio-Formats
> library for reading microscopy file formats. Many of you know this  
> software
> as a suite of ImageJ plugins which allow you to import pixels and  
> metadata
> in more than 70 formats into ImageJ.
>
> Recently, together with the Marine Biological Laboratory (MBL) at  
> Woods Hole
> and the Broad Institute of MIT and Harvard, LOCI submitted a  
> successful
> proposal to NIH to fund ImageJ development (for details, see
> http://imagejdev.org/funding). We also have letters of support from  
> both
> Wayne Rasband and the Fiji development group (http://pacific.mpi- 
> cbg.de/) at
> the Max Planck Institute of Molecular Cell Biology and Genetics  
> (MPI-CBG).
> The project is still in the early planning stage, but we have  
> launched a
> website (http://imagejdev.org/) describing the project aims, with  
> we will
> heavily expand upon in coming weeks.
>
> As of now, the actively involved people include: Wayne Rasband of NIH;
> Curtis Rueden of LOCI and Grant Harris of MBL as technical project  
> leads;
> Lee Kamentsky and Adam Fraser of Broad's CellProfiler project; an  
> additional
> 3-4 LOCI full-time staff programmers being brought on board within  
> the next
> month; Fiji developers Albert Cardona, Johannes Schindelin and Stephan
> Preibisch; and principal investigators Kevin Eliceiri (LOCI), Anne  
> Carpenter
> (Broad) and Rudolf Oldenbourg (MBL).
>
> There has been a recent surge of interest in ImageJ and related  
> projects:
> ImageJ itself, Fiji/ImageJA, ImageJX, VisBio, TrakEM2, Endrov, and  
> now of
> course Imagejdev.org. There are also many other projects with at  
> least some
> interest in ImageJ as it evolves into the future: BioImageXD,  
> CellProfiler,
> FARSIGHT, Micro-Manager, OME, and many more. As such, I have CCed
> participants in all of these projects, in the hope of maintaining  
> an open
> dialogue as the project moves forward. Please forward on to anyone  
> else who
> might be interested.
>
> The mission of imagejdev.org is:
>   * To lead ImageJ development with a clear vision.
>   * To continue developing one official version of ImageJ to keep  
> the user
> community unified and happy.
>   * To collaborate with other interested parties and institutions  
> wherever
> useful.
>   * To ensure ImageJ remains useful and relevant to the broadest  
> possible
> community.
>   * To maintain backwards compatibility with the current ImageJ as  
> close to
> 100% as possible.
>   * To avoid duplication of effort and instead leverage each  
> others' work
> wherever practical.
>   * To provide a central online resource for ImageJ: program  
> downloads, a
> plugin repository, developer resources and more.
>
> These goals will require careful planning and hard work to deliver,  
> but will
> be well worth the effort. There is great potential to use ImageJ as a
> library, provide interoperability, or otherwise share code and  
> ideas between
> these efforts. Now is the time to guide ImageJ's future development.
>
> For those interested in the technical goals, they are:
>
> Aim I – Improve the ImageJ core architecture
>    a. Separate the data model from the user interface
>       * Interface-driven, MVC design. Support AWT, Swing, headless/
> console,
> etc. [see: http://imagejdev.org/plan]
>       * Grant Harris has successfully refactored ImageJ's GUI into an
> interface-centric design and replaced the AWT interface with Swing.  
> [see:
> http://imagejdev.org/files/imagejdev.org/ImageJX_Mar09.pdf]
>       * Raymond Martin is also actively researching this issue. [see:
> http://n2.nabble.com/ImageJ-development-involvement-contributions- 
> td4102492.html
> ]
>    b. Introduce an extensions framework for algorithms
>       * Dimiter Prodanov proposed a revised PluginPlus interface on  
> the
> ImageJX mailing list that would serve as a reasonable starting  
> point for
> this aim, though there are many other questions and issues  
> surrounding the
> architecture of such an extensions framework. [see:
> http://groups.google.com/group/imagejx/browse_thread/thread/ 
> 3ac4cd10a7f1ec3c
> ]
>    c. Broaden the image data model
>       * Stephan Preibisch of Fiji has developed a Generic Image  
> Processing
> Library that could serve as a foundation for the broadened image  
> data model.
>
> Aim II – Expand functionality by interfacing ImageJ with existing
> open-source programs
>
> Aim III – Grow community-driven development while maintaining  
> compatibility
>
> For more details, you can read about the aims at: http://
> imagejdev.org/aims.
> Soon, we will also post the accepted grant proposal in its entirety.
>
> Over the next few days, Grant Harris and I will be responding to a  
> number of
> technical discussions that have cropped up on the ImageJ and ImageJX
> development lists, as well as replying to a few private emails from  
> some of
> you as well. We apologize for the delay on these replies, but it  
> has been a
> very hectic time. Moving forward, you can expect many additions to the
> imagejdev.org website and associated tools, and a solidifying  
> development
> plan as we meet with colleagues and discussion the best way forward  
> for
> these efforts.
>
> In the meantime, please let us know if you have any questions or  
> ideas for
> collaboration!
>
> Regards,
> Curtis

Pablo S. Aguilar, PhD

Institut Pasteur de Montevideo
2020 Mataojo
Montevideo, 11400
Uruguay

[hidden email]

Ph#: 59-82-522-0910 ext. 155
Fx#: 59-82-522-4185

[nckrzan]

Hi,

do You known some pluggin for the analysis of surface tension - pendant
drop method?

Regards
Marcel Krzan

[Daniel Hornung]

Marcel Krzan PhD wrote:
> Hi,
>
> do You known some pluggin for the analysis of surface tension - pendant
> drop method?
I don't know about the pendant drop method, but maybe you could modify this plugin?
http://bigwww.epfl.ch/demo/dropanalysis/

HTH,
Daniel Hornung

[Raymond Martin-2]

Hi,

Documentation indicates for version 1.43m:

"Results tables (in tab-delimited text format) with an ".xls" extension can be
opened using File>Open and drag and drop."

I believe the more appropriate format is comma-separated values (CSV)
with a .csv extension (tab-delimited format is considered one subtype of CSV).
CSV is more of a standard format that almost any spreadsheet application
can import or export.

Regards,

Raymond

[dscho]

Hi,

On Thu, 10 Dec 2009, Raymond Martin wrote:

> Documentation indicates for version 1.43m:
>
> "Results tables (in tab-delimited text format) with an ".xls" extension
> can be opened using File>Open and drag and drop."
>
> I believe the more appropriate format is comma-separated values (CSV)
> with a .csv extension (tab-delimited format is considered one subtype of
> CSV).

As you probably guessed: the extension .xls does not mean that ImageJ
can open Excel files.  The files are still interpreted as tab-separated
values.

Ciao,
Johannes

[Prodanov Dimiter]

Indeed, Let's all contribute!

Dimiter

-----Original Message-----
From: Pablo S. Aguilar [mailto:[hidden email]]
Sent: Wednesday 9 December 2009 09:54
Subject: Re: Funded ImageJ development effort: Imagejdev.org

these are great news! congratulations to all!

On Dec 8, 2009, at 10:16 PM, Curtis Rueden wrote:

> Hi everyone,
>
> Most of you know me, but for those who don't, my name is Curtis  
> Rueden of
> the Laboratory for Optical and Computational Instrumentation (LOCI)  
> at the
> University of Wisconsin-Madison. Together with Glencoe Software and  
> the Open
> Microscopy Environment (OME) consortium, LOCI releases the Bio-Formats
> library for reading microscopy file formats. Many of you know this  
> software
> as a suite of ImageJ plugins which allow you to import pixels and  
> metadata
> in more than 70 formats into ImageJ.
>
> Recently, together with the Marine Biological Laboratory (MBL) at  
> Woods Hole
> and the Broad Institute of MIT and Harvard, LOCI submitted a  
> successful
> proposal to NIH to fund ImageJ development (for details, see
> http://imagejdev.org/funding). We also have letters of support from  
> both
> Wayne Rasband and the Fiji development group (http://pacific.mpi- 
> cbg.de/) at
> the Max Planck Institute of Molecular Cell Biology and Genetics  
> (MPI-CBG).
> The project is still in the early planning stage, but we have  
> launched a
> website (http://imagejdev.org/) describing the project aims, with  
> we will
> heavily expand upon in coming weeks.
>
> As of now, the actively involved people include: Wayne Rasband of NIH;
> Curtis Rueden of LOCI and Grant Harris of MBL as technical project  
> leads;
> Lee Kamentsky and Adam Fraser of Broad's CellProfiler project; an  
> additional
> 3-4 LOCI full-time staff programmers being brought on board within  
> the next
> month; Fiji developers Albert Cardona, Johannes Schindelin and Stephan
> Preibisch; and principal investigators Kevin Eliceiri (LOCI), Anne  
> Carpenter
> (Broad) and Rudolf Oldenbourg (MBL).
>
> There has been a recent surge of interest in ImageJ and related  
> projects:
> ImageJ itself, Fiji/ImageJA, ImageJX, VisBio, TrakEM2, Endrov, and  
> now of
> course Imagejdev.org. There are also many other projects with at  
> least some
> interest in ImageJ as it evolves into the future: BioImageXD,  
> CellProfiler,
> FARSIGHT, Micro-Manager, OME, and many more. As such, I have CCed
> participants in all of these projects, in the hope of maintaining  
> an open
> dialogue as the project moves forward. Please forward on to anyone  
> else who
> might be interested.
>
> The mission of imagejdev.org is:
>   * To lead ImageJ development with a clear vision.
>   * To continue developing one official version of ImageJ to keep  
> the user
> community unified and happy.
>   * To collaborate with other interested parties and institutions  
> wherever
> useful.
>   * To ensure ImageJ remains useful and relevant to the broadest  
> possible
> community.
>   * To maintain backwards compatibility with the current ImageJ as  
> close to
> 100% as possible.
>   * To avoid duplication of effort and instead leverage each  
> others' work
> wherever practical.
>   * To provide a central online resource for ImageJ: program  
> downloads, a
> plugin repository, developer resources and more.
>
> These goals will require careful planning and hard work to deliver,  
> but will
> be well worth the effort. There is great potential to use ImageJ as a
> library, provide interoperability, or otherwise share code and  
> ideas between
> these efforts. Now is the time to guide ImageJ's future development.
>
> For those interested in the technical goals, they are:
>
> Aim I - Improve the ImageJ core architecture
>    a. Separate the data model from the user interface
>       * Interface-driven, MVC design. Support AWT, Swing, headless/
> console,
> etc. [see: http://imagejdev.org/plan]
>       * Grant Harris has successfully refactored ImageJ's GUI into an
> interface-centric design and replaced the AWT interface with Swing.  
> [see:
> http://imagejdev.org/files/imagejdev.org/ImageJX_Mar09.pdf]
>       * Raymond Martin is also actively researching this issue. [see:
> http://n2.nabble.com/ImageJ-development-involvement-contributions- 
> td4102492.html
> ]
>    b. Introduce an extensions framework for algorithms
>       * Dimiter Prodanov proposed a revised PluginPlus interface on  
> the
> ImageJX mailing list that would serve as a reasonable starting  
> point for
> this aim, though there are many other questions and issues  
> surrounding the
> architecture of such an extensions framework. [see:
> http://groups.google.com/group/imagejx/browse_thread/thread/ 
> 3ac4cd10a7f1ec3c
> ]
>    c. Broaden the image data model
>       * Stephan Preibisch of Fiji has developed a Generic Image  
> Processing
> Library that could serve as a foundation for the broadened image  
> data model.
>
> Aim II - Expand functionality by interfacing ImageJ with existing
> open-source programs
>
> Aim III - Grow community-driven development while maintaining  
> compatibility
>
> For more details, you can read about the aims at: http://
> imagejdev.org/aims.
> Soon, we will also post the accepted grant proposal in its entirety.
>
> Over the next few days, Grant Harris and I will be responding to a  
> number of
> technical discussions that have cropped up on the ImageJ and ImageJX
> development lists, as well as replying to a few private emails from  
> some of
> you as well. We apologize for the delay on these replies, but it  
> has been a
> very hectic time. Moving forward, you can expect many additions to the
> imagejdev.org website and associated tools, and a solidifying  
> development
> plan as we meet with colleagues and discussion the best way forward  
> for
> these efforts.
>
> In the meantime, please let us know if you have any questions or  
> ideas for
> collaboration!
>
> Regards,
> Curtis

Pablo S. Aguilar, PhD

Institut Pasteur de Montevideo
2020 Mataojo
Montevideo, 11400
Uruguay

[hidden email]

Ph#: 59-82-522-0910 ext. 155
Fx#: 59-82-522-4185

[Wayne Rasband]

 > Documentation indicates for version 1.43m:
 >
 > "Results tables (in tab-delimited text format) with an
 > ".xls" extension can be opened using File>Open and drag and
 > drop."
 >
 > I believe the more appropriate format is comma-separated
 > values (CSV) with a .csv extension (tab-delimited format is
 > considered one subtype of CSV). CSV is more of a standard
 > format that almost any spreadsheet application can import
 > or export.

The ImageJ 1.43n daily build adds support for saving results tables as
.csv (comma-separated values) files and for opening them using drag and
drop. You can make ".csv" the default extension for saving tables in
Edit>Options>Input-Output.

-wayne