ImageJ 2.0.0-beta1 released

Previous Topic Next Topic
 
classic Classic list List threaded Threaded
19 messages Options
Reply | Threaded
Open this post in threaded view
|

ImageJ 2.0.0-beta1 released

ctrueden
Hi everyone,

Today, the ImageJDev team is proud to release the first beta of ImageJ2,
version 2.0.0-beta1!

ImageJ 2.0.0-beta1 is a "beta"-quality release, meaning the code is not
finished. The design is more stable than before but still subject to change
until the final 2.0.0 release. It is recommended that people continue to
use ImageJ v1.x for critical work.

The ImageJ2 user interface is modeled after ImageJ v1.x as much as
possible. However, under the hood, ImageJ2 is a complete redesign of
ImageJ. It provides backward compatibility with older versions of ImageJ by
bundling the latest v1.x code and translating between "legacy" and "modern"
image structures.

The beta still has many bugs and limitations, but we have achieved several
substantial milestones:

   - Support for most ImageJ1 plugins and macros
   - Many new pixel types (thanks to ImgLib2)
   - Multidimensional data beyond 5D (thanks to ImgLib2)
   - Import and export of all SCIFIO-supported file formats
   - Improved region of interest (ROI) tools
   - Truly headless: image processing is separate from user interface
   - Automatic updates: once you download beta1, ImageJ can update itself
   - Easily install additional plugins, including Fiji (over 350 plugins!)
   - 175 new and/or reimplemented core ImageJ2 plugins so far
   - 125+ bugs fixed


Many legacy ImageJ plugins and macros work; many others do not. There are
still many bugs. In particular, there are a few issues specifically
regarding 2.0.0-beta1:

   - On Windows & Linux, you must have Java already installed; ImageJ2 is
   not bundled with Java, nor will it download it for you.
   - On Mac OS X 10.5 Leopard, there is a bug that prevents ImageJ2 from
   launching successfully. This bug will be fixed in the next beta release,
   and is already fixed in the development version.
   - On Windows, when ImageJ2 first starts, a console message ("Falling
   back to system Java") appears, which is merely informative and is safe to
   ignore. This message will no longer be displayed in the next beta release,
   and is already fixed in the development version.


For further details on this release, including a discussion of new
features, please see our blog post:
  http://developer.imagej.net/2012/04/09/imagej-v200-beta1

You can download the release from:
  http://developer.imagej.net/downloads

That page also has a table of planned future releases and roadmap links for
the project.

For more details on the ImageJ developments, see the web site at:
  http://developer.imagej.net/

Regards,
Curtis Rueden
ImageJDev project lead
Laboratory for Optical and Computational Instrumentation
University of Wisconsin-Madison
Reply | Threaded
Open this post in threaded view
|

Re: [fiji-devel] ImageJ 2.0.0-beta1 released

Albert Cardona-2
Adding myself to the cheer! Great milestone! Now is the time to use
it, report, and polish!

Albert

--
http://albert.rierol.net
http://www.ini.uzh.ch/~acardona/
Reply | Threaded
Open this post in threaded view
|

Re: [fiji-devel] ImageJ 2.0.0-beta1 released

Leon Espinosa-3
Good news !!

What is the right list to report ? This list with a specific thread ?



thank you all for these amazing tools (IJ, FIJI, IJ2, CP...) !!!
Leon Espinosa

Le 10 avr. 2012 à 16:39, Albert Cardona a écrit :

> Adding myself to the cheer! Great milestone! Now is the time to use
> it, report, and polish!
>
> Albert
>
> --
> http://albert.rierol.net
> http://www.ini.uzh.ch/~acardona/
Reply | Threaded
Open this post in threaded view
|

Re: [fiji-devel] ImageJ 2.0.0-beta1 released

ctrueden
Hi Leon,


What is the right list to report ? This list with a specific thread ?
>

For beta2, we are working on a "Report a bug" mechanism that will work from
within ImageJ2, similar to Fiji's, which will file a ticket into the Trac
system (http://trac.imagej.net/).

In the meantime, using this list is fine, as is imagej-devel—whichever is
easier for you!

Thanks,
Curtis


On Tue, Apr 10, 2012 at 11:06 AM, Leon Espinosa
<[hidden email]>wrote:

> Good news !!
>
> What is the right list to report ? This list with a specific thread ?
>
>
>
> thank you all for these amazing tools (IJ, FIJI, IJ2, CP...) !!!
> Leon Espinosa
>
> Le 10 avr. 2012 à 16:39, Albert Cardona a écrit :
>
> > Adding myself to the cheer! Great milestone! Now is the time to use
> > it, report, and polish!
> >
> > Albert
> >
> > --
> > http://albert.rierol.net
> > http://www.ini.uzh.ch/~acardona/
>
Reply | Threaded
Open this post in threaded view
|

ImageJ 2.0.0-beta1 (minimum requirements)

Herbie-6
Dear ImageJ-2 architects!
Dear Albert!

First of all, congratulations for the beta and many thanks for your work!

Second, I should like to report that apparently
there is a problem with launching ImageJ-2 under
OSX-Tiger (10.4.11), i.e. not only, as mentioned,
with OSX-Leopard (10.5.x).

Hence, I should like to suggest a note on the
download web-page that deals with the minimum
requirements.

Thanks

Herbie
_______________________________

>Hi Leon,
>What is the right list to report ? This list with a specific thread ?
>>
>For beta2, we are working on a "Report a bug" mechanism that will work from
>within ImageJ2, similar to Fiji's, which will file a ticket into the Trac
>system (http://trac.imagej.net/).
>
>In the meantime, using this list is fine, as is imagej-devel-whichever is
>easier for you!
>
>Thanks,
>Curtis
>
>
>On Tue, Apr 10, 2012 at 11:06 AM, Leon Espinosa
><[hidden email]>wrote:
>
>>  Good news !!
>>
>  > What is the right list to report ? This list with a specific thread ?
>>
>  >thank you all for these amazing tools (IJ, FIJI, IJ2, CP...) !!!
>  > Leon Espinosa
>>
>>  Le 10 avr. 2012 à 16:39, Albert Cardona a écrit :
>>
>>  > Adding myself to the cheer! Great milestone! Now is the time to use
>>  > it, report, and polish!
>>  >
>>  > Albert
>>  >
>>  > --
>>  > http://albert.rierol.net
>  > > http://www.ini.uzh.ch/~acardona/
Reply | Threaded
Open this post in threaded view
|

Re: [fiji-devel] ImageJ 2.0.0-beta1 released

Stephan Saalfeld
In reply to this post by ctrueden
Congratulations to the ImageJDev team!

All the best,
Stephan




On Mon, 2012-04-09 at 14:07 -0500, Curtis Rueden wrote:

> Hi everyone,
>
> Today, the ImageJDev team is proud to release the first beta of ImageJ2,
> version 2.0.0-beta1!
>
> ImageJ 2.0.0-beta1 is a "beta"-quality release, meaning the code is not
> finished. The design is more stable than before but still subject to change
> until the final 2.0.0 release. It is recommended that people continue to
> use ImageJ v1.x for critical work.
>
> The ImageJ2 user interface is modeled after ImageJ v1.x as much as
> possible. However, under the hood, ImageJ2 is a complete redesign of
> ImageJ. It provides backward compatibility with older versions of ImageJ by
> bundling the latest v1.x code and translating between "legacy" and "modern"
> image structures.
>
> The beta still has many bugs and limitations, but we have achieved several
> substantial milestones:
>
>    - Support for most ImageJ1 plugins and macros
>    - Many new pixel types (thanks to ImgLib2)
>    - Multidimensional data beyond 5D (thanks to ImgLib2)
>    - Import and export of all SCIFIO-supported file formats
>    - Improved region of interest (ROI) tools
>    - Truly headless: image processing is separate from user interface
>    - Automatic updates: once you download beta1, ImageJ can update itself
>    - Easily install additional plugins, including Fiji (over 350 plugins!)
>    - 175 new and/or reimplemented core ImageJ2 plugins so far
>    - 125+ bugs fixed
>
>
> Many legacy ImageJ plugins and macros work; many others do not. There are
> still many bugs. In particular, there are a few issues specifically
> regarding 2.0.0-beta1:
>
>    - On Windows & Linux, you must have Java already installed; ImageJ2 is
>    not bundled with Java, nor will it download it for you.
>    - On Mac OS X 10.5 Leopard, there is a bug that prevents ImageJ2 from
>    launching successfully. This bug will be fixed in the next beta release,
>    and is already fixed in the development version.
>    - On Windows, when ImageJ2 first starts, a console message ("Falling
>    back to system Java") appears, which is merely informative and is safe to
>    ignore. This message will no longer be displayed in the next beta release,
>    and is already fixed in the development version.
>
>
> For further details on this release, including a discussion of new
> features, please see our blog post:
>   http://developer.imagej.net/2012/04/09/imagej-v200-beta1
>
> You can download the release from:
>   http://developer.imagej.net/downloads
>
> That page also has a table of planned future releases and roadmap links for
> the project.
>
> For more details on the ImageJ developments, see the web site at:
>   http://developer.imagej.net/
>
> Regards,
> Curtis Rueden
> ImageJDev project lead
> Laboratory for Optical and Computational Instrumentation
> University of Wisconsin-Madison
>
Reply | Threaded
Open this post in threaded view
|

Re: ImageJ 2.0.0-beta1 (minimum requirements)

dscho
In reply to this post by Herbie-6
Dear Herbie,

On Wed, 11 Apr 2012, Herbie wrote:

> Second, I should like to report that apparently there is a problem with
> launching ImageJ-2 under OSX-Tiger (10.4.11), i.e. not only, as
> mentioned, with OSX-Leopard (10.5.x).

Yes, the problem with Tiger is actually exactly the same as that with
Leopard (and for that matter, also Panther -- 10.3.x): due to an oversight
when porting the Fiji Launcher into the ImageJ code base, the executable
did not work correctly on any MacOSX version prior to 10.6.x.

Sorry about that!

But as Curtis said, the problem has been identified and fixed and beta2
will work correctly on above-mentioned MacOSX versions!

Ciao,
Johannes
Reply | Threaded
Open this post in threaded view
|

make text larger in Outlines from Analyze Particles?

Franklin Shaffer-2
I'm using Analyze Particles tool in ImageJ with the "Show Outlines" options.  The text in the Outlines images is very small.  
Does anyone know how to make the text larger in the Outlines image?

I tried increasing the text size in Edit-->Options-->Fonts but it did not change the size of text in the Outlines image.

Thanks!
Frank

Franklin Shaffer
Senior Research Engineer
USDOE National Energy Technology Laboratory
Computational Science Division
Mail Stop 84-202
626 Cochran's Mill Road
Pittsburgh, PA 15236
 
[hidden email]
Office:  412-386-5964
Cell:  724-970-7262



Franklin Shaffer.vcf (403 bytes) Download Attachment
Reply | Threaded
Open this post in threaded view
|

Re: ImageJ 2.0.0-beta1 released

Arindam Chatterjee
In reply to this post by ctrueden
Congratulations to the team!

One issue that I have faced with the previous version has been a copy-paste
of CF_DIB format images (The image gets distorted). I have shared this
earlier with the list on the current version of ImageJ, but wondering if it
is being tackled in this version?

Thanks!
Arindam

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Curtis
Rueden
Sent: Monday, April 09, 2012 2:07 PM
To: [hidden email]
Subject: ImageJ 2.0.0-beta1 released

Hi everyone,

Today, the ImageJDev team is proud to release the first beta of ImageJ2,
version 2.0.0-beta1!

ImageJ 2.0.0-beta1 is a "beta"-quality release, meaning the code is not
finished. The design is more stable than before but still subject to change
until the final 2.0.0 release. It is recommended that people continue to use
ImageJ v1.x for critical work.


The ImageJ2 user interface is modeled after ImageJ v1.x as much as possible.
However, under the hood, ImageJ2 is a complete redesign of ImageJ. It
provides backward compatibility with older versions of ImageJ by bundling
the latest v1.x code and translating between "legacy" and "modern"
image structures.

The beta still has many bugs and limitations, but we have achieved several
substantial milestones:

   - Support for most ImageJ1 plugins and macros
   - Many new pixel types (thanks to ImgLib2)
   - Multidimensional data beyond 5D (thanks to ImgLib2)
   - Import and export of all SCIFIO-supported file formats
   - Improved region of interest (ROI) tools
   - Truly headless: image processing is separate from user interface
   - Automatic updates: once you download beta1, ImageJ can update itself
   - Easily install additional plugins, including Fiji (over 350 plugins!)
   - 175 new and/or reimplemented core ImageJ2 plugins so far
   - 125+ bugs fixed


Many legacy ImageJ plugins and macros work; many others do not. There are
still many bugs. In particular, there are a few issues specifically
regarding 2.0.0-beta1:

   - On Windows & Linux, you must have Java already installed; ImageJ2 is
   not bundled with Java, nor will it download it for you.
   - On Mac OS X 10.5 Leopard, there is a bug that prevents ImageJ2 from
   launching successfully. This bug will be fixed in the next beta release,
   and is already fixed in the development version.
   - On Windows, when ImageJ2 first starts, a console message ("Falling
   back to system Java") appears, which is merely informative and is safe to
   ignore. This message will no longer be displayed in the next beta
release,
   and is already fixed in the development version.


For further details on this release, including a discussion of new features,
please see our blog post:
  http://developer.imagej.net/2012/04/09/imagej-v200-beta1

You can download the release from:
  http://developer.imagej.net/downloads

That page also has a table of planned future releases and roadmap links for
the project.

For more details on the ImageJ developments, see the web site at:
  http://developer.imagej.net/

Regards,
Curtis Rueden
ImageJDev project lead
Laboratory for Optical and Computational Instrumentation University of
Wisconsin-Madison
Reply | Threaded
Open this post in threaded view
|

Re: make text larger in Outlines from Analyze Particles?

Rasband, Wayne (NIH/NIMH) [E]
In reply to this post by Franklin Shaffer-2
On Apr 11, 2012, at 11:52 AM, Franklin Shaffer wrote:

> I'm using Analyze Particles tool in ImageJ with the "Show Outlines" options.  The text in the Outlines images is very small.  
> Does anyone know how to make the text larger in the Outlines image?
>
> I tried increasing the text size in Edit-->Options-->Fonts but it did not change the size of text in the Outlines image.

Use the "Overlay Outlines" option. Then you will be able to change the text size, color and background in the Image>Overlay>Labels dialog box.

-wayne
Reply | Threaded
Open this post in threaded view
|

Re: make text larger in Outlines from Analyze Particles?

Franklin Shaffer-2
Hi Wayne,
I'm using Analyze Particles on a sequence of images.  If I select "Show Outlines" it overlays all of the outlines in the entire sequence onto each image.  But I can adjust the size of the text.
What I need to do is select "Outlines" then increase the text size.  Is there any way to do that?
Thank you!
Frank

>>> "Rasband, Wayne (NIH/NIMH) [E]" <[hidden email]> 4/11/2012 1:58 PM >>>
On Apr 11, 2012, at 11:52 AM, Franklin Shaffer wrote:

> I'm using Analyze Particles tool in ImageJ with the "Show Outlines" options.  The text in the Outlines images is very small.  
> Does anyone know how to make the text larger in the Outlines image?
>
> I tried increasing the text size in Edit-->Options-->Fonts but it did not change the size of text in the Outlines image.

Use the "Overlay Outlines" option. Then you will be able to change the text size, color and background in the Image>Overlay>Labels dialog box.

-wayne
Reply | Threaded
Open this post in threaded view
|

ImageJ 2.0.0-beta1 16 bit conversion

Knecht, David
In reply to this post by ctrueden
I am trying to use the new release of ImageJ 2.0 for the first time.  I am trying to convert a series of 16 bit images to 8 bit but I now have a choice of signed and unsigned.  I don't know what that means and the difference in order to choose.  Can you clarify?  Thanks- Dave

On Apr 10, 2012, at 9:53 PM, Curtis Rueden wrote:

> Hi Leon,
>
>
> What is the right list to report ? This list with a specific thread ?
>>
>
> For beta2, we are working on a "Report a bug" mechanism that will work from
> within ImageJ2, similar to Fiji's, which will file a ticket into the Trac
> system (http://trac.imagej.net/).
>
> In the meantime, using this list is fine, as is imagej-devel—whichever is
> easier for you!
>
> Thanks,
> Curtis
>
>
> On Tue, Apr 10, 2012 at 11:06 AM, Leon Espinosa
> <[hidden email]>wrote:
>
>> Good news !!
>>
>> What is the right list to report ? This list with a specific thread ?
>>
>>
>>
>> thank you all for these amazing tools (IJ, FIJI, IJ2, CP...) !!!
>> Leon Espinosa
>>
>> Le 10 avr. 2012 à 16:39, Albert Cardona a écrit :
>>
>>> Adding myself to the cheer! Great milestone! Now is the time to use
>>> it, report, and polish!
>>>
>>> Albert
>>>
>>> --
>>> http://albert.rierol.net
>>> http://www.ini.uzh.ch/~acardona/
>>

Visiting Professor David Knecht
Beatson Institute for Cancer Research
University of Glasgow
Switchback Road, Bearsden
Glasgow Scotland G61 1BD
UK
Reply | Threaded
Open this post in threaded view
|

Re: ImageJ 2.0.0-beta1 16 bit conversion

dscho
Hi David,

On Mon, 16 Apr 2012, David Knecht wrote:

> I am trying to use the new release of ImageJ 2.0 for the first time.  I
> am trying to convert a series of 16 bit images to 8 bit but I now have a
> choice of signed and unsigned.  I don't know what that means and the
> difference in order to choose.  Can you clarify?  Thanks- Dave

It simply means that the range of values is no longer restricted to
0..65535 (which is unsigned; you cannot have negative numbers) but from
-32768..32767 (where numbers can be signed, but the upper bound is now
lower). Both ranges have an entropy of 16 bit, hence the name.

So if you need to stay compatible with IJ1 plugins (which have no notion
of signed 16-bit), please convert to unsigned 16-bit.

Ciao,
Johannes
Reply | Threaded
Open this post in threaded view
|

Re: ImageJ 2.0.0-beta1 released

Yang YU
In reply to this post by Arindam Chatterjee
Congratulations!

Where can I find the headless usage tutorial?

For example, if I use ImageJ to convert .lsm to .tif, how to do it in
headless way?

Thanks,
Yang



On Wed, Apr 11, 2012 at 12:10 PM, Arindam Chatterjee <[hidden email]>wrote:

> Congratulations to the team!
>
> One issue that I have faced with the previous version has been a copy-paste
> of CF_DIB format images (The image gets distorted). I have shared this
> earlier with the list on the current version of ImageJ, but wondering if it
> is being tackled in this version?
>
> Thanks!
> Arindam
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Curtis
> Rueden
> Sent: Monday, April 09, 2012 2:07 PM
> To: [hidden email]
> Subject: ImageJ 2.0.0-beta1 released
>
> Hi everyone,
>
> Today, the ImageJDev team is proud to release the first beta of ImageJ2,
> version 2.0.0-beta1!
>
> ImageJ 2.0.0-beta1 is a "beta"-quality release, meaning the code is not
> finished. The design is more stable than before but still subject to change
> until the final 2.0.0 release. It is recommended that people continue to
> use
> ImageJ v1.x for critical work.
>
>
> The ImageJ2 user interface is modeled after ImageJ v1.x as much as
> possible.
> However, under the hood, ImageJ2 is a complete redesign of ImageJ. It
> provides backward compatibility with older versions of ImageJ by bundling
> the latest v1.x code and translating between "legacy" and "modern"
> image structures.
>
> The beta still has many bugs and limitations, but we have achieved several
> substantial milestones:
>
>   - Support for most ImageJ1 plugins and macros
>   - Many new pixel types (thanks to ImgLib2)
>   - Multidimensional data beyond 5D (thanks to ImgLib2)
>   - Import and export of all SCIFIO-supported file formats
>   - Improved region of interest (ROI) tools
>   - Truly headless: image processing is separate from user interface
>   - Automatic updates: once you download beta1, ImageJ can update itself
>   - Easily install additional plugins, including Fiji (over 350 plugins!)
>   - 175 new and/or reimplemented core ImageJ2 plugins so far
>   - 125+ bugs fixed
>
>
> Many legacy ImageJ plugins and macros work; many others do not. There are
> still many bugs. In particular, there are a few issues specifically
> regarding 2.0.0-beta1:
>
>   - On Windows & Linux, you must have Java already installed; ImageJ2 is
>   not bundled with Java, nor will it download it for you.
>   - On Mac OS X 10.5 Leopard, there is a bug that prevents ImageJ2 from
>   launching successfully. This bug will be fixed in the next beta release,
>   and is already fixed in the development version.
>   - On Windows, when ImageJ2 first starts, a console message ("Falling
>   back to system Java") appears, which is merely informative and is safe to
>   ignore. This message will no longer be displayed in the next beta
> release,
>   and is already fixed in the development version.
>
>
> For further details on this release, including a discussion of new
> features,
> please see our blog post:
>  http://developer.imagej.net/2012/04/09/imagej-v200-beta1
>
> You can download the release from:
>  http://developer.imagej.net/downloads
>
> That page also has a table of planned future releases and roadmap links for
> the project.
>
> For more details on the ImageJ developments, see the web site at:
>  http://developer.imagej.net/
>
> Regards,
> Curtis Rueden
> ImageJDev project lead
> Laboratory for Optical and Computational Instrumentation University of
> Wisconsin-Madison
>
Reply | Threaded
Open this post in threaded view
|

Re: ImageJ 2.0.0-beta1 released

dscho
Dear Yang,

On Mon, 16 Apr 2012, Yang YU wrote:

> Congratulations!

Thanks!

> Where can I find the headless usage tutorial?

At this point in the beta phase, we do not target headless usage, although
it is being worked on actively. Read: at the moment, there is
unfortunately no end-user interface to perform the conversion you mention:

> For example, if I use ImageJ to convert .lsm to .tif, how to do it in
> headless way?

However, headless operations are certainly one of the big aims of the
project. I will ask you to test when we have an end-user command line
interface ;-)

Ciao,
Johannes
Reply | Threaded
Open this post in threaded view
|

Re: ImageJ 2.0.0-beta1 released

Leon Espinosa-3
Dear developers, there are some problems with the display that I have note in both Mac OS 10.6 and WXP :

- Filters preview shows nothing (but the filter works fine after "ok")

- The Adjust Threshold window is not showing the overlay of selected values (red, Over/under and B/W) But the particles analyzer works if it is launched after a blind (or auto) settings (the same for "Window Level" adjustment)

- "blobs.gif" open with inverted LUT but it this this is not show in hte info bar "(256x254; unsigned-8bit; 63,5 KiB;)" instead "(256x254; unsigned-8bit (inverting LUT) ; 63,5 KiB;)"

- The display refreshing is very slow (for example 2-3 seconds to display "duplicate" blobs.gif).

- "Duplicate" command duplicates the whole image not only the selection.

- "undo" is not working after a '"crop" command

-  The IJ1 macro record doesn't work and the IJ2 says strange commands :
Started recording...
  >> Module: imagej.legacy.plugin.LegacyPlugin
    context = imagej.ImageJ@224478fe  {ImageJ}
    imageDisplayService = imagej.data.display.DefaultImageDisplayService@24cc17f1  {ImageDisplayService}
    legacyService = imagej.legacy.LegacyService@11a5ee7c  {LegacyService}
    uiService = imagej.ui.UIService@4c53ccba  {UIService}

Thank you...


All the best,

Leon






Le 17 avr. 2012 à 00:37, Johannes Schindelin a écrit :

> Dear Yang,
>
> On Mon, 16 Apr 2012, Yang YU wrote:
>
>> Congratulations!
>
> Thanks!
>
>> Where can I find the headless usage tutorial?
>
> At this point in the beta phase, we do not target headless usage, although
> it is being worked on actively. Read: at the moment, there is
> unfortunately no end-user interface to perform the conversion you mention:
>
>> For example, if I use ImageJ to convert .lsm to .tif, how to do it in
>> headless way?
>
> However, headless operations are certainly one of the big aims of the
> project. I will ask you to test when we have an end-user command line
> interface ;-)
>
> Ciao,
> Johannes
Reply | Threaded
Open this post in threaded view
|

Re: ImageJ 2.0.0-beta1 released

Barry DeZonia
Hi Leon,

Thank you for trying the ImageJ2 beta and reporting these issues. I have
updated existing tickets and hatched new ones as needed (listed below). If
you would like to be CCed on these tickets (such that you are updated when
their status changes) let me know. I thought the reply email address might
be a list.

The following issues have existing tickets:

Improve undo/redo functionality

http://code.imagej.net/trac/imagej/ticket/13


Rewrite interactive plugins

http://code.imagej.net/trac/imagej/ticket/981


The following tickets were hatched:


Adjust threshold not working

http://code.imagej.net/trac/imagej/ticket/112<http://code.imagej.net/trac/imagej/ticket/1126#comment:2>
2


IJ2 does not support inverted luts the same as IJ1

http://code.imagej.net/trac/imagej/ticket/112<http://code.imagej.net/trac/imagej/ticket/1126#comment:2>
3


Display refresh is slow

http://code.imagej.net/trac/imagej/ticket/112<http://code.imagej.net/trac/imagej/ticket/1126#comment:2>
4


Duplicate command does not respect selection

http://code.imagej.net/trac/imagej/ticket/112<http://code.imagej.net/trac/imagej/ticket/1126#comment:2>
5


Recording macros problematic

http://code.imagej.net/trac/imagej/ticket/1126<http://code.imagej.net/trac/imagej/ticket/1126#comment:2>

On Tue, Apr 17, 2012 at 2:46 AM, Leon Espinosa
<[hidden email]>wrote:

> Dear developers, there are some problems with the display that I have note
> in both Mac OS 10.6 and WXP :
>
> - Filters preview shows nothing (but the filter works fine after "ok")
>
> - The Adjust Threshold window is not showing the overlay of selected
> values (red, Over/under and B/W) But the particles analyzer works if it is
> launched after a blind (or auto) settings (the same for "Window Level"
> adjustment)
>
> - "blobs.gif" open with inverted LUT but it this this is not show in hte
> info bar "(256x254; unsigned-8bit; 63,5 KiB;)" instead "(256x254;
> unsigned-8bit (inverting LUT) ; 63,5 KiB;)"
>
> - The display refreshing is very slow (for example 2-3 seconds to display
> "duplicate" blobs.gif).
>
> - "Duplicate" command duplicates the whole image not only the selection.
>
> - "undo" is not working after a '"crop" command
>
> -  The IJ1 macro record doesn't work and the IJ2 says strange commands :
> Started recording...
>  >> Module: imagej.legacy.plugin.LegacyPlugin
>    context = imagej.ImageJ@224478fe  {ImageJ}
>    imageDisplayService =
> imagej.data.display.DefaultImageDisplayService@24cc17f1 {ImageDisplayService}
>    legacyService = imagej.legacy.LegacyService@11a5ee7c  {LegacyService}
>    uiService = imagej.ui.UIService@4c53ccba  {UIService}
>
> Thank you...
>
>
> All the best,
>
> Leon
>
>
>
>
>
>
> Le 17 avr. 2012 à 00:37, Johannes Schindelin a écrit :
>
> > Dear Yang,
> >
> > On Mon, 16 Apr 2012, Yang YU wrote:
> >
> >> Congratulations!
> >
> > Thanks!
> >
> >> Where can I find the headless usage tutorial?
> >
> > At this point in the beta phase, we do not target headless usage,
> although
> > it is being worked on actively. Read: at the moment, there is
> > unfortunately no end-user interface to perform the conversion you
> mention:
> >
> >> For example, if I use ImageJ to convert .lsm to .tif, how to do it in
> >> headless way?
> >
> > However, headless operations are certainly one of the big aims of the
> > project. I will ask you to test when we have an end-user command line
> > interface ;-)
> >
> > Ciao,
> > Johannes
>
Reply | Threaded
Open this post in threaded view
|

Re: ImageJ 2.0.0-beta1 released

Yang YU
In reply to this post by dscho
Hi Ciao,

Thank you for your kind response. If CLI of ImageJ is ready, I love to give
it a shot.

Cheers,
Yang

On Mon, Apr 16, 2012 at 6:37 PM, Johannes Schindelin <
[hidden email]> wrote:

> Dear Yang,
>
> On Mon, 16 Apr 2012, Yang YU wrote:
>
> > Congratulations!
>
> Thanks!
>
> > Where can I find the headless usage tutorial?
>
> At this point in the beta phase, we do not target headless usage, although
> it is being worked on actively. Read: at the moment, there is
> unfortunately no end-user interface to perform the conversion you mention:
>
> > For example, if I use ImageJ to convert .lsm to .tif, how to do it in
> > headless way?
>
> However, headless operations are certainly one of the big aims of the
> project. I will ask you to test when we have an end-user command line
> interface ;-)
>
> Ciao,
> Johannes
>
Reply | Threaded
Open this post in threaded view
|

Re: ImageJ 2.0.0-beta1 released

Birgit M=?UTF-8?Q?=C3=B6ller?=
In reply to this post by ctrueden
Dear Yang,
in reply to your question about headless usage of ImageJ 2.0 functionality I would like to point you to our software packages Alida and MiToBo. Alida aims to support the development of data analysis algorithms by providing an infrastructure that allows to automatically generate various kinds of interfaces for implemented data analysis operators without additional effort. MiToBo is a library based on Alida which is designed for biomedical image analysis and ships with
several plugins compatible to ImageJ 1.0 (and which by itself is also available as ImageJ 1.0 plugin).

The most interesting point for you is that Alida in principal already subsumes the functionality to automatically generate graphical and commandline interfaces for ImageJ 2.0 plugins as well, i.e. allows for headless usage of ImageJ 2.0. Thereby "in principal" refers to the fact that the complete infrastructure is already there, and we have already some few prototypical plugins compatible with ImageJ 2.0. But, for supporting the large variety of possible plugin parameter data types
Alida relies on a provider mechanism that offers large flexibility in handling arbitrary data types as plugin parameters without need to modify Alida's core.
Yet for full support of ImageJ 2.0 plugins in general we are lacking some of these providers, but we are in the process of implementing them. In particular, we will present Alida and MiToBo at the ISBI 2012 Satellite Workshop on Biomedical Image Analysis in Barcelona in two weeks. We hope to clarify some key issues of the ImageJ 2.0 concept with the help of the developers of ImageJ 2.0 there, which are necessary for us to complete the list of providers, and by this also Alida's ImageJ 2.0 support.

If you are even so interested to take a look at Alida and MiToBo, you are invited to visit our webpages:

http://www.informatik.uni-halle.de/alida
http://www.informatik.uni-halle.de/mitobo

A new release of MiToBo will be available next week prior to ISBI. The currently released version of Alida does not yet support ImageJ 2.0, but we are happy to supply you with our current development version with inital ImageJ 2.0 support and a few demo plugins. We expect to release a new version of Alida/MiToBo with enhanced ImageJ 2.0 support shortly after the end of the conference.
Ciao,

 Birgit

------------------------------------------------------------------------
Dr. rer. nat. Birgit Moeller

Pattern Recognition & Bioinformatics Group
Institute of Computer Science, Faculty of Natural Sciences III
Martin Luther University Halle-Wittenberg / Germany
------------------------------------------------------------------------