drawing in ImageJ

[jvander]

I use ImageJ for processing tasks but still use NIH Image for precision drawing tasks.  I exploit the
ability to draw on a small (e.g. 128 by 128 pixel image window) and I use the ability to draw at the
pixel level.  I also like to use image processing tasks (e.g. skeletonize, thresholding, etc.) as part
of the object creation task.

ImageJ lags far behind NIH Image in drawing capabilities and I believe Wayne has indicated that
this is not destined to be an area of development in ImageJ.  I can certainly appreciate that it is not
a priority for most users and I have just gotten used to using NIH Image for object creation and
ImageJ for analysis.

Unfortunately, the new Intel macs will not support 'Classic' applications like NIH Image, so down
the road I see a problem.

My questions are:

Are there others who will be crippled by this and might that spur someone to further develop
drawing plug-ins for ImageJ?

Is it reasonable to believe that there will be ways of running 'Classic' apps in the next year or so on
an intel Mac?

Or might it be possible in the futuer  to run the WIndows version of NIH Image on an Intel Mac?  (It
is painfully slow in emulatin on a current Mac).



Any thoughts or comments are welcome.

thanks

[Jeff Brandenburg]

On Mar 16, 2006, at 12:16 PM, Joseph Vandergracht wrote:
> Is it reasonable to believe that there will be ways of running
> 'Classic' apps in the next year or so on
> an intel Mac?

Yes, it seems likely.  There are Mac emulators that run on Linux, and
there are lots of people who want to get them running on OS X for just
this purpose.  Performance may be better or worse than you're seeing
with Virtual PC on the Mac; I wouldn't know what to expect.

> Or might it be possible in the futuer  to run the WIndows version of
> NIH Image on an Intel Mac?  (It
> is painfully slow in emulatin on a current Mac).

Well, it's now possible to run Windows XP itself natively on an Intel
Mac:

http://www.engadget.com/2006/03/16/windows-xp-on-mac-solution-posted/

However, bringing up your Mac as a Windows box probably isn't what you
wanted.  (As I pointed out to someone else yesterday, you can also
unplug it and use it as a nifty doorstop, but that, too, negates many
of the advantages of the Mac.)

It stands to reason that Virtual PC could perform much better on an
Intel Mac, since you'd no longer be emulating x86 instructions on a
PowerPC, but Microsoft hasn't had much to say about making an Intel
version of VPC available.

> Any thoughts or comments are welcome.

Can you describe in any more detail what your drawing tasks are like,
and what parts of NIH Image make those tasks easier?  (I'll confess
that I haven't really done any homework on this, because I've never run
NIH Image.)
--
        -jeffB (Jeff Brandenburg, Duke Center for In-Vivo Microscopy)

[Tony Collins-2]

Hi Joseph,

I'm not sure I understand exactly what you're after, but it sounds like
you need to use the "Pencil" tool from the toolbar.

This started life as a standalone macro (2003?) but is now included
(along with brush, eraser, spray and flood-fill) in the StartUpMacros.
This should be included in new installations but old installtions can be
updated by downloading this:
http://rsb.info.nih.gov/ij/macros/StartupMacros.txt
to "imagej/macros" folder.

Double clicking the toolbar button allows you to change the "width" for
these tools.

Regards,

Tony



Joseph Vandergracht wrote:

> I use ImageJ for processing tasks but still use NIH Image for precision drawing tasks.  I exploit the
> ability to draw on a small (e.g. 128 by 128 pixel image window) and I use the ability to draw at the
> pixel level.  I also like to use image processing tasks (e.g. skeletonize, thresholding, etc.) as part
> of the object creation task.
>
> ImageJ lags far behind NIH Image in drawing capabilities and I believe Wayne has indicated that
> this is not destined to be an area of development in ImageJ.  I can certainly appreciate that it is not
> a priority for most users and I have just gotten used to using NIH Image for object creation and
> ImageJ for analysis.
>
> Unfortunately, the new Intel macs will not support 'Classic' applications like NIH Image, so down
> the road I see a problem.
>
> My questions are:
>
> Are there others who will be crippled by this and might that spur someone to further develop
> drawing plug-ins for ImageJ?
>
> Is it reasonable to believe that there will be ways of running 'Classic' apps in the next year or so on
> an intel Mac?
>
> Or might it be possible in the futuer  to run the WIndows version of NIH Image on an Intel Mac?  (It
> is painfully slow in emulatin on a current Mac).
>
>
>
> Any thoughts or comments are welcome.
>
> thanks

--
Tony Collins, Ph.D.
Facility Manager
Wright Cell Imaging Facility
Toronto Western Research Institute
13-407 McLaughlin Pavilion
399 Bathurst Street
Toronto, ON. M5T 2S8
tel. [phone] fax: [phone]
http://www.uhnresearch.ca/wcif

[nitya thiyagarajan]

I am trying to open a metamorph-generated timelapse image stack (nd file)
from Image-J, through the "nd stack builder" plugin. This experiment
has about 10 stage positions, two wavelengths, 3 z planes for each
wavelength and about 90 time points. I am able to build the time series
stack after doing the desired z projection. However, I am not able to do it
for just one desired position and/or wavelength (even if I specify the
desired position and wavelength from the pulldown menu).  In other words,
the plug-in is always wanting all the sequential time point stacks for all
wavelengths and positions starting from position1, wavelength 1, timepoint 1
(it can do 1, 1-2, 1-3 etc, but not just for 2 or 3 only or the second
wavelength only). Does any one know if I can have this plugin to build only
the time series stack for the desired position and wavelength? (I have tried
changing the nd file code to make it read the experiment has having only one
position and wavelength, and it does show up as 1 position/1 wavelength when
I open it, but still is not able to build the stack). Any tips on this issue
will be greatly appreciated.


Thank you
Regards
Nitya Thiyagarajan
Graduate Research Assistant
UMKC-Dental School


On 3/17/06, Jeff Brandenburg <[hidden email]> wrote:

>
> On Mar 16, 2006, at 12:16 PM, Joseph Vandergracht wrote:
> > Is it reasonable to believe that there will be ways of running
> > 'Classic' apps in the next year or so on
> > an intel Mac?
>
> Yes, it seems likely.  There are Mac emulators that run on Linux, and
> there are lots of people who want to get them running on OS X for just
> this purpose.  Performance may be better or worse than you're seeing
> with Virtual PC on the Mac; I wouldn't know what to expect.
>
> > Or might it be possible in the futuer  to run the WIndows version of
> > NIH Image on an Intel Mac?  (It
> > is painfully slow in emulatin on a current Mac).
>
> Well, it's now possible to run Windows XP itself natively on an Intel
> Mac:
>
> http://www.engadget.com/2006/03/16/windows-xp-on-mac-solution-posted/
>
> However, bringing up your Mac as a Windows box probably isn't what you
> wanted.  (As I pointed out to someone else yesterday, you can also
> unplug it and use it as a nifty doorstop, but that, too, negates many
> of the advantages of the Mac.)
>
> It stands to reason that Virtual PC could perform much better on an
> Intel Mac, since you'd no longer be emulating x86 instructions on a
> PowerPC, but Microsoft hasn't had much to say about making an Intel
> version of VPC available.
>
> > Any thoughts or comments are welcome.
>
> Can you describe in any more detail what your drawing tasks are like,
> and what parts of NIH Image make those tasks easier?  (I'll confess
> that I haven't really done any homework on this, because I've never run
> NIH Image.)
> --
>        -jeffB (Jeff Brandenburg, Duke Center for In-Vivo Microscopy)
>

[jvander]

Tony,

Thanks for the comments.  I am embarrassed that I had not given the new drawing tools more of a
look before posting.  I had experimented with drawing in ImageJ a short while ago and was
frustrated compared to NIH Image drawing ccapabilities.

After your post, I spent a bit more time and find that I can indeed do everything that I need to.  
There is a bit of a familiarity curve with getting used to minor differences in implementation, but
the major capabilities are indeed there.

Thanks once again.

Joe van der Gracht
HoloSpex, Inc.

______________________

Hi Joseph,

I'm not sure I understand exactly what you're after, but it sounds like
you need to use the "Pencil" tool from the toolbar.

This started life as a standalone macro (2003?) but is now included
(along with brush, eraser, spray and flood-fill) in the StartUpMacros.
This should be included in new installations but old installtions can be
updated by downloading this:
http://rsb.info.nih.gov/ij/macros/StartupMacros.txt
to "imagej/macros" folder.

Double clicking the toolbar button allows you to change the "width" for
these tools.

Regards,

Tony

[Albert Cardona]

Joseph,

ImageJ itself may not be very useful for drawing, but remember it is built on
top of java. Explore the ij.gui.ImageCanvas.paint(Graphics g) in a class that
extends ImageCanvas, and the java.awt.Graphics methods. There is a lot that
can be done directly on the Graphics object.

Albert

[jvander]

Albert,

Actually it does most of what I need.  One thing it does lack is a tool for drawing straight line.

If it ever proves too much of a problem, I will take your advice and look at the extension to Images
Canvas.

thanks,

Joe van der Gracht

On Sat, 18 Mar 2006 11:25:43 -0800, Albert Cardona <[hidden email]> wrote:

>Joseph,
>
>ImageJ itself may not be very useful for drawing, but remember it is built on
>top of java. Explore the ij.gui.ImageCanvas.paint(Graphics g) in a class that
>extends ImageCanvas, and the java.awt.Graphics methods. There is a lot that
>can be done directly on the Graphics object.
>
>Albert
>===========================================================
==============

[Wayne Rasband]

> Actually it does most of what I need.  One thing it does lack is a
> tool for drawing straight line.
>
> If it ever proves too much of a problem, I will take your advice
> and look at the extension to Images Canvas.

To draw a straight line, create a straight line selection and press "d"
(Edit>Draw) or "f" (Edit>Fill). To draw a line wider than one pixel,
double click on the straight line tool icon, set the line width, create
a line selection, and press "f". Hold down the shift key as you create
the selection to constrain it to be horizontal or vertical.

-wayne

[Tony Collins-2]

Hi Joseph,

Try selecting a stright line, edit the nodes unitl it's exactly where
you want it then hit the 'd' key on the keyboard (or right click
'Draw'). It'll draw the straight line in the foreground colour.

It may be possible to write a toolbar macro to draw the line as soon as
you finish selecting it - but I would guess this would not allow such
precise drawing.

Regards,

Tony
 

Joseph Vandergracht wrote:

> Albert,
>
> Actually it does most of what I need.  One thing it does lack is a tool for drawing straight line.
>
> If it ever proves too much of a problem, I will take your advice and look at the extension to Images
> Canvas.
>
> thanks,
>
> Joe van der Gracht
>
> On Sat, 18 Mar 2006 11:25:43 -0800, Albert Cardona <[hidden email]> wrote:
>
>  
>> Joseph,
>>
>> ImageJ itself may not be very useful for drawing, but remember it is built on
>> top of java. Explore the ij.gui.ImageCanvas.paint(Graphics g) in a class that
>> extends ImageCanvas, and the java.awt.Graphics methods. There is a lot that
>> can be done directly on the Graphics object.
>>
>> Albert
>> ===========================================================
>>    
> ==============
>  

[jvander]

Thanks Tony and Wayne for the tip about drawing a line.  I tried it and it works as advertised.

Before your posts, I had had the idea of selecting a line and then using edit>cut, but it would not
permit cutting with a line selection.  Your tip solved the problems.

Joe