http://imagej.273.s1.nabble.com/Waiting-for-run-command-to-complete-before-proceeding-with-macro-execution-tp3701048.html
macros that did batch rotations on 4d datasets. I'm trying to do this
times of heavier CPU usage or Java garbage collector operation. Is
1117 W. Johnson St.
> There are 14 messages totalling 1231 lines in this issue.
>
> Topics of the day:
>
> 1. AW: Out of available memory? Help! (2)
> 2. Image J - overlay (5)
> 3. Test of radialness
> 4. Create an image composed of the profile plot???
> 5. Out of available memory? Help! (3)
> 6. Nearest Neighbour Analysis (2)
>
> ----------------------------------------------------------------------
>
> Date: Thu, 2 Nov 2006 10:20:23 +0100
> From: "Lucas, Falk /BDF HAM" <
[hidden email]>
> Subject: AW: Out of available memory? Help!
>
> Hi,
>
> we have encountered this issue too and found an solution, but only
> for some of our machines...
>
> We had an early version (1.31) on hte machines and I set up an
> script for just overwriting hte old version with a new one, which
> results in the same error message you get.
> Solution: Delete the ImagJ Folder completly and install/copy the
> current version again.
> However, if your account (on a PC) is just associated with the
> user group (minimum rights), this message can still be there. We
> never encountered the message if the user is in the main user or
> admin group.
>
> Falk
>
> -----Ursprüngliche Nachricht-----
> Von: ImageJ Interest Group [mailto:
[hidden email]] Im Auftrag
> von Jonathan Thomas
> Gesendet: Mittwoch, 1. November 2006 23:23
> An:
[hidden email]
> Betreff: Out of available memory? Help!
>
> (cliffs at bottom)
>
> I am currently trying to use ImageJ to do image segmentation on
> some ~11MB RGB images. The images load fine into ImageJ, but if I
> attempt to do any filtering on them ImageJ throws this error:
>
> <Out of memory>
> <All available memory (63MB) has been>
> <used. Instructions for making more>
> <available can be found in the "Memory" > <sections of the
> installation notes at> <
http://rsb.info.nih.gov/ij/docs/install/>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>
> I then poked through the options and raised the memory alotted to
> 500MB, closed ImageJ and reopened it attempted the same operation
> and got an identical error. Even mentioning 63MB. Note that the
> default was not 63 MB nor was the max memory set anywhere near 63MB
> after I changed it.
>
>
> So I came here, and I see people recommending changing the command
> given to the executable, so I checked my ImageJ.cfg and it reads:
>
> .
> C:\Program Files\Java\j2re1.4.2_03\bin\javaw.exe
> -Xmx500m -cp ij.jar ij.ImageJ
>
> In a previous thread someone mentioned a similar problem and
> modifying this line fixed the problem but I believe that java
> should have plenty of memory the way I have it configured.
>
> So that's my problem, I'd appreciate any help you guys can give me.
>
> If you have read this far here is some more information that may be
> helpful:
>
> 2.99Ghz Pentium D
> 2GB Ram
>
> ImageJ 1.36b
> Java 1.5.0_06
> About ImageJ displays 55MB of 500MB (11%) while the error message
> is still in the log.
>
> The java is on this machine, while the ImageJ is being run from a
> network drive. The same error arrizes when I run ImageJ as an
> applet from the NIH page.
>
> I have contacted the sys admin and he assures me that there is no
> constraint put on memory used by a user, with the exception of the
> physical memory on the machine and what is being used by other
> software.
>
> Software running in the background or not has no effect on the
> error message.
>
> I have replicated this error on 2 machines, each using their own
> local java but the same ImageJ off the same network drive. I have
> also replicated it running ImageJ as an applet on both machines.
>
> Curiously when I look at the size of the image in windows it is
> listed as 11MB, but ImageJ claims it's 27MB. (perhaps this is
> extra space for a
> buffer?) One image is 2915x2456 pixel tiff. The others are
> similar. All tiffs, all RGB, all produce the same error.
>
> If you have made it this far I truly commend you. Thank you for
> the attention and here's a quote for your efforts.
>
> "'That is indisputable,' was the answer, 'but in this country it is
> a good thing to kill an admiral from time to time to encourage the
> others.'"
> -Voltaire (François-Marie Arouet), Candide
>
> Thank you for any help you can give me.
> -Stumped in StonyBrook
>
>
>
>
>
> finally cliffnotes:
> 1. ImageJ throws an out of memory error when I try to analyze some
> large tiff images 2. The machine has plenty of memory and so does
> java.
> 3. Solutions to similar problems from this listserv do not help.
> 4. Recent software, reproducible.
> 5. HELP!
> 6. quote for your efforts, thanks!
>
> _____________________ Confidentiality _____________________
>
> This electronic transmission is strictly confidential and intended
> solely for the addressee. It may contain information which is covered
> by legal, professional or other privilege. If you are not the
> intended
> addressee, you must not disclose, copy or take any action in reliance
> of this transmission. If you have received this transmission in
> error,
> please notify us and delete the received data as soon as possible.
>
> This footnote also confirms that this email message has been swept
> for the presence of computer viruses.
> _______________________________________________________
>
> ------------------------------
>
> Date: Thu, 2 Nov 2006 14:09:50 +0100
> From: Michael Weber <
[hidden email]>
> Subject: Re: AW: Out of available memory? Help!
>
> Hi,
>
> it usually works for us if we:
>
> - define the amount of RAM in the config (~75% of system memory)
> - have this amount of RAM free (double check with the task manager, if
> you're a Windows user)
> - use the newest Java version
> - run only one instance of ImageJ
>
> Maybe this helps.
>
> cheers,
> Michael
>
>
> Lucas, Falk /BDF HAM schrieb:
>> Hi,
>>
>> we have encountered this issue too and found an solution, but only
>> for some of our machines...
>>
>> We had an early version (1.31) on hte machines and I set up an
>> script for just overwriting hte old version with a new one, which
>> results in the same error message you get.
>> Solution: Delete the ImagJ Folder completly and install/copy the
>> current version again.
>> However, if your account (on a PC) is just associated with the
>> user group (minimum rights), this message can still be there. We
>> never encountered the message if the user is in the main user or
>> admin group.
>>
>> Falk
>>
>> -----Ursprüngliche Nachricht-----
>> Von: ImageJ Interest Group [mailto:
[hidden email]] Im Auftrag
>> von Jonathan Thomas
>> Gesendet: Mittwoch, 1. November 2006 23:23
>> An:
[hidden email]
>> Betreff: Out of available memory? Help!
>>
>> (cliffs at bottom)
>>
>> I am currently trying to use ImageJ to do image segmentation on
>> some ~11MB RGB images. The images load fine into ImageJ, but if I
>> attempt to do any filtering on them ImageJ throws this error:
>>
>> <Out of memory>
>> <All available memory (63MB) has been>
>> <used. Instructions for making more>
>> <available can be found in the "Memory" > <sections of the
>> installation notes at> <
http://rsb.info.nih.gov/ij/docs/install/>
>>
>> I then poked through the options and raised the memory alotted to
>> 500MB, closed ImageJ and reopened it attempted the same operation
>> and got an identical error. Even mentioning 63MB. Note that the
>> default was not 63 MB nor was the max memory set anywhere near
>> 63MB after I changed it.
>>
>>
>> So I came here, and I see people recommending changing the command
>> given to the executable, so I checked my ImageJ.cfg and it reads:
>>
>> .
>> C:\Program Files\Java\j2re1.4.2_03\bin\javaw.exe
>> -Xmx500m -cp ij.jar ij.ImageJ
>>
>> In a previous thread someone mentioned a similar problem and
>> modifying this line fixed the problem but I believe that java
>> should have plenty of memory the way I have it configured.
>>
>> So that's my problem, I'd appreciate any help you guys can give me.
>>
>> If you have read this far here is some more information that may be
>> helpful:
>>
>> 2.99Ghz Pentium D
>> 2GB Ram
>>
>> ImageJ 1.36b
>> Java 1.5.0_06
>> About ImageJ displays 55MB of 500MB (11%) while the error message
>> is still in the log.
>>
>> The java is on this machine, while the ImageJ is being run from a
>> network drive. The same error arrizes when I run ImageJ as an
>> applet from the NIH page.
>>
>> I have contacted the sys admin and he assures me that there is no
>> constraint put on memory used by a user, with the exception of the
>> physical memory on the machine and what is being used by other
>> software.
>>
>> Software running in the background or not has no effect on the
>> error message.
>>
>> I have replicated this error on 2 machines, each using their own
>> local java but the same ImageJ off the same network drive. I have
>> also replicated it running ImageJ as an applet on both machines.
>>
>> Curiously when I look at the size of the image in windows it is
>> listed as 11MB, but ImageJ claims it's 27MB. (perhaps this is
>> extra space for a
>> buffer?) One image is 2915x2456 pixel tiff. The others are
>> similar. All tiffs, all RGB, all produce the same error.
>>
>> If you have made it this far I truly commend you. Thank you for
>> the attention and here's a quote for your efforts.
>>
>> "'That is indisputable,' was the answer, 'but in this country it
>> is a good thing to kill an admiral from time to time to encourage
>> the others.'"
>> -Voltaire (François-Marie Arouet), Candide
>>
>> Thank you for any help you can give me.
>> -Stumped in StonyBrook
>>
>>
>>
>>
>>
>> finally cliffnotes:
>> 1. ImageJ throws an out of memory error when I try to analyze some
>> large tiff images 2. The machine has plenty of memory and so does
>> java.
>> 3. Solutions to similar problems from this listserv do not help.
>> 4. Recent software, reproducible.
>> 5. HELP!
>> 6. quote for your efforts, thanks!
>>
>> _____________________ Confidentiality _____________________
>>
>> This electronic transmission is strictly confidential and intended
>> solely for the addressee. It may contain information which is
>> covered
>> by legal, professional or other privilege. If you are not the
>> intended
>> addressee, you must not disclose, copy or take any action in reliance
>> of this transmission. If you have received this transmission in
>> error,
>> please notify us and delete the received data as soon as possible.
>>
>> This footnote also confirms that this email message has been swept
>> for the presence of computer viruses.
>> _______________________________________________________
>
> ------------------------------
>
> Date: Thu, 2 Nov 2006 14:24:50 -0000
> From: "O'Brien.Joseph" <Joseph.O'
[hidden email]>
> Subject: Image J - overlay
>
> Dear Image J community.
>
> It's a cold afternoon here in the UK and Im struggling with the
> program.. Can u help?
>
> The question is.......Can imageJ perform an 'overlay' function?
>
> "What is overlay ?" I hear you ask.
> Other software performs overlay by mixing pixels i.e pixel 1 from
> col 1, row1 belongs to ct image. Then pixel 2 from col 2, row 1
> belongs to nuc med image. Then pixel 3 from col 3, row1 belongs to
> ct image. And so on.
>
> I want to overaly a nucmed functional image over a CT structural
> image.
>
> Can it be done?
>
> Kind regards in advance
>
> Yours shiveringly
>
> Joe O'Brien
> Clinical Scientist (Nuclear Medicine)
> Department of Physics and Nuclear Medicine
> City Hospital
> Dudley Road
> Birmingham
> UK
>
>
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:
[hidden email]] On Behalf
> Of Michael Weber
> Sent: 02 November 2006 13.10
> To:
[hidden email]
> Subject: Re: AW: Out of available memory? Help!
>
>
> Hi,
>
> it usually works for us if we:
>
> - define the amount of RAM in the config (~75% of system memory)
> - have this amount of RAM free (double check with the task manager, if
> you're a Windows user)
> - use the newest Java version
> - run only one instance of ImageJ
>
> Maybe this helps.
>
> cheers,
> Michael
>
>
> Lucas, Falk /BDF HAM schrieb:
>> Hi,
>>
>> we have encountered this issue too and found an solution, but only
>> for
>> some of our machines...
>>
>> We had an early version (1.31) on hte machines and I set up an script
>> for just overwriting hte old version with a new one, which results
>> in the same error message you get.
>> Solution: Delete the ImagJ Folder completly and install/copy the
>> current version again.
>> However, if your account (on a PC) is just associated with the
>> user group (minimum rights), this message can still be there. We
>> never encountered the message if the user is in the main user or
>> admin group.
>>
>> Falk
>>
>> -----Ursprüngliche Nachricht-----
>> Von: ImageJ Interest Group [mailto:
[hidden email]] Im Auftrag
>> von
>> Jonathan Thomas
>> Gesendet: Mittwoch, 1. November 2006 23:23
>> An:
[hidden email]
>> Betreff: Out of available memory? Help!
>>
>> (cliffs at bottom)
>>
>> I am currently trying to use ImageJ to do image segmentation on some
>> ~11MB RGB images. The images load fine into ImageJ, but if I attempt
>> to do any filtering on them ImageJ throws this error:
>>
>> <Out of memory>
>> <All available memory (63MB) has been>
>> <used. Instructions for making more>
>> <available can be found in the "Memory" > <sections of the
>> installation notes at> <
http://rsb.info.nih.gov/ij/docs/install/>
>>
>> I then poked through the options and raised the memory alotted to
>> 500MB, closed ImageJ and reopened it attempted the same operation and
>> got an identical error. Even mentioning 63MB. Note that the default
>> was not 63 MB nor was the max memory set anywhere near 63MB after I
>> changed it.
>>
>>
>> So I came here, and I see people recommending changing the command
>> given to the executable, so I checked my ImageJ.cfg and it reads:
>>
>> .
>> C:\Program Files\Java\j2re1.4.2_03\bin\javaw.exe
>> -Xmx500m -cp ij.jar ij.ImageJ
>>
>> In a previous thread someone mentioned a similar problem and
>> modifying
>> this line fixed the problem but I believe that java should have
>> plenty
>> of memory the way I have it configured.
>>
>> So that's my problem, I'd appreciate any help you guys can give me.
>>
>> If you have read this far here is some more information that may be
>> helpful:
>>
>> 2.99Ghz Pentium D
>> 2GB Ram
>>
>> ImageJ 1.36b
>> Java 1.5.0_06
>> About ImageJ displays 55MB of 500MB (11%) while the error message is
>> still in the log.
>>
>> The java is on this machine, while the ImageJ is being run from a
>> network drive. The same error arrizes when I run ImageJ as an applet
>> from the NIH page.
>>
>> I have contacted the sys admin and he assures me that there is no
>> constraint put on memory used by a user, with the exception of the
>> physical memory on the machine and what is being used by other
>> software.
>>
>> Software running in the background or not has no effect on the error
>> message.
>>
>> I have replicated this error on 2 machines, each using their own
>> local
>> java but the same ImageJ off the same network drive. I have also
>> replicated it running ImageJ as an applet on both machines.
>>
>> Curiously when I look at the size of the image in windows it is
>> listed
>> as 11MB, but ImageJ claims it's 27MB. (perhaps this is extra
>> space for a
>> buffer?) One image is 2915x2456 pixel tiff. The others are
>> similar. All tiffs, all RGB, all produce the same error.
>>
>> If you have made it this far I truly commend you. Thank you for the
>> attention and here's a quote for your efforts.
>>
>> "'That is indisputable,' was the answer, 'but in this country it is a
>> good thing to kill an admiral from time to time to encourage the
>> others.'" -Voltaire (François-Marie Arouet), Candide
>>
>> Thank you for any help you can give me.
>> -Stumped in StonyBrook
>>
>>
>>
>>
>>
>> finally cliffnotes:
>> 1. ImageJ throws an out of memory error when I try to analyze some
>> large tiff images 2. The machine has plenty of memory and so does
>> java. 3. Solutions to similar problems from this listserv do not
>> help.
>> 4. Recent software, reproducible. 5. HELP! 6. quote for your efforts,
>> thanks!
>>
>> _____________________ Confidentiality _____________________
>>
>> This electronic transmission is strictly confidential and intended
>> solely for the addressee. It may contain information which is
>> covered
>> by legal, professional or other privilege. If you are not the
>> intended
>> addressee, you must not disclose, copy or take any action in reliance
>> of this transmission. If you have received this transmission in
>> error,
>> please notify us and delete the received data as soon as possible.
>>
>> This footnote also confirms that this email message has been swept
>> for the presence of computer viruses.
>> _______________________________________________________
>
> ------------------------------
>
> Date: Thu, 2 Nov 2006 16:39:56 +0100
> From: Johannes Schindelin <
[hidden email]>
> Subject: Re: Image J - overlay
>
> Hi,
>
> On Thu, 2 Nov 2006, O'Brien.Joseph wrote:
>
>> It's a cold afternoon here in the UK [...]
>
> Funny, I was in Scotland until Tuesday, and it was warmer than here in
> Germany!
>
>> The question is.......Can imageJ perform an 'overlay' function?
>
> You might want to copy the image to be overlayed, and play with
> "Edit/Paste Control..." I got what I wanted with "Max".
>
> Hth,
> Dscho
>
> ------------------------------
>
> Date: Thu, 2 Nov 2006 08:28:09 -0800
> From: "Batishko, Charles R" <
[hidden email]>
> Subject: Re: Test of radialness
>
> I had a problem like this a number of years ago. I don't have a
> standard metric, but the way I did it was as follows.
>
> I segmented the objects and measured the angle of the major axis
> for each. I defined straight lines at those angles and found the
> set of intersections between each pair of lines. I measured the
> tightness (density) of the cluster of intersection points. The
> tighter the cluster, the more radial. The more diffuse the cluster,
> the less radial. One would need to have some kind of distrubuted
> population of samples so as to define a distribution, and a
> threshold that might then discriminate between radial and non-
> radial. But that would need to be associated with the physical
> reality. For example, my work involved whether to not the segmented
> features emanated from a point source or an extended source. Based
> on reality, one would need to define a finite threshold
> differentiating between "point" and "extended" sources - probably
> based on measurement uncertainty that leads to there being no such
> thing as a point source where physical measurements are concerned.
>
> Probably not the answer you wanted, but perhaps will trigger
> thoughts from others, or help you think of it in terms that lead to
> a solution.
>
> Chuck
>
>> -----Original Message-----
>> From: ImageJ Interest Group [mailto:
[hidden email]] On
>> Behalf Of Bulent Celasun
>> Sent: Wednesday, November 01, 2006 10:55 AM
>> To:
[hidden email]
>> Subject: Test of radialness
>>
>> Dear All,
>>
>> Think of an image of an orange's cut surface (the one
>> resembling a wheel).
>> Then, imagine thresholding the juicy lobes that are separated
>> from each other.
>> You now have objects distributed radially around a central point.
>> (Petals of a flower seen from above can also serve the same purpose).
>>
>> Question:
>> Is there a measure of "radialness" of the thresholded objects
>> similar to the one called as "circularity factor" or "roundness".
>> To be useful, such a measure should be tolerant to changing
>> the number and the distance of the objects to the center
>> (i.e. adding "radial" objects of differing sizes and shapes
>> here and there should not alter it much), but responsive to
>> changes in their axes.
>>
>> In other words; can I define and measure "radialness" as a
>> variable in ImageJ?
>> If yes, how?
>>
>> Thanks,
>>
>> Bülent Celasun, MD
>>
>>
>> Department of Pathology
>> Baskent Uni. School of Medicine,
>> Ankara, Turkey
>>
>
> ------------------------------
>
> Date: Wed, 1 Nov 2006 21:47:22 -0800
> From: Harry Parker <
[hidden email]>
> Subject: Re: Create an image composed of the profile plot???
>
> I suggest looking at the source for the plugin, "Random Ovals"
> under the Graphics heading on the Plugin page. It shows how to draw
> circles ( = ovals with the same width and height).
>
> --
> Harry Parker
> Senior Systems Engineer
> Dialog Imaging Systems, Inc.
>
> ----- Original Message ----
> From: Liisa Palomaa <
[hidden email]>
> To:
[hidden email]
> Sent: Monday, October 30, 2006 8:57:22 PM
> Subject: Create an image composed of the profile plot???
>
> Hi again...
>
> I got the help I neede to create a new image and set the
> pixelvalues :) Thanks
>
> Now I have a new question- when creating a new image.
> Is it possible to generate an image composed of the pixelvalues of a
> profile plot( plot values)? So that in the new image all the points
> (radius) that are at say distance 10 from the center has a pixelvalue
> 200.
>
> Thanks in advance
> //Liisa
>
> ------------------------------
>
> Date: Thu, 2 Nov 2006 12:19:54 -0500
> From: Wayne Rasband <
[hidden email]>
> Subject: Re: Out of available memory? Help!
>
> How do you run ImageJ? Double-clicking on ij.jar instead of on
> ImageJ.exe would cause this problem. Java programs are limited to 64MB
> when you run them by double clicking on their JAR file.
>
> A 2915x2456 color image does require 27MB of memory. To do the
> calculations, open a text window (shift-n), paste in the following
> line
>
> round(2915*2456*4/(1024*1024)) + " MB"
>
> and press ctrl-r (Run Macro).
>
> -wayne
>
>> (cliffs at bottom)
>>
>> I am currently trying to use ImageJ to do image segmentation on some
>> ~11MB
>> RGB images. The images load fine into ImageJ, but if I attempt to do
>> any
>> filtering on them ImageJ throws this error:
>>
>> <Out of memory>
>> <All available memory (63MB) has been>
>> <used. Instructions for making more>
>> <available can be found in the "Memory" >
>> <sections of the installation notes at>
>> <
http://rsb.info.nih.gov/ij/docs/install/>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>
>> I then poked through the options and raised the memory alotted to
>> 500MB,
>> closed ImageJ and reopened it attempted the same operation and got an
>> identical error. Even mentioning 63MB. Note that the default was
>> not
>> 63
>> MB nor was the max memory set anywhere near 63MB after I changed it.
>>
>>
>> So I came here, and I see people recommending changing the command
>> given
>> to the executable, so I checked my ImageJ.cfg and it reads:
>>
>> .
>> C:\Program Files\Java\j2re1.4.2_03\bin\javaw.exe
>> -Xmx500m -cp ij.jar ij.ImageJ
>>
>> In a previous thread someone mentioned a similar problem and
>> modifying
>> this line fixed the problem but I believe that java should have
>> plenty
>> of
>> memory the way I have it configured.
>>
>> So that's my problem, I'd appreciate any help you guys can give me.
>>
>> If you have read this far here is some more information that may be
>> helpful:
>>
>> 2.99Ghz Pentium D
>> 2GB Ram
>>
>> ImageJ 1.36b
>> Java 1.5.0_06
>> About ImageJ displays 55MB of 500MB (11%) while the error message is
>> still
>> in the log.
>>
>> The java is on this machine, while the ImageJ is being run from a
>> network
>> drive. The same error arrizes when I run ImageJ as an applet from
>> the
>> NIH
>> page.
>>
>> I have contacted the sys admin and he assures me that there is no
>> constraint put on memory used by a user, with the exception of the
>> physical memory on the machine and what is being used by other
>> software.
>>
>> Software running in the background or not has no effect on the error
>> message.
>>
>> I have replicated this error on 2 machines, each using their own
>> local
>> java but the same ImageJ off the same network drive. I have also
>> replicated it running ImageJ as an applet on both machines.
>>
>> Curiously when I look at the size of the image in windows it is
>> listed
>> as
>> 11MB, but ImageJ claims it's 27MB. (perhaps this is extra space
>> for a
>> buffer?) One image is 2915x2456 pixel tiff. The others are similar.
>> All
>> tiffs, all RGB, all produce the same error.
>>
>> If you have made it this far I truly commend you. Thank you for the
>> attention and here's a quote for your efforts.
>>
>> "'That is indisputable,' was the answer, 'but in this country it is a
>> good
>> thing to kill an admiral from time to time to encourage the others.'"
>> -Voltaire (François-Marie Arouet), Candide
>>
>> Thank you for any help you can give me.
>> -Stumped in StonyBrook
>>
>>
>>
>>
>>
>> finally cliffnotes:
>> 1. ImageJ throws an out of memory error when I try to analyze some
>> large
>> tiff images
>> 2. The machine has plenty of memory and so does java.
>> 3. Solutions to similar problems from this listserv do not help.
>> 4. Recent software, reproducible.
>> 5. HELP!
>> 6. quote for your efforts, thanks!
>
> ------------------------------
>
> Date: Thu, 2 Nov 2006 12:35:57 -0500
> From: "DeBarr, Gabriel" <
[hidden email]>
> Subject: Re: Image J - overlay
>
> You could use a "CustomCanvas" and override the "public void
> paint(Graphics g)" to fill in your overlay. This would allow you to
> non-destructively layer one set of data on top of another. e.g.:
> <code>
> //a custom canvas to apply a non-destructive graphic overlay to image
> display
> CustomCanvas(ImagePlus imp) {
> super(imp);
> }//~ctor
>
> public void paint(Graphics g) {
> super.paint(g);
> drawOverlay(g);
> }//~cc paint
>
> void drawOverlay(Graphics g) {
> //draw the graphic overlay (non-destructively) showing user's selected
> points.
> g.setColor(Color.blue);
> if(pending) {//draw crosshair for current
> location
> g.drawLine(screenX((int)cl_x-2),
> screenY((int)cl_y), screenX((int)cl_x+2), screenY((int)cl_y));
> g.drawLine(screenX((int)cl_x),
> screenY((int)cl_y-2), screenX((int)cl_x), screenY((int)cl_y+2));
> }
> if(n_pts>0) {//draw crosshair cursors over
> previously selected locations
> int i,lx,ly;
> for(i=0;i<n_pts;i++) {
> if(i<3)
>
> g.setColor(Color.green);//our transform defining points
> else
>
> g.setColor(Color.yellow);//the rest of them
>
> lx=(int)((mPointDouble)mPoints.elementAt(i)).getX();
>
> ly=(int)((mPointDouble)mPoints.elementAt(i)).getY();
> g.drawLine(screenX(lx-2),
> screenY(ly), screenX(lx+2), screenY(ly));
> g.drawLine(screenX(lx),
> screenY(ly-2), screenX(lx), screenY(ly+2));
> }
> }
> }//~cc drawOverlay
>
> }//~ custom canvas class
> </code>
>
> Another option would be to just create a new image, as a composite of
> your data sets.
>
> -Gabriel
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:
[hidden email]]On Behalf Of
> Johannes Schindelin
> Sent: Thursday, November 02, 2006 10:40 AM
> To:
[hidden email]
> Subject: Re: Image J - overlay
>
>
> Hi,
>
> On Thu, 2 Nov 2006, O'Brien.Joseph wrote:
>
>> It's a cold afternoon here in the UK [...]
>
> Funny, I was in Scotland until Tuesday, and it was warmer than here in
> Germany!
>
>> The question is.......Can imageJ perform an 'overlay' function?
>
> You might want to copy the image to be overlayed, and play with
> "Edit/Paste Control..." I got what I wanted with "Max".
>
> Hth,
> Dscho
>
> **********************************************************************
> ******************
>
> Note: If the reader of this message is not the intended recipient,
> or an employee or agent responsible for delivering this message to
> the intended recipient, you are hereby notified that any
> dissemination, distribution or copying of this communication is
> strictly prohibited. If you have received this communication in
> error, please notify us immediately by replying to the message and
> deleting it from your computer. Thank you.
>
> **********************************************************************
> ******************
>
> ------------------------------
>
> Date: Thu, 2 Nov 2006 10:15:20 -0800
> From: "DeBarr, Gabriel" <
[hidden email]>
> Subject: Re: Image J - overlay
>
> You could use a "CustomCanvas" and override the "public void
> paint(Graphics g)" to fill in your overlay. This would allow you to
> non-destructively layer one set of data on top of another. e.g.:
> <code>
> //a custom canvas to apply a non-destructive graphic overlay to image
> display
> CustomCanvas(ImagePlus imp) {
> super(imp);
> }//~ctor
>
> public void paint(Graphics g) {
> super.paint(g);
> drawOverlay(g);
> }//~cc paint
>
> void drawOverlay(Graphics g) {
> //draw the graphic overlay (non-destructively) showing user's selected
> points.
> g.setColor(Color.blue);
> if(pending) {//draw crosshair for current
> location
> g.drawLine(screenX((int)cl_x-2),
> screenY((int)cl_y), screenX((int)cl_x+2), screenY((int)cl_y));
> g.drawLine(screenX((int)cl_x),
> screenY((int)cl_y-2), screenX((int)cl_x), screenY((int)cl_y+2));
> }
> if(n_pts>0) {//draw crosshair cursors over
> previously selected locations
> int i,lx,ly;
> for(i=0;i<n_pts;i++) {
> if(i<3)
>
> g.setColor(Color.green);//our transform defining points
> else
>
> g.setColor(Color.yellow);//the rest of them
>
> lx=(int)((mPointDouble)mPoints.elementAt(i)).getX();
>
> ly=(int)((mPointDouble)mPoints.elementAt(i)).getY();
> g.drawLine(screenX(lx-2),
> screenY(ly), screenX(lx+2), screenY(ly));
> g.drawLine(screenX(lx),
> screenY(ly-2), screenX(lx), screenY(ly+2));
> }
> }
> }//~cc drawOverlay
>
> }//~ custom canvas class
> </code>
>
> Another option would be to just create a new image, as a composite of
> your data sets.
>
> -Gabriel
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:
[hidden email]]On Behalf Of
> Johannes Schindelin
> Sent: Thursday, November 02, 2006 10:40 AM
> To:
[hidden email]
> Subject: Re: Image J - overlay
>
>
> Hi,
>
> On Thu, 2 Nov 2006, O'Brien.Joseph wrote:
>
>> It's a cold afternoon here in the UK [...]
>
> Funny, I was in Scotland until Tuesday, and it was warmer than here in
> Germany!
>
>> The question is.......Can imageJ perform an 'overlay' function?
>
> You might want to copy the image to be overlayed, and play with
> "Edit/Paste Control..." I got what I wanted with "Max".
>
> Hth,
> Dscho
>
> **********************************************************************
> ******************
>
> Note: If the reader of this message is not the intended recipient,
> or an employee or agent responsible for delivering this message to
> the intended recipient, you are hereby notified that any
> dissemination, distribution or copying of this communication is
> strictly prohibited. If you have received this communication in
> error, please notify us immediately by replying to the message and
> deleting it from your computer. Thank you.
>
> **********************************************************************
> ******************
>
> ------------------------------
>
> Date: Thu, 2 Nov 2006 15:17:30 -0500
> From: Jon Thomas <
[hidden email]>
> Subject: Re: Out of available memory? Help!
>
> Thanks! That solved the problem. I was running it from the .jar.
> As far
> as the memory usage the 27MB must be correct. Windows must be
> doing some
> compression or some such. Either way, thank you very much for the
> help.
>
> -Jon
>
>
> On 11/2/06, Wayne Rasband <
[hidden email]> wrote:
>>
>> How do you run ImageJ? Double-clicking on ij.jar instead of on
>> ImageJ.exe would cause this problem. Java programs are limited to
>> 64MB
>> when you run them by double clicking on their JAR file.
>>
>> A 2915x2456 color image does require 27MB of memory. To do the
>> calculations, open a text window (shift-n), paste in the following
>> line
>>
>> round(2915*2456*4/(1024*1024)) + " MB"
>>
>> and press ctrl-r (Run Macro).
>>
>> -wayne
>>
>>> (cliffs at bottom)
>>>
>>> I am currently trying to use ImageJ to do image segmentation on some
>>> ~11MB
>>> RGB images. The images load fine into ImageJ, but if I attempt
>>> to do
>>> any
>>> filtering on them ImageJ throws this error:
>>>
>>> <Out of memory>
>>> <All available memory (63MB) has been>
>>> <used. Instructions for making more>
>>> <available can be found in the "Memory" >
>>> <sections of the installation notes at>
>>> <
http://rsb.info.nih.gov/ij/docs/install/>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>
>>> I then poked through the options and raised the memory alotted to
>>> 500MB,
>>> closed ImageJ and reopened it attempted the same operation and
>>> got an
>>> identical error. Even mentioning 63MB. Note that the default
>>> was not
>>> 63
>>> MB nor was the max memory set anywhere near 63MB after I changed it.
>>>
>>>
>>> So I came here, and I see people recommending changing the command
>>> given
>>> to the executable, so I checked my ImageJ.cfg and it reads:
>>>
>>> .
>>> C:\Program Files\Java\j2re1.4.2_03\bin\javaw.exe
>>> -Xmx500m -cp ij.jar ij.ImageJ
>>>
>>> In a previous thread someone mentioned a similar problem and
>>> modifying
>>> this line fixed the problem but I believe that java should have
>>> plenty
>>> of
>>> memory the way I have it configured.
>>>
>>> So that's my problem, I'd appreciate any help you guys can give me.
>>>
>>> If you have read this far here is some more information that may be
>>> helpful:
>>>
>>> 2.99Ghz Pentium D
>>> 2GB Ram
>>>
>>> ImageJ 1.36b
>>> Java 1.5.0_06
>>> About ImageJ displays 55MB of 500MB (11%) while the error message is
>>> still
>>> in the log.
>>>
>>> The java is on this machine, while the ImageJ is being run from a
>>> network
>>> drive. The same error arrizes when I run ImageJ as an applet
>>> from the
>>> NIH
>>> page.
>>>
>>> I have contacted the sys admin and he assures me that there is no
>>> constraint put on memory used by a user, with the exception of the
>>> physical memory on the machine and what is being used by other
>>> software.
>>>
>>> Software running in the background or not has no effect on the error
>>> message.
>>>
>>> I have replicated this error on 2 machines, each using their own
>>> local
>>> java but the same ImageJ off the same network drive. I have also
>>> replicated it running ImageJ as an applet on both machines.
>>>
>>> Curiously when I look at the size of the image in windows it is
>>> listed
>>> as
>>> 11MB, but ImageJ claims it's 27MB. (perhaps this is extra space
>>> for a
>>> buffer?) One image is 2915x2456 pixel tiff. The others are
>>> similar.
>>> All
>>> tiffs, all RGB, all produce the same error.
>>>
>>> If you have made it this far I truly commend you. Thank you for the
>>> attention and here's a quote for your efforts.
>>>
>>> "'That is indisputable,' was the answer, 'but in this country it
>>> is a
>>> good
>>> thing to kill an admiral from time to time to encourage the
>>> others.'"
>>> -Voltaire (Fran=E7ois-Marie Arouet), Candide
>>>
>>> Thank you for any help you can give me.
>>> -Stumped in StonyBrook
>>>
>>>
>>>
>>>
>>>
>>> finally cliffnotes:
>>> 1. ImageJ throws an out of memory error when I try to analyze some
>>> large
>>> tiff images
>>> 2. The machine has plenty of memory and so does java.
>>> 3. Solutions to similar problems from this listserv do not help.
>>> 4. Recent software, reproducible.
>>> 5. HELP!
>>> 6. quote for your efforts, thanks!
>>
>
> ------------------------------
>
> Date: Thu, 2 Nov 2006 13:50:41 -0600
> From: Justin McGrath <
[hidden email]>
> Subject: Re: Image J - overlay
>
> I create overlays by adding the values of the pixels together with
> image calculator.
> i.e.
> imageCalculator("Add create", "Red","Result of Masked");
>
> I mulitpy the overlay by a fraction so it looks transparent and
> reduces the chance of values over 255.
>
> Justin
>
>
> On 11/2/06, DeBarr, Gabriel <
[hidden email]> wrote:
>> You could use a "CustomCanvas" and override the "public void
>> paint(Graphics g)" to fill in your overlay. This would allow you to
>> non-destructively layer one set of data on top of another. e.g.:
>> <code>
>> //a custom canvas to apply a non-destructive graphic overlay to image
>> display
>> CustomCanvas(ImagePlus imp) {
>> super(imp);
>> }//~ctor
>>
>> public void paint(Graphics g) {
>> super.paint(g);
>> drawOverlay(g);
>> }//~cc paint
>>
>> void drawOverlay(Graphics g) {
>> //draw the graphic overlay (non-destructively) showing user's
>> selected
>> points.
>> g.setColor(Color.blue);
>> if(pending) {//draw crosshair for current
>> location
>> g.drawLine(screenX((int)cl_x-2),
>> screenY((int)cl_y), screenX((int)cl_x+2), screenY((int)cl_y));
>> g.drawLine(screenX((int)cl_x),
>> screenY((int)cl_y-2), screenX((int)cl_x), screenY((int)cl_y+2));
>> }
>> if(n_pts>0) {//draw crosshair cursors over
>> previously selected locations
>> int i,lx,ly;
>> for(i=0;i<n_pts;i++) {
>> if(i<3)
>>
>> g.setColor(Color.green);//our transform defining points
>> else
>>
>> g.setColor(Color.yellow);//the rest of them
>>
>> lx=(int)((mPointDouble)mPoints.elementAt(i)).getX();
>>
>> ly=(int)((mPointDouble)mPoints.elementAt(i)).getY();
>> g.drawLine(screenX(lx-2),
>> screenY(ly), screenX(lx+2), screenY(ly));
>> g.drawLine(screenX(lx),
>> screenY(ly-2), screenX(lx), screenY(ly+2));
>> }
>> }
>> }//~cc drawOverlay
>>
>> }//~ custom canvas class
>> </code>
>>
>> Another option would be to just create a new image, as a composite of
>> your data sets.
>>
>> -Gabriel
>>
>> -----Original Message-----
>> From: ImageJ Interest Group [mailto:
[hidden email]]On Behalf Of
>> Johannes Schindelin
>> Sent: Thursday, November 02, 2006 10:40 AM
>> To:
[hidden email]
>> Subject: Re: Image J - overlay
>>
>>
>> Hi,
>>
>> On Thu, 2 Nov 2006, O'Brien.Joseph wrote:
>>
>>> It's a cold afternoon here in the UK [...]
>>
>> Funny, I was in Scotland until Tuesday, and it was warmer than
>> here in
>> Germany!
>>
>>> The question is.......Can imageJ perform an 'overlay' function?
>>
>> You might want to copy the image to be overlayed, and play with
>> "Edit/Paste Control..." I got what I wanted with "Max".
>>
>> Hth,
>> Dscho
>>
>> *********************************************************************
>> *******************
>>
>> Note: If the reader of this message is not the intended
>> recipient, or an employee or agent responsible for delivering this
>> message to the intended recipient, you are hereby notified that
>> any dissemination, distribution or copying of this communication
>> is strictly prohibited. If you have received this communication in
>> error, please notify us immediately by replying to the message and
>> deleting it from your computer. Thank you.
>>
>> *********************************************************************
>> *******************
>>
>
> ------------------------------
>
> Date: Thu, 2 Nov 2006 14:43:09 -0800
> From: "David W. Robinson" <
[hidden email]>
> Subject: Nearest Neighbour Analysis
>
> Hi there,
>
> We have 2D images of neurons and we would like to conduct a nearest
> neighbor analysis. We can use point picker to get the XY
> coordinates of
> the cell bodies we wish to analyze but have not yet found a plugin or
> method for using ImageJ to compute the nearest neighbor value. Does
> anyone know how we can achieve this in either ImageJ or with some
> other
> program?
>
> Thank you
>
> David
>
> --
> David W. Robinson, Ph.D.
> Vice Provost for Academic Technology
> Assistant Professor and Director, Educational Communications
> Center for Research on Occupational and Environmental Toxicology, L606
> Oregon Health & Science University
> 3181 Sam Jackson Park Road
> Portland OR 97239
>
> Tel 503-494-7361
> Fax 503-494-4352
>
>
[hidden email]
>
> ------------------------------
>
> Date: Thu, 2 Nov 2006 09:04:14 -0800
> From: Harry Parker <
[hidden email]>
> Subject: Re: Out of available memory? Help!
>
> I had a similar problem when running ImageJ locally on my Windows
> PC. =0A=
> =0AI had renamed ImageJ to something like "ImageJv1.3" to allow
> myself muti=
> ple versions for testing.=0AIt appeared to work well in every
> respect, EXCE=
> PT it did not read the config file memory allocation option!
> =0A=0AChanging =
> the name back to "ImageJ" fixed the problem.=0A=0AI found that I
> could do w=
> hat I wanted to do by renaming links to the ImageJ versions in
> different di=
> rectories.=0A=0ADid you rename ImageJ?=0A =0A-- =0AHarry Parker
> =0ASenior=
> Systems Engineer =0ADialog Imaging Systems, Inc.=0A=0A-----
> Original Mess=
> age ----=0AFrom: Jonathan Thomas <
[hidden email]>=0ATo:
> IMAGEJ@LIST=
> .NIH.GOV=0ASent: Wednesday, November 1, 2006 5:23:24 PM=0ASubject:
> Out of a=
> vailable memory? Help!=0A=0A(cliffs at bottom)=0A=0AI am currently
> trying t=
> o use ImageJ to do image segmentation on some ~11MB =0ARGB images.
> The ima=
> ges load fine into ImageJ, but if I attempt to do any =0Afiltering
> on them =
> ImageJ throws this error:=0A=0A<Out of memory>=0A<All available
> memory (63M=
> B) has been>=0A<used. Instructions for making more>=0A<available
> can be fou=
> nd in the "Memory" >=0A<sections of the installation notes
> at>=0A<
http://rs=> b.info.nih.gov/ij/docs/install/
> >=0A>>>>>>>>>>>>>>>>>>>>>>>>>>>=0A=0AI then =
> poked through the options and raised the memory alotted to 500MB,
> =0Aclosed=
> ImageJ and reopened it attempted the same operation and got an
> =0Aidentica=
> l error. Even mentioning 63MB. Note that the default was not 63
> =0AMB nor=
> was the max memory set anywhere near 63MB after I changed
> it.=0A=0A=0ASo I=
> came here, and I see people recommending changing the command
> given =0Ato =
> the executable, so I checked my ImageJ.cfg and it reads:=0A=0A.=0AC:
> \Progra=
> m Files\Java\j2re1.4.2_03\bin\javaw.exe=0A-Xmx500m -cp ij.jar
> ij.ImageJ=0A=
> =0AIn a previous thread someone mentioned a similar problem and
> modifying =
> =0Athis line fixed the problem but I believe that java should have
> plenty o=
> f =0Amemory the way I have it configured.=0A=0ASo that's my
> problem, I'd ap=
> preciate any help you guys can give me.=0A=0AIf you have read this
> far here=
> is some more information that may be =0Ahelpful:=0A=0A2.99Ghz
> Pentium D=0A=
> 2GB Ram=0A=0AImageJ 1.36b=0AJava 1.5.0_06=0AAbout ImageJ displays
> 55MB of 5=
> 00MB (11%) while the error message is still =0Ain the log.=0A=0AThe
> java is=
> on this machine, while the ImageJ is being run from a network
> =0Adrive. T=
> he same error arrizes when I run ImageJ as an applet from the NIH
> =0Apage.=
> =0A=0AI have contacted the sys admin and he assures me that there
> is no =0A=
> constraint put on memory used by a user, with the exception of the
> =0Aphysi=
> cal memory on the machine and what is being used by other
> software.=0A=0ASo=
> ftware running in the background or not has no effect on the error
> =0Amessa=
> ge.=0A=0AI have replicated this error on 2 machines, each using
> their own l=
> ocal =0Ajava but the same ImageJ off the same network drive. I
> have also =
> =0Areplicated it running ImageJ as an applet on both
> machines.=0A=0ACurious=
> ly when I look at the size of the image in windows it is listed as
> =0A11MB,=
> but ImageJ claims it's 27MB. (perhaps this is extra space for a
> =0Abuffer=
> ?) One image is 2915x2456 pixel tiff. The others are similar.
> All =0Atif=
> fs, all RGB, all produce the same error.=0A=0AIf you have made it
> this far =
> I truly commend you. Thank you for the =0Aattention and here's a
> quote for=
> your efforts.=0A=0A"'That is indisputable,' was the answer, 'but
> in this c=
> ountry it is a good =0Athing to kill an admiral from time to time
> to encour=
> age the others.'"=0A-Voltaire (Fran=E7ois-Marie Arouet), Candide
> =0A=0AThan=
> k you for any help you can give me.=0A-Stumped in
> StonyBrook=0A=0A=0A=0A=0A=
> =0Afinally cliffnotes:=0A1. ImageJ throws an out of memory error
> when I try=
> to analyze some large =0Atiff images=0A2. The machine has plenty
> of memory=
> and so does java.=0A3. Solutions to similar problems from this
> listserv do=
> not help.=0A4. Recent software, reproducible.=0A5. HELP!=0A6.
> quote for yo=
> ur efforts, thanks!=0A=0A=0A=0A=0A=0A=0A
>
> ------------------------------
>
> Date: Thu, 2 Nov 2006 19:33:55 -0600
> From: Michael Miller <
[hidden email]>
> Subject: Re: Nearest Neighbour Analysis
>
> Hello,
>
> I've written a number of plugins for ImageJ in Java that: trace pixel
> neighborhoods on a greyscale image to try to find the nearest local
> maxima,
> search skeletal branchings for the nearest "node", as well as
> looked at
> mesh/particle components. So I strongly suspect what you are trying
> to do
> can be done within ImageJ.
>
> I think generally the best advice at this stage would be for you to
> post a
> few links to some of your images that represent a good sample of
> what you
> have. Then I can at least respond more completely. If you're
> tracing along
> neuron network connections, then I can almost definately help you. :-)
>
> If your pictured neurons are isolated, my first guess would be to
> use the
> Particle Analyzer to identify the exact single-coordinate centers
> of each
> neuron, construct a list of those centers, and then at that point a
> first
> year Informatics student could pair up all the closest neurons :-)
>
> Cheers,
> -Mike Miller
>
[hidden email]
>
> ----- Original Message -----
> From: "David W. Robinson" <
[hidden email]>
> To: <
[hidden email]>
> Sent: Thursday, November 02, 2006 4:43 PM
> Subject: Nearest Neighbour Analysis
>
>
>> Hi there,
>>
>> We have 2D images of neurons and we would like to conduct a nearest
>> neighbor analysis. We can use point picker to get the XY
>> coordinates of
>> the cell bodies we wish to analyze but have not yet found a plugin or
>> method for using ImageJ to compute the nearest neighbor value.
>> Does anyone
>> know how we can achieve this in either ImageJ or with some other
>> program?
>>
>> Thank you
>>
>> David
>>
>> --
>> David W. Robinson, Ph.D.
>> Vice Provost for Academic Technology
>> Assistant Professor and Director, Educational Communications
>> Center for Research on Occupational and Environmental Toxicology,
>> L606
>> Oregon Health & Science University
>> 3181 Sam Jackson Park Road
>> Portland OR 97239
>>
>> Tel 503-494-7361
>> Fax 503-494-4352
>>
>>
[hidden email]
>
> ------------------------------
>
> End of IMAGEJ Digest - 1 Nov 2006 to 2 Nov 2006 (#2006-295)
> ***********************************************************