ImageJ

"Magnetic lasso"-like tool

_‹ Previous Topic Next Topic _›

Classic

List

Threaded

6 messages Options

Vera, Pedro L.

"Magnetic lasso"-like tool

Greetings all:
I'm using ImageJ to measure DAB immunostaining intensity and I would like to trace (using a mouse) and select certain areas for measurement. Currently, the freehand tool works but it's very cumbersome and also fairly innacurate. Adobe Photoshop has a "magnetic lasso" tool that outlines and snaps to differences in pixel intensity and I have found it very useful for the kind of tracing that I am doing. Is there a similar plugin for ImageJ? I have searched the plugin list but have been unable to find one.

Thanks.

Pedro

Jean-Yves Tinevez-2

Re: "Magnetic lasso"-like tool

On Sep 22, 2009, at 11:39 AM, Vera, Pedro L. wrote:

> Greetings all:
> I'm using ImageJ to measure DAB immunostaining intensity and I would
> like to trace (using a mouse) and select certain areas for
> measurement. Currently, the freehand tool works but it's very
> cumbersome and also fairly innacurate. Adobe Photoshop has a
> "magnetic lasso" tool that outlines and snaps to differences in
> pixel intensity and I have found it very useful for the kind of
> tracing that I am doing. Is there a similar plugin for ImageJ? I
> have searched the plugin list but have been unable to find one.

The Fiji package has blow\lasso tool that works quite ok, tough they
are announced as non-fully functional.
I think it similar to what you are looking for.

http://pacific.mpi-cbg.de/wiki/index.php/Lasso_selection

cheers
jy

Volker Baecker

Re: "Magnetic lasso"-like tool

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Another one is the LiveWire, that can be found here:
http://ivussnakes.sourceforge.net/index.php?option=com_content&view=article&id=46&Itemid=53
Cheers,
Volker

Jean-Yves Tinevez wrote:

> On Sep 22, 2009, at 11:39 AM, Vera, Pedro L. wrote:
>
>> Greetings all:
>> I'm using ImageJ to measure DAB immunostaining intensity and I would
>> like to trace (using a mouse) and select certain areas for
>> measurement. Currently, the freehand tool works but it's very
>> cumbersome and also fairly innacurate. Adobe Photoshop has a "magnetic
>> lasso" tool that outlines and snaps to differences in pixel intensity
>> and I have found it very useful for the kind of tracing that I am
>> doing. Is there a similar plugin for ImageJ? I have searched the
>> plugin list but have been unable to find one.
>
> The Fiji package has blow\lasso tool that works quite ok, tough they are
> announced as non-fully functional.
> I think it similar to what you are looking for.
>
> http://pacific.mpi-cbg.de/wiki/index.php/Lasso_selection
>
> cheers
> jy
>

-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.9 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org

iEYEARECAAYFAkq4oOUACgkQ0gXPLVKexCdZFgCfV3gMQv6XeMQur0hgmC4IqDrK
eQQAnAy4DDN4E5Urvq1Fhtc35YMiQpJm
=79Uq
-----END PGP SIGNATURE-----

--
passerelle antivirus du campus CNRS de Montpellier
--

Vera, Pedro L.

Re: "Magnetic lasso"-like tool

Thanks for the suggestions. I installed the LiveWire plugin, since it seemed like it would do what I was looking for. However, I'm getting all kinds of errors (both in a windows box and a linux box). Following are the error msg (from the windows install). Btw, I'm running ImageJ 1.43f. It seems that the java version is a problem, but I don't get any other error msg when I run ImageJ.

java.lang.UnsupportedClassVersionError: Bad version number in .class file
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(Unknown Source)
at java.security.SecureClassLoader.defineClass(Unknown Source)
at java.net.URLClassLoader.defineClass(Unknown Source)
at java.net.URLClassLoader.access$100(Unknown Source)
at java.net.URLClassLoader$1.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at ij.IJ.runUserPlugIn(IJ.java:177)
at ij.IJ.runPlugIn(IJ.java:146)
at ij.Executer.runCommand(Executer.java:122)
at ij.Executer.run(Executer.java:59)
at ij.IJ.run(IJ.java:244)
at ij.macro.Functions.doRun(Functions.java:551)
at ij.macro.Functions.doFunction(Functions.java:74)
at ij.macro.Interpreter.doStatement(Interpreter.java:200)
at ij.macro.Interpreter.doBlock(Interpreter.java:511)
at ij.macro.Interpreter.runMacro(Interpreter.java:127)
at ij.macro.MacroRunner.run(MacroRunner.java:126)
at java.lang.Thread.run(Unknown Source)

I would appreciate any suggestions on how to fix this.

Best regards,
Pedro

________________________________________
From: ImageJ Interest Group [[hidden email]] On Behalf Of Volker Baecker [[hidden email]]
Sent: Tuesday, September 22, 2009 6:03 AM
To: [hidden email]
Subject: Re: "Magnetic lasso"-like tool

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Another one is the LiveWire, that can be found here:
http://ivussnakes.sourceforge.net/index.php?option=com_content&view=article&id=46&Itemid=53
Cheers,
Volker

Jean-Yves Tinevez wrote:

Gabriel Landini

Re: "Magnetic lasso"-like tool

On Tuesday 22 September 2009 14:58:19 Vera, Pedro L. wrote:
> Thanks for the suggestions. I installed the LiveWire plugin, since it seemed
like it would do what I was looking for. However, I'm getting all kinds of
errors (both in a windows box and a linux box). Following are the error msg
(from the windows install). Btw, I'm running ImageJ 1.43f. It seems that the
java version is a problem, but I don't get any other error msg when I run
ImageJ.

It is been some time since I tried last, but I also had problems using the
LiveWire plugin (under linux).

ImageJ's magic wand has recently been enhanced by means of a tolerance setting
(double click on the magic wand icon). It is probably not what you are looking
for, but it might help anyway.

BTW, when I read postings from other users trying to quantify dab intensity I
point them to this very informative message (last part) posted some time ago
to this list:

https://list.nih.gov/cgi-bin/wa?A2=ind0902&L=IMAGEJ&P=R18412&I=-3

I hope it helps.

G.

Volker Baecker

Re: "Magnetic lasso"-like tool

In reply to this post by Vera, Pedro L.

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Hello,
the plugin needs java 1.6. I don't know the version from the site,
please contact the author for information about it.
If it doesn't work with java 1.6, you can try the version that comes
with "mri cell image analyzer" from
http://www.mri.cnrs.fr/index.php?m=42
if you don't mind to install a lot of stuff that you didn't want (make a
backup of your imagej folder before installing). You can start the
LiveWire 1d or 2d from the Tracing toolset.
Best regards,
Volker Bäcker

Vera, Pedro L. wrote:

> Thanks for the suggestions. I installed the LiveWire plugin, since it seemed like it would do what I was looking for. However, I'm getting all kinds of errors (both in a windows box and a linux box). Following are the error msg (from the windows install). Btw, I'm running ImageJ 1.43f. It seems that the java version is a problem, but I don't get any other error msg when I run ImageJ.
>
> java.lang.UnsupportedClassVersionError: Bad version number in .class file
> at java.lang.ClassLoader.defineClass1(Native Method)
> at java.lang.ClassLoader.defineClass(Unknown Source)
> at java.security.SecureClassLoader.defineClass(Unknown Source)
> at java.net.URLClassLoader.defineClass(Unknown Source)
> at java.net.URLClassLoader.access$100(Unknown Source)
> at java.net.URLClassLoader$1.run(Unknown Source)
> at java.security.AccessController.doPrivileged(Native Method)
> at java.net.URLClassLoader.findClass(Unknown Source)
> at java.lang.ClassLoader.loadClass(Unknown Source)
> at java.lang.ClassLoader.loadClass(Unknown Source)
> at ij.IJ.runUserPlugIn(IJ.java:177)
> at ij.IJ.runPlugIn(IJ.java:146)
> at ij.Executer.runCommand(Executer.java:122)
> at ij.Executer.run(Executer.java:59)
> at ij.IJ.run(IJ.java:244)
> at ij.macro.Functions.doRun(Functions.java:551)
> at ij.macro.Functions.doFunction(Functions.java:74)
> at ij.macro.Interpreter.doStatement(Interpreter.java:200)
> at ij.macro.Interpreter.doBlock(Interpreter.java:511)
> at ij.macro.Interpreter.runMacro(Interpreter.java:127)
> at ij.macro.MacroRunner.run(MacroRunner.java:126)
> at java.lang.Thread.run(Unknown Source)
>
> I would appreciate any suggestions on how to fix this.
>
> Best regards,
> Pedro
>
> ________________________________________
> From: ImageJ Interest Group [[hidden email]] On Behalf Of Volker Baecker [[hidden email]]
> Sent: Tuesday, September 22, 2009 6:03 AM
> To: [hidden email]
> Subject: Re: "Magnetic lasso"-like tool
>
> Another one is the LiveWire, that can be found here:
> http://ivussnakes.sourceforge.net/index.php?option=com_content&view=article&id=46&Itemid=53
> Cheers,
> Volker
>
> Jean-Yves Tinevez wrote:
>> On Sep 22, 2009, at 11:39 AM, Vera, Pedro L. wrote:
>
>>> Greetings all:
>>> I'm using ImageJ to measure DAB immunostaining intensity and I would
>>> like to trace (using a mouse) and select certain areas for
>>> measurement. Currently, the freehand tool works but it's very
>>> cumbersome and also fairly innacurate. Adobe Photoshop has a "magnetic
>>> lasso" tool that outlines and snaps to differences in pixel intensity
>>> and I have found it very useful for the kind of tracing that I am
>>> doing. Is there a similar plugin for ImageJ? I have searched the
>>> plugin list but have been unable to find one.
>> The Fiji package has blow\lasso tool that works quite ok, tough they are
>> announced as non-fully functional.
>> I think it similar to what you are looking for.
>
>> http://pacific.mpi-cbg.de/wiki/index.php/Lasso_selection
>
>> cheers
>> jy
>

- --
passerelle antivirus du campus CNRS de Montpellier
- --

-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.9 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org

iEYEARECAAYFAkq5+aEACgkQ0gXPLVKexCeBGACdHnFBYJlB0IA7WhMdaACxNK/D
1C0An3hyUybwbOvohlf7y2k3kOLowlN2
=gAV4
-----END PGP SIGNATURE-----

--
passerelle antivirus du campus CNRS de Montpellier
--