Plugin directory on the server
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Plugin directory on the server
 
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Hello,
My students will use ImageJ in my lab (on Windows). In the lab, applications are generally installed on client computers and students data are stored on the server. Is there a way to configure that the plugin directory is stored on the server? I only found the path to the plugin directory within the source files. Thanks, Wolfgang |
Antwort: Plugin directory on the server
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HI,
There is something related to that in the archives: The "plugins.dir" property specifies the location of the parent of the plugins directory. This property can be set from either the command line or from within a Java program that starts ImageJ. For example, if you run ImageJ with the command java -Dplugins.dir=/Users/wayne -cp ij.jar ij.ImageJ it will look for the plugins folder in the /Users/wayne/ directory. This property can also be set in a program that launches ImageJ: System.getProperties().setProperty("plugins.dir", "/Users/wayne/ImageJ"); new ImageJ(null); |---------+--------------------------------> | | Wolfgang Lux | | | <wolfgang.lux@FH-DUES| | | SELDORF.DE> | | | Gesendet von: ImageJ | | | Interest Group | | | <[hidden email]>| | | | | | | | | 31.05.2006 10:33 | | | Bitte antworten an | | | ImageJ Interest Group| |---------+--------------------------------> >-------------------------------------------------------------------------------------------------------------------------------| | | | An: [hidden email] | | Kopie: (Blindkopie: Joachim Wesner/DEWET/LMSCentral/Leica) | | Thema: Plugin directory on the server | >-------------------------------------------------------------------------------------------------------------------------------| Hello, My students will use ImageJ in my lab (on Windows). In the lab, applications are generally installed on client computers and students data are stored on the server. Is there a way to configure that the plugin directory is stored on the server? I only found the path to the plugin directory within the source files. Thanks, Wolfgang ______________________________________________________________________ This email has been scanned by the MessageLabs Email Security System. For more information please visit http://www.messagelabs.com/email ______________________________________________________________________ |
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In reply to this post by Wolfgang Lux-2
Hi,
On Wed, 31 May 2006, Wolfgang Lux wrote: > Is there a way to configure that the plugin directory is stored on the > server? Yes. You can pass the command line option "-ijpath x:/hello" and ImageJ will look in x:/hello/plugins for the plugins. You could also try some trickery with Java properties, but that is more complicated. Alternatively, you could patch ImageJ to read the plugin path from IJ_Props.txt, which is contained in the JAR file. Hth, Dscho |
Re: Plugin directory on the server
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Hi,
this is interesting: > Yes. You can pass the command line option "-ijpath x:/hello" and ImageJ > will look in x:/hello/plugins for the plugins. So by doing this, ImageJ will load also the ij.jar from the server? Would it also be possible to load the newest ij.jar directly from http://rsb.info.nih.gov/ij/upgrade/ij.jar every time IJ starts? I'm wondering about an easy way to keep around 20 machines with IJ updated... Michael -- Michael Weber (B.Sc.) ..MTZ (before 12.30 pm).. Technische Universität Medical Theoretical Centre, Haus 91 Fiedlerstr. 42 D-01307 Dresden e-mail: [hidden email] phone: +49 351 4586426 ..MPI (after 12.30 pm).. Max Planck Institute of Molecular Cell Biology and Genetics Light Microscopy Facility Pfotenhauer Str. 108 D-01307 Dresden e-mail: [hidden email] phone: +49 351 2102837 |
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In reply to this post by Joachim Wesner
Dear all,
I am trying to send a string through the serial port which, when in Hyperterminal, looks like the following example: 50398384728<ENTER> This is how I have it coded in my Macro: ----- EOL = "\n"; run("serial plugin", "genericcmd=50398384728" + EOL); ----- My EOL is sometimes temperamental, having changed it to "\r\n" too! Regardless of the "serial plugin" used, what is the correct notation for an end of line character in ImageJ under both Windows and Unix systems? Cheers, Andy |
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In reply to this post by Michael Weber-4
Hi,
On Wed, 31 May 2006, Michael Weber wrote: > this is interesting: > > > Yes. You can pass the command line option "-ijpath x:/hello" and ImageJ will > > look in x:/hello/plugins for the plugins. > > So by doing this, ImageJ will load also the ij.jar from the server? No. Just the plugins. And I do not know if you are free to use whatever protocol you like. In my example, I wrote "x:/hello", because I assumed that the original poster uses Windows. Ciao, Dscho |
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In reply to this post by Michael Weber-4
Hi Michael,
Would it also be possible to load the newest ij.jar directly from > > http://rsb.info.nih.gov/ij/upgrade/ij.jar > > every time IJ starts? It shouldn't be difficult to write a little Java wrapper that checks the server for an upgrade using URL.getResourceAsStream, then launches ImageJ via reflection (to prevent the ClassLoader from loading the ImageJ classes from ij.jar before the new one is downloaded). It would be most friendly to only download ij.jar again if the datestamp is newer. Alternately, you could set up ImageJ via Java Web Start, which automatically keeps the software up-to-date with what's on the server. I did some work on deploying ImageJ via JWS a couple of weeks ago, and was planning on finishing that up soon, when I have time. Has anyone else successfully deployed ImageJ with JWS? If not, I'll post my results once I have them. -Curtis |
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In reply to this post by Weller Andrew Francis
Andy,
I am not familiar with the serial plugin, however the generally accepted end of data termination that a device expects is "carriage return" (ASCII 13) and / or "line feed" (ASCII 10). The plugin may already be sending one or more of these characters as part of the plugin code so an extra one may be confusing the listening device. This confusion may continue to the next input so it becomes "temperamental", so after each trial you may have to reset the listen device. You could build the termination sequence using: CR=fromCharCode(13); LF=fromCharCode(10); and then create the string outside of the serial plugin command and append nothing or CR or LF or CR+LF or LF+CR for example gencmd= "genericcmd=50398384728" + CR + LF; run("serial plugin", gencmd); good luck, John Cahill On 5/31/06, Andy Weller <[hidden email]> wrote: > Dear all, > > I am trying to send a string through the serial port which, when in > Hyperterminal, looks like the following example: > > 50398384728<ENTER> > > This is how I have it coded in my Macro: > > ----- > EOL = "\n"; > > run("serial plugin", "genericcmd=50398384728" + EOL); > ----- > > My EOL is sometimes temperamental, having changed it to "\r\n" too! > Regardless of the "serial plugin" used, what is the correct notation for > an end of line character in ImageJ under both Windows and Unix systems? > > Cheers, Andy > |
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In reply to this post by Weller Andrew Francis
Hi Andy,
I seem to remember that you should use plugin without terminator. Close hyperterminal-session before use plugin!! by Nicola ---------- Initial Header ----------- From : "ImageJ Interest Group" [hidden email] To : [hidden email] Cc : Date : Wed, 31 May 2006 13:41:41 +0200 Subject : End of line? > Dear all, > > I am trying to send a string through the serial port which, when in > Hyperterminal, looks like the following example: > > 50398384728<ENTER> > > This is how I have it coded in my Macro: > > ----- > EOL = "\n"; > run("serial plugin", "genericcmd=50398384728" + EOL); > ----- > > My EOL is sometimes temperamental, having changed it to "\r\n" too! > Regardless of the "serial plugin" used, what is the correct notation for > an end of line character in ImageJ under both Windows and Unix systems? > > Cheers, Andy > |
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hello,
i repeat my question about estimating particle orientation based on shape descriptor and center of mass. if there is a particle which starts as a round particle and grows to become elongated and the front of this particle is wider than the width of particle at the beginning is it possible to write a macro or is there any plugin which can draw a vector which start in the one end of particle( this part where it startet to grow) and ends in center of mass( or in the opposite end of particle than it was said to be begggining)? can i ask you to help to construct this kind of procedure?> with best regards, thanks in advance jarek |
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Hi,
what do you mean by "grow"? In time? So you have 2 related images, one with small almost round particles and one later, when it has "grown" to the final asymmetric shape? OR you mean that the width of particle "grows" (widens) along the vector you are referring to - in ONE image ? In the latter case, one could probably look at the center of mass of the particles after and before eroding to find that vector and then look along that vetor to find the exact end of the particle on the thin side. Or look at the sceletonize operator, if the particles are probably like a "bulb" resp. a "pear" it would also probably also give something close to the vector you are interested in (but still with an ambiguity relative to forward/backward, but that again could probably be solved by looking at the center of mass), you still would need some extra processing to find the edges Hope this could help JW |---------+---------------------------> | | Jarek Grodek | | | <[hidden email]| | | BLIN.PL> | | | Gesendet von: | | | ImageJ Interest | | | Group | | | <[hidden email]| | | .GOV> | | | | | | | | | 01.06.2006 10:41| | | Bitte antworten | | | an ImageJ | | | Interest Group | |---------+---------------------------> >-------------------------------------------------------------------------------------------------------------------------------| | | | An: [hidden email] | | Kopie: | | Thema: particle orientation | >-------------------------------------------------------------------------------------------------------------------------------| hello, i repeat my question about estimating particle orientation based on shape descriptor and center of mass. if there is a particle which starts as a round particle and grows to become elongated and the front of this particle is wider than the width of particle at the beginning is it possible to write a macro or is there any plugin which can draw a vector which start in the one end of particle( this part where it startet to grow) and ends in center of mass( or in the opposite end of particle than it was said to be begggining)? can i ask you to help to construct this kind of procedure?> with best regards, thanks in advance jarek ______________________________________________________________________ This email has been scanned by the MessageLabs Email Security System. For more information please visit http://www.messagelabs.com/email ______________________________________________________________________ |
Re: Antwort: particle orientation
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hello, yes it is a one image indeed!
i was thinking also about skeletonnize operatingbut still just like you mentioned i had a problem to make imagej "see" where the vestor starts and where should it stop. thanks for reply. does anyone else has some more ideas? thanks in advance, jarek > Hi, > > what do you mean by "grow"? In time? So you have 2 related images, one > with > small almost round particles and one later, when it has "grown" to the > final asymmetric shape? > > OR you mean that the width of particle "grows" (widens) along the vector > you are referring to - in ONE image ? > > In the latter case, one could probably look at the center of mass of the > particles after and before eroding to find that vector and then look along > that vetor to find the exact end of the particle > on the thin side. > > Or look at the sceletonize operator, if the particles are probably like a > "bulb" resp. a "pear" it would also probably also give something close to > the vector you are interested in (but still with an > ambiguity relative to forward/backward, but that again could probably be > solved by looking at the center of mass), you still would need some extra > processing to find the edges > > Hope this could help > > JW > > > > |---------+---------------------------> > | | Jarek Grodek | > | | <[hidden email]| > | | BLIN.PL> | > | | Gesendet von: | > | | ImageJ Interest | > | | Group | > | | <[hidden email]| > | | .GOV> | > | | | > | | | > | | 01.06.2006 10:41| > | | Bitte antworten | > | | an ImageJ | > | | Interest Group | > |---------+---------------------------> > >-------------------------------------------------------------------------------------------------------------------------------| > | > | > | An: [hidden email] > | > | Kopie: > | > | Thema: particle orientation > | > >-------------------------------------------------------------------------------------------------------------------------------| > > > > > hello, > i repeat my question about estimating particle orientation based on shape > descriptor and center of mass. > > if there is a particle which starts as a round particle and grows to > become elongated and the front of this particle is wider than the width of > particle at the beginning is it possible to write a macro or is there any > plugin which can draw a vector which start in the one end of particle( > this part where it startet to grow) and ends in center of mass( or in the > opposite end of particle than it was said to be begggining)? > > can i ask you to help to construct this kind of procedure?> > > with best regards, thanks in advance > > jarek > > > > ______________________________________________________________________ > This email has been scanned by the MessageLabs Email Security System. > For more information please visit http://www.messagelabs.com/email > ______________________________________________________________________ > > |
Antwort: Re: Antwort: particle orientation
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Hi,
OK, I see! Yep I think using the skeleton to find the approx. vector and then using enough erosion will probably reduce each particle to one small spot in the "center" of the wide end which should tell you the "right" orientation of that vector. Joachim |---------+---------------------------> | | Jarek Grodek | | | <[hidden email]| | | BLIN.PL> | | | Gesendet von: | | | ImageJ Interest | | | Group | | | <[hidden email]| | | .GOV> | | | | | | | | | 01.06.2006 11:52| | | Bitte antworten | | | an ImageJ | | | Interest Group | |---------+---------------------------> >-------------------------------------------------------------------------------------------------------------------------------| | | | An: [hidden email] | | Kopie: | | Thema: Re: Antwort: particle orientation | >-------------------------------------------------------------------------------------------------------------------------------| hello, yes it is a one image indeed! i was thinking also about skeletonnize operatingbut still just like you mentioned i had a problem to make imagej "see" where the vestor starts and where should it stop. thanks for reply. does anyone else has some more ideas? thanks in advance, jarek > Hi, > > what do you mean by "grow"? In time? So you have 2 related images, one > with > small almost round particles and one later, when it has "grown" to the > final asymmetric shape? > > OR you mean that the width of particle "grows" (widens) along the vector > you are referring to - in ONE image ? > > In the latter case, one could probably look at the center of mass of the > particles after and before eroding to find that vector and then look > that vetor to find the exact end of the particle > on the thin side. > > Or look at the sceletonize operator, if the particles are probably like a > "bulb" resp. a "pear" it would also probably also give something close to > the vector you are interested in (but still with an > ambiguity relative to forward/backward, but that again could probably be > solved by looking at the center of mass), you still would need some extra > processing to find the edges > > Hope this could help > > JW > > > > |---------+---------------------------> > | | Jarek Grodek | > | | <[hidden email]| > | | BLIN.PL> | > | | Gesendet von: | > | | ImageJ Interest | > | | Group | > | | <[hidden email]| > | | .GOV> | > | | | > | | | > | | 01.06.2006 10:41| > | | Bitte antworten | > | | an ImageJ | > | | Interest Group | > |---------+---------------------------> > >-------------------------------------------------------------------------------------------------------------------------------| > | > | > | An: [hidden email] > | > | Kopie: > | > | Thema: particle orientation > | > >-------------------------------------------------------------------------------------------------------------------------------| > > > > > hello, > i repeat my question about estimating particle orientation based on shape > descriptor and center of mass. > > if there is a particle which starts as a round particle and grows to > become elongated and the front of this particle is wider than the width > particle at the beginning is it possible to write a macro or is there any > plugin which can draw a vector which start in the one end of particle( > this part where it startet to grow) and ends in center of mass( or in the > opposite end of particle than it was said to be begggining)? > > can i ask you to help to construct this kind of procedure?> > > with best regards, thanks in advance > > jarek > > > > ______________________________________________________________________ > This email has been scanned by the MessageLabs Email Security System. > For more information please visit http://www.messagelabs.com/email > ______________________________________________________________________ > > ______________________________________________________________________ This email has been scanned by the MessageLabs Email Security System. For more information please visit http://www.messagelabs.com/email ______________________________________________________________________ |
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In reply to this post by Jarek Grodek
Hmm... there are a couple of ways that you could do this. One, that comes to mind, would be to use the [1st] moments of the object::
Centroid {Cx,Cy} = {Sx/A,Sy/A} where Sx = sum(x values in object), Sy = sum(y values in object) and A=area You could, then, easily update this as your particle "grows" by updating Sx, Sy, and A, then calculating the new centroid. A vector from the first centroid to the second would just be {(Cx2-Cx1),(Cy2-Cy1)} (a least-squares fit for a the major axis of growth is left as an exercise for the person who wishes to apply it.) One way in which you could draw this is by writing an override of the ImageCanvas.Paint(Graphics g) to include something like: class CustomCanvas extends ImageCanvas { //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) { g.drawLine(screenX((int)(Cx1+0.5)), screenY((int)(Cy1+0.5)), screenX((int)(Cx2+0.5)), screenY((int)(Cy2+0.5))); }//~drawOverlay } You could make the line [y=m*x+b] drawn any length that you like, since you have the slope m = (Cy2-Cy1)/(Cx2-Cx1), and intercept b = Cy1-m*Cx1, you could, for example, work out : Y2 = min(y[max],m*x[max]+b) and X2 = (Y2-b)/m and use those values, in place of Cx2 and Cy2 in the above code snippet, to draw a vector from the original centroid to the endpoint furthest from it, in the direction of growth. As I wrote, in opening, there are many ways in which this could be approached. This is not, necessarily, the best (need more info for that - e.g. how many stages of growth are included, what other processing are you doing, &c.), but it's the first that came to mind. I hope that it helps. -gd -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]]On Behalf Of Jarek Grodek Sent: Thursday, June 01, 2006 4:41 AM To: [hidden email] Subject: particle orientation hello, i repeat my question about estimating particle orientation based on shape descriptor and center of mass. if there is a particle which starts as a round particle and grows to become elongated and the front of this particle is wider than the width of particle at the beginning is it possible to write a macro or is there any plugin which can draw a vector which start in the one end of particle( this part where it startet to grow) and ends in center of mass( or in the opposite end of particle than it was said to be begggining)? can i ask you to help to construct this kind of procedure?> with best regards, thanks in advance jarek **************************************************************************************** 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. **************************************************************************************** |
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In reply to this post by Jarek Grodek
Jarek,
It seems to me that you could get at the orientation of the desired vector by computing the second moment of the area (the moment of inertia of the cross section) for your objects. The principal directions of the object can be determined in such a calculation. These directions essentially specify "major and minor axes" for your object. I believe that what you're describing is a vector oriented along the first principal axis. A search on google gave these two links: http://www.hopkinsmedicine.org/FAE/mmacro.htm http://rsb.info.nih.gov/ij/plugins/moments.html Also, on the old NIH Image list, I recall that Matthew Warfel submitted some code for these types of calculations. Typing in his name yielded this - a link to the code you would need: http://www.hopkinsmedicine.org/FAE/MomentMacroJ_v1_2.txt Hope this helps, --Mike IMPORTANT NOTICE: This communication, including any attachment, contains important information that may be confidential or privileged, and is intended solely for the entity or individual to whom it is addressed. If you are not the intended recipient, you should contact the sender and delete this message. Any unauthorized disclosure, copying, or distribution of this message is strictly prohibited. Nothing in this email, including any attachment, is intended to be a legally binding signature. |
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Is it possible to count the number of pixels within a specified region that have the same color?
Thanks so much! ~Katherine |
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The plugin "Color Inspector 3D" on the ImageJ web site may do what you want.
Katherine Huang <[hidden email]> wrote: Is it possible to count the number of pixels within a specified region that have the same color? Thanks so much! ~Katherine -- Harry Parker Systems Engineer Dialog Imaging Systems, Inc. --------------------------------- Yahoo! Messenger with Voice. PC-to-Phone calls for ridiculously low rates. |
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In reply to this post by Michael Roberts-4
Michael Roberts napisał(a):
> Jarek, > > It seems to me that you could get at the orientation of the desired > vector by computing the second moment of the area (the moment of > inertia of the cross section) for your objects. The principal > directions of the object can be determined in such a calculation. > These directions essentially specify "major and minor axes" for your > object. I believe that what you're describing is a vector oriented > along the first principal axis. > > A search on google gave these two links: > > http://www.hopkinsmedicine.org/FAE/mmacro.htm > http://rsb.info.nih.gov/ij/plugins/moments.html > > Also, on the old NIH Image list, I recall that Matthew Warfel > submitted some code for these types of calculations. Typing in his > name yielded this - a link to the code you would need: > > http://www.hopkinsmedicine.org/FAE/MomentMacroJ_v1_2.txt > > Hope this helps, > --Mike > > > > > IMPORTANT NOTICE: This communication, including any attachment, > contains important information that may be confidential or privileged, > and is intended solely for the entity or individual to whom it is > addressed. If you are not the intended recipient, you should contact > the sender and delete this message. Any unauthorized disclosure, > copying, or distribution of this message is strictly prohibited. > Nothing in this email, including any attachment, is intended to be a > legally binding signature. > > > thanks for suggestions, i've checked those macros and still not found satysfying answer for my problem. those two macros seem to fit major and minor axis according to bounding rectangle. it would be ok when particles were oriented in staright horiz/vertical order, but it is not true, i want to analyze direction of "growth" where angle of this direction vary from 0 to 360 degrees. greatfully expecting any help to resolve this problem. thanks in advance, jarek |
internship loctaion searching and trainee position proposition
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hello NIH group,
i'd like to ask you for help in finding institute, facility or organisation working with image analysis for eventual possibility of internship for PhD student. i'm a PhD student in Institute of Agrophysics of Polish Academy of Sciences. In my work i process and analyze x-ray images of biological materials. the main topic up till now was processing and analysis of x-ray images of wheat kernels infested by granary weevil, but it is not the only object of my interest. i like to work with images of microstructure of biological materials and looking for possibility of internship with the trainee position. i want to set theses for my doctoral work about analysis of plant tissues images analysis versus physical properties of these materials. i work with ImageJ for 8 months already and find it very fruitful and powerful tool for anaysing. if anyone has some information or can help with reaching contact to any institute which can offer trainee position, please do not hesitate and let me know. thanks in advance, with best regards, jarek grodek |
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In reply to this post by Jarek Grodek
jarek wrote:
> Michael Roberts napisał(a): >> Jarek, >> >> It seems to me that you could get at the orientation of the desired >> vector by computing the second moment of the area (the moment of >> inertia of the cross section) for your objects. The principal >> directions of the object can be determined in such a calculation. >> These directions essentially specify "major and minor axes" for your >> object. I believe that what you're describing is a vector oriented >> along the first principal axis. >> >> A search on google gave these two links: >> >> http://www.hopkinsmedicine.org/FAE/mmacro.htm >> http://rsb.info.nih.gov/ij/plugins/moments.html >> >> Also, on the old NIH Image list, I recall that Matthew Warfel >> submitted some code for these types of calculations. Typing in his >> name yielded this - a link to the code you would need: >> >> http://www.hopkinsmedicine.org/FAE/MomentMacroJ_v1_2.txt >> >> Hope this helps, >> --Mike >> >> >> >> >> IMPORTANT NOTICE: This communication, including any attachment, >> contains important information that may be confidential or >> privileged, and is intended solely for the entity or individual to >> whom it is addressed. If you are not the intended recipient, you >> should contact the sender and delete this message. Any unauthorized >> disclosure, copying, or distribution of this message is strictly >> prohibited. Nothing in this email, including any attachment, is >> intended to be a legally binding signature. >> >> >> > hello, > thanks for suggestions, i've checked those macros and still not found > satysfying answer for my problem. those two macros seem to fit major > and minor axis according to bounding rectangle. it would be ok when > particles were oriented in staright horiz/vertical order, but it is > not true, i want to analyze direction of "growth" where angle of this > direction vary from 0 to 360 degrees. greatfully expecting any help to > resolve this problem. > > thanks in advance, > jarek I'm confident that the moment-of-inertia in the first link does not strictly fit particles oriented in the vertical or horizontal direction. In the first link, there is an image showing the principal axes of a bone specimen cross section, and these orientations are non-vertical/horizontal. However, as you can see, the 2 axes are perpendicular to one another. My thinking was that portions of this code could be used to pull out the first principal orientation angle (the angle of the major axis orientation) in order to get the required information for your direction of growth vector. You'd also want to pull out the centroid location. This would take a little coding on your part, but not much. Perhaps I'm not understanding your problem, however. For instance, if your particles are able to grow in multiple directions then the approach I've suggested will be of little help. On the other hand, if a given particle has a single angle indicating the predominant growth direction, I think some of code in the first link may be useful. Good luck, --Mike |
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