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.

sudo mkdir -p /etc/.java/.systemPrefs/
sudo touch /etc/.java/.systemPrefs/.system.lock
touch /etc/.java/.systemPrefs/.systemRootModFile

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

Download and install Sun's version.

Source code

µManager is officially 1.4.*, but they keep the repository in micromanager2/

cd /storage/big1/kdb/projects/micromanager/micromanager1.4/
svn co https://valelab.ucsf.edu/svn/micromanager2/trunk/

cd /storage/big1/kdb/projects/micromanager/micromanager1.4/
svn co https://valelab.ucsf.edu/svn/3rdpartypublic/

GitHub

git clone https://github.com/micro-manager/micro-manager

3rd Party Installs

yum install zlib-static swig libtool libdc1394-devel  gcc gcc-c++ libgphoto2.x86_64 libgphoto2-devel.x86_64 freeimage-devel.x86_64 boost-devel.x86_64  ant.x86_64  python-devel.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

itc18

copy the ITC18.h to /usr/local/include/ copy libitc18.0.1.so to /usr/local/lib

Make a softlink

ln -s /usr/local/lib/libitc18.0.1.so /usr/local/lib/libitc18.so

Make sure /usr/local/lib is in your library path.

if not, add "/etc/ld.so.conf.d/itc18.conf" to /etc/ld.so.conf.d/ with "/usr/local/lib/" as the contents

Compiling code

./autogen.sh
./configure JNI_CPPFLAGS="-I/usr/java/latest/include -I/usr/java/latest/include/linux" --libdir=/usr/local/lib

VESM

./autogen.sh 
./configure --with-java="/usr/lib/jvm/java"
make fetchdeps
make

See http://sourceforge.net/p/micro-manager/mailman/message/34561785/

Installation

chmod a+rw config.log

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

 make install

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"
 
# Andor USB and Bitflow cameras
SYSFS{idVendor}=="136e", MODE="0666"
SUBSYSTEM=="video4linux", KERNEL=="video[0-3]*", ATTR{name}=="bitflow", GROUP="users"

# Spectra X-Cite
ATTRS{idVendor}=="0403", ATTRS{idProduct}=="6001", 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

RPM Build

cd /storage/big1/kdb/projects/micromanager/micromanager2/trunk; svn update
tar --exclude-vcs -cvzf /storage/big1/kdb/public_html/micro-manager/micro-manager-`cat version.txt`.tar.gz ./

cd /storage/big1/kdb/projects/micromanager/
tar --exclude-vcs -cvzf /storage/big1/kdb/public_html/micro-manager/3rdpartypublic.tar.gz 3rdpartypublic/classext/ 

./configure JAVAC="/usr/java/latest/bin/javac" JAVA_HOME="/usr/java/latest" JNI_CPPFLAGS="-I/usr/java/latest/include -\I/usr/java/latest/include/linux" --prefix=/usr/ --with-ij-jar=/usr/share/java/imagej.jar