Micromanager
This is for installing Micromanager on a Fedora Linux system
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/
3rd Party Installs
yum install zlib-static swig libtool gcc-c++
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
./configure --with-imagej=/usr/local/ImageJ/ ./mmUnixBuild.sh 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