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(New page: == General remarks == We assume installation of ImageJ in "/usr/local/ImageJ". In addition to ImageJ and Micro-Manager, you need the following programmes: * svn for obtaining the reposit...)
 
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== Steps ==
 
== Steps ==
  
1. '''Installing ImageJ'''</p>
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1. '''Installing ImageJ'''
 +
 
 
Get the Linux version of ImageJ from http://rsb.info.nih.gov/ij/download.html, move it to "/usr/local" and unpack it as described in http://rsb.info.nih.gov/ij/docs/install/linux.html. You will have a directory "/usr/local/ImageJ" with everything needed to run ImageJ (you can start ImageJ from the terminal: "cd /usr/local/ImageJ", followed by "./run").
 
Get the Linux version of ImageJ from http://rsb.info.nih.gov/ij/download.html, move it to "/usr/local" and unpack it as described in http://rsb.info.nih.gov/ij/docs/install/linux.html. You will have a directory "/usr/local/ImageJ" with everything needed to run ImageJ (you can start ImageJ from the terminal: "cd /usr/local/ImageJ", followed by "./run").
 +
 
2. '''Get Micro-Manager from the repository'''
 
2. '''Get Micro-Manager from the repository'''
  Make a directory somewhere (e.g. "~/src"), move to it ("cd ~/src") and get Micro-Manager with the command "svn checkout htpps://valelab.ucsf.edu/svn/micromanager2/branches/micromanager1.3". This will download all the necessary files from the repository into "~/src/micromanager1.3/".
+
 
 +
Make a directory somewhere (e.g. "~/src"), move to it ("cd ~/src") and get Micro-Manager with the command "svn checkout htpps://valelab.ucsf.edu/svn/micromanager2/branches/micromanager1.3". This will download all the necessary files from the repository into "~/src/micromanager1.3/".
 +
 
 
3. '''Beanshell and swingx'''
 
3. '''Beanshell and swingx'''
  Move to the new directory ("cd micromanager1.3") and copy beanshell and swingx from "~/src/micromanager1.3/classext" to the "plugins" directory of your ImageJ installation: "sudo cp classext/bsh-2.0b4.jar /usr/local/ImageJ/plugins" and "sudo cp classext/swingx-0.9.5.jar /usr/local/ImageJ/plugins".
+
 
 +
Move to the new directory ("cd micromanager1.3") and copy beanshell and swingx from "~/src/micromanager1.3/classext" to the "plugins" directory of your ImageJ installation: "sudo cp classext/bsh-2.0b4.jar /usr/local/ImageJ/plugins" and "sudo cp classext/swingx-0.9.5.jar /usr/local/ImageJ/plugins".
 +
 
 
4. '''Create a new micro-manager directory in /usr/lib'''
 
4. '''Create a new micro-manager directory in /usr/lib'''
  "sudo mkdir /usr/lib/micro-manager"
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 +
"sudo mkdir /usr/lib/micro-manager"
 +
 
 
5. '''mmUnixBuild.sh'''
 
5. '''mmUnixBuild.sh'''
  From within "~/src/micromanager1.3", type "./mmUnixBuild.sh".
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 +
From within "~/src/micromanager1.3", type "./mmUnixBuild.sh".
 +
 
 
6. '''Run configure'''
 
6. '''Run configure'''
  "./configure --with-imagej=/usr/local/ImageJ". You have to add the option (--with-imagej), because the default assumes a different localisation of ImageJ.
+
 
 +
"./configure --with-imagej=/usr/local/ImageJ". You have to add the option (--with-imagej), because the default assumes a different localisation of ImageJ.
 +
 
 
7. '''Run make'''
 
7. '''Run make'''
  "make"
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 +
"make"
 +
 
 
8. '''Install as superuser'''
 
8. '''Install as superuser'''
  "sudo make install"
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 +
"sudo make install"
 +
 
 
9. Run '''ldconfig'''
 
9. Run '''ldconfig'''
  "ldconfig"
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 +
"ldconfig"
 +
 
 
10. '''The starting script'''
 
10. '''The starting script'''
    Starting ImageJ with the scripts provided in the ImageJ directory (run, script, see 1 above) will start ImageJ, but Micro-Manager, although now in the plugins directory, will not work properly because the path to /usr/lib/micro-manager is missing. Write your own script containing the 4 lines given below ("mmscript"), save and move it to /usr/local/ImageJ.
 
11. Running Micro-Manager cd to "/usr/local/ImageJ" and start ImageJ with your new script ("./mmscript &"). In the plugins menu of ImageJ, start Micro-Manager –> Micro-Manager Studio.
 
  
mmscript:
+
Starting ImageJ with the scripts provided in the ImageJ directory (run, script, see 1 above) will start ImageJ, but Micro-Manager, although now in the plugins directory, will not work properly because the path to /usr/lib/micro-manager is missing. Write your own script containing the 4 lines given below ("mmscript"), save and move it to /usr/local/ImageJ.
 +
 
 +
11. '''Running Micro-Manager'''
 +
 
 +
cd to "/usr/local/ImageJ" and start ImageJ with your new script ("./mmscript &"). In the plugins menu of ImageJ, start Micro-Manager –> Micro-Manager Studio.
 +
 
 +
 
 +
== mmscript: ==
  
#!/bin/bash
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#!/bin/bash
cd /user/local/ImageJ
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cd /user/local/ImageJ
export LD_LIBRARY_PATH=.:/usr/local/lib:/usr/lib/micro-manager:/usr/local/ImageJ
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export LD_LIBRARY_PATH=.:/usr/local/lib:/usr/lib/micro-manager:/usr/local/ImageJ
java -mx1200m -Djava.library.path=/usr/lib/micro-manager:/usr/local/ImageJ -Dplugins.dir=/usr/local/ImageJ -cp /usr/local/ImageJ/ij.jar:usr/local/jdk1.5.0_04/lib/tools.jar ij.ImageJ
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java -mx1200m -Djava.library.path=/usr/lib/micro-manager:/usr/local/ImageJ -Dplugins.dir=/usr/local/ImageJ -cp /usr/local/ImageJ/ij.jar:usr/local/jdk1.5.0_04/lib/tools.jar ij.ImageJ

Revision as of 06:59, 15 July 2009

General remarks

We assume installation of ImageJ in "/usr/local/ImageJ". In addition to ImageJ and Micro-Manager, you need the following programmes:

  • svn for obtaining the repository
  • sun-java6-sdk or better/equivalent
  • autoconf
  • automake
  • swig
  • libace
  • libace-dev
  • g++
  • libtool

In addition, note that:

  • File versions might have changed, check before using the names given in the instructions.
  • Some operations have to be performed as "superuser" ("sudo …").
  • Permissions of the new ImageJ directory might have to be set properly.


Steps

1. Installing ImageJ

Get the Linux version of ImageJ from http://rsb.info.nih.gov/ij/download.html, move it to "/usr/local" and unpack it as described in http://rsb.info.nih.gov/ij/docs/install/linux.html. You will have a directory "/usr/local/ImageJ" with everything needed to run ImageJ (you can start ImageJ from the terminal: "cd /usr/local/ImageJ", followed by "./run").

2. Get Micro-Manager from the repository

Make a directory somewhere (e.g. "~/src"), move to it ("cd ~/src") and get Micro-Manager with the command "svn checkout htpps://valelab.ucsf.edu/svn/micromanager2/branches/micromanager1.3". This will download all the necessary files from the repository into "~/src/micromanager1.3/".

3. Beanshell and swingx

Move to the new directory ("cd micromanager1.3") and copy beanshell and swingx from "~/src/micromanager1.3/classext" to the "plugins" directory of your ImageJ installation: "sudo cp classext/bsh-2.0b4.jar /usr/local/ImageJ/plugins" and "sudo cp classext/swingx-0.9.5.jar /usr/local/ImageJ/plugins".

4. Create a new micro-manager directory in /usr/lib

"sudo mkdir /usr/lib/micro-manager"

5. mmUnixBuild.sh

From within "~/src/micromanager1.3", type "./mmUnixBuild.sh".

6. Run configure

"./configure --with-imagej=/usr/local/ImageJ". You have to add the option (--with-imagej), because the default assumes a different localisation of ImageJ.

7. Run make

"make"

8. Install as superuser

"sudo make install"

9. Run ldconfig

"ldconfig"

10. The starting script

Starting ImageJ with the scripts provided in the ImageJ directory (run, script, see 1 above) will start ImageJ, but Micro-Manager, although now in the plugins directory, will not work properly because the path to /usr/lib/micro-manager is missing. Write your own script containing the 4 lines given below ("mmscript"), save and move it to /usr/local/ImageJ.

11. Running Micro-Manager

cd to "/usr/local/ImageJ" and start ImageJ with your new script ("./mmscript &"). In the plugins menu of ImageJ, start Micro-Manager –> Micro-Manager Studio.


mmscript:

#!/bin/bash
cd /user/local/ImageJ
export LD_LIBRARY_PATH=.:/usr/local/lib:/usr/lib/micro-manager:/usr/local/ImageJ
java -mx1200m -Djava.library.path=/usr/lib/micro-manager:/usr/local/ImageJ -Dplugins.dir=/usr/local/ImageJ -cp /usr/local/ImageJ/ij.jar:usr/local/jdk1.5.0_04/lib/tools.jar ij.ImageJ
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