Micromanager

This is for installing Micromanager on a Fedora Linux system

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Java Issues

Java needs the following directory, if it doesn't already exist.

/etc/.java/.systemPrefs/

Micro-Manager doesn't work well with Icedtea Java.

Download and install Sun's version.

Source code

cd /storage/big1/kdb/projects/svn/micromanager2/trunk
svn co https://valelab.ucsf.edu/svn/micromanager2/trunk/

cd /storage/big1/kdb/projects/svn/micromanager2/
svn co https://valelab.ucsf.edu/svn/3rdpartypublic/

zlib

Static zlib is neede

yum install zlib-static.x86_64

bsh

copy bsh-2.0b4.jar to /usr/share/java

 ln -sf /usr/share/java/bsh-2.0b4.jar /usr/share/java/bsh.jar

dc1394

need libdc1394-devel installed if you want to use firewire devices

Compiling code

./mmUnixBuild.sh
./configure --with-imagej=/usr/local/ImageJ/
make

Installation

chmod a+rw config.log

As **root**:\\ I had to mkdir /usr/lib64/micro-manager before running

 make install

The micromanager libraries want to be installed in /usr/lib/micro-manager, but I wanted them installed in a 64 library path.

Add the following to /etc/ld.so.conf.d/micro-manager.

  echo "/usr/lib64/micro-manager" > /etc/ld.so.conf.d/micro-manager-x86_64.conf

Each user must be part of the UUCP dialout group in order to use the serial ports, perhaps make a udev rule later.

To the file macros/StartupMacros.txt in your ImageJ directory, add the following:

 macro "AutoRun" {
   run("Micro-Manager Studio");
 }

udev rules vi /etc/udev/rules.d/micromanager.rules

# ITC18
ATTRS{idVendor}=="1482", ATTRS{idProduct}=="0011", MODE="0666"
 
# "Velleman K8055-0"
ATTRS{idVendor}=="10cf", ATTRS{idProduct}=="5500", MODE="0666"
 
#Velleman K8055-1
ATTRS{idVendor}=="10cf", ATTRS{idProduct}=="5501", MODE="0666"
 
#Velleman K8055-2
ATTRS{idVendor}=="10cf", ATTRS{idProduct}=="5502", MODE="0666"
 
#Velleman K8055-3
ATTRS{idVendor}=="10cf", ATTRS{idProduct}=="5503", MODE="0666"
 
#Velleman K8061-0
ATTRS{idVendor}=="10cf", ATTRS{idProduct}=="8061", MODE="0666"
 
#Ludl Mac 5000
ATTRS{idVendor}=="6969", ATTRS{idProduct}=="1235", MODE="0666"
 
#ASI MS-2000
ATTRS{idVendor}=="0b54", ATTRS{idProduct}=="2000", MODE="0666"
 
#Spectral LMM5
ATTRS{idVendor}=="1bdb", ATTRS{idProduct}=="0300", MODE="0666"
 
#Nikon AZ100m
ATTRS{idVendor}=="04b0", ATTRS{idProduct}=="7804", MODE="0666"
 
#Zeiss AxioObserver Z1
ATTRS{idVendor}=="0758", ATTRS{idProduct}=="1004", MODE="0666"

Running

/usr/java/latest/bin/java -Xmx512m -Djava.library.path=/usr/lib64/micro-manager/ -cp ij.jar ij.ImageJ

my script:

 #!/bin/bash
 export IMAGEJDIR=/usr/local/ImageJ
 export MMDIR=/usr/lib64/micro-manager 
 #export LD_DEBUG=files
 cd $IMAGEJDIR
 
 /usr/java/latest/bin/java -Xmx10000m -Djava.library.path=$MMDIR -cp $IMAGEJDIR/ij.jar ij.ImageJ