Micro-Manager on the Raspberry Pi

Micro-Manager is an open source platform for controlling microscope hardware, automating image acquisition, and tracking metadata about how images are acquired. In biomedical imaging research, it serves as an incredibly important tool because it is free and open source, which means that scientists can benefit from the contributions of others to the software without paying costly licensing fees.

I recently managed to compile Micro-Manager version 2.0 on the Raspberry Pi. I did this for a small hobby project I am working on to build a cheap yet effective tool for at-home microscope projects and hacking. Though I am not yet convinced that Micro-Manager will be the best tool for this particular job given it's relatively heavy footprint on the Pi's slower hardware, I thought that I would post my notes so that others could benefit from my experience.

Software versions

I am working with a Raspberry Pi 3 Model B:

pi@raspberrypi:~ $ uname -a & gcc -dumpversion & make -v & ldd --version
Linux raspberrypi 4.4.38-v7+ #938 SMP Thu Dec 15 15:22:21 GMT 2016 armv7l GNU/Linux

pi@raspberrypi:~ $ gcc -dumpversion

pi@raspberrypi:~ $ make -v
GNU Make 4.0

pi@raspberrypi:~ $ ldd --version
ldd (Debian GLIBC 2.19-18+deb8u7) 2.19

Setup a network share for 3rd party libraries

We need to compile Micro-Manager because binares for the Pi's ARM processor are not distributed by the Micro-Manager team (probably because too few people have ever wanted them). To compile Micro-Manager, we need to checkout a rather large set of 3rd party libraries. When I last checked, these libraries occupied 6.7 GB of space on my laptop, a size which can be prohibitive when using the Micro-SD cards that provide storage for the Pi.

To circumvent this problem, I checked out the 3rdpartypublic SVN repository onto my laptop and created a network share from this directory. Then, I mounted the share on my Pi in the directory just above that containing the Micro-Manager source code.

To get started, first have a look at my post on connecting a Pi to a Linux home network for ideas if you haven't already connected the Pi to your other machines at home: http://kmdouglass.github.io/posts/connecting-a-raspberry-pi-to-a-home-linux-network.html

Once the Pi and the laptop are on the same network, checkout the SVN 3rdpartypublic repository onto your laptop or home server. You may need to do this a few times until completion because the downloads can timeout after a few minutes:

svn checkout https://valelab4.ucsf.edu/svn/3rdpartypublic/

Next, we need to setup the network share. If your laptop or server is running Windows, then you will probably need to setup Samba on the Pi to share files between them. I however am running a Linux home network, so I decided to use NFS (Network File Sharing) to share the directory between my laptop--which runs Debian Linux--and the Pi. I installed NFS on my laptop with:

sudo apt-get install nfs-kernel-server nfs-common

Once installed, I added the following line to the newly created /etc/exports file:


The first part is the directory to share, i.e. where the 3rdpartypublic directory is stored on my laptop. The second part contains the static IP address of the Pi on my home network. The /24 was REQUIRED for my client (the Pi) to mount the share. /24 simply denotes a network mask of; if you have a different mask on your network, then you can find a good discussion on this topic here: https://arstechnica.com/civis/viewtopic.php?t=751834 Finally, (...) specifies shared options and ro means read only.

After editing the file, export the folder and restart the NFS server:

sudo exportfs -arv
sudo /etc/init.d/nfs-kernel-server restart

On the client (the Pi), the NFS client software was already installed. However, I had to restart the rpcbind service before I could mount the share:

sudo /etc/init.d/rpcbind restart

Finally, I added a line to the /etc/fstab file on the Pi to make mounting the 3rdpartypublic share easier: /home/pi/src/micro-manager/3rdpartypublic nfs user,noauto 0 0

The first part indicates the IP of the laptop and the share to mount. The second part, /home/pi/src/micro-manager/3rdpartypublic is the directory on the Pi where the share will be mounted. I placed this one directory above where the MM source code is, (/home/pi/src/micro-manager/micro-manager on my machine). nfs indicates the type of share to mount, and user,noauto permits any user to mount the share (not just root), though this share will not be automatically mounted when the Pi starts. The final two zeros are explained in the fstab comments but aren't really important for us. To mount the share, type the following on the Pi:

sudo mount /home/pi/src/micro-manager/3rdpartypublic

In case you're interested in learning more about the intricacies of Linux home networking, I found the following sources of information to be incredibly helpful.

  1. https://www.howtoforge.com/install_nfs_server_and_client_on_debian_wheezy
  2. https://www.youtube.com/watch?v=luqq8DUqqCw
  3. http://nfs.sourceforge.net/nfs-howto/ar01s03.html#config_server_setup
  4. http://www.tecmint.com/how-to-setup-nfs-server-in-linux/

Building MM

Once I was able to mount the share containing 3rd party libraries, I installed the following packages on the Pi and checked out the Micro-Manager source code:

sudo apt-get install autoconf automake libtool pkg-config swig ant libboost-dev libboost-all-dev
cd ~/src/micro-manager
git clone https://github.com/micro-manager/micro-manager.git
cd micro-manager
git checkout mm2

The last command switches to the mm2 branch where the Micro-Manager 2.0 source code is found. Note that it may not be necessary to install all of the boost libraries with sudo apt-get install libboost-all-dev, but I did this anyway because I encountered multiple errors due to missing boost library files the first few times I tried compiling.

The next step follows the normal Micro-Manager build routine using make, with the exception of the configuration step. From inside the Micro-Manager source code directory on the Pi, run the following commands one at a time:

PYTHON=/usr/bin/python3 ./configure --prefix=/opt/micro-manager --with-ij-jar=/usr/share/java/ij.jar --with-python=/usr/include/python3.4 --with-boost-libdir=/usr/lib/arm-linux-gnueabihf --with-boost=/usr/include/boost
make fetchdeps
sudo make install

In the configuration step, I set the Python interpreter to Python 3 because I greatly prefer it over Python 2. This is done by setting the PYTHON environment variable before running configure. --prefix=/opt/micro-manager/ indicates the preferred installation directory of Micro-Manager. --with-ij-jar=/usr/share/java/ij.jar is the path to the ImageJ Java library, though I am uncertain whether this was necessary. (I installed ImageJ with a sudo apt-get install imagej a while ago.) --with-python=/usr/include/python3.4 should point to the directory containing the Python.h header file for the version of Python you are compiling against. with-boost-libdir should point to the directory containing the boost libraries (.so files). This was critical for getting MM2 to build. If you are unsure where they are located, you can search for them with sudo find / -name "libboost*". Finally, the last option, with-boost, may or may not be necessary. I set it to the directory containing the boost headers but never checked to see whether MM compiles without it.

If all goes well, Micro-Manager will compile and install without problems. Compilation time on my Pi took around one hour.

Set the maximum amount of direct memory

In the next step, we need to make a minor edit to the Micro-Manager Linux start script. Edit the script (/opt/micro-manager/bin/micromanager) to reduce the maximum direct memory to something reasonable:

/usr/lib/jvm/jdk-8-oracle-arm32-vfp-hflt/bin/java -Xmx1024M \
  -XX:MaxDirectMemorySize=1000G \
   -classpath "$CLASSPATH" \
   -Dmmcorej.library.loading.stderr.log=yes \
   -Dmmcorej.library.path="/opt/micro-manager/lib/micro-manager" \
   -Dorg.micromanager.plugin.path="/opt/micro-manager/share/micro-manager/mmplugins" \

Change 1000G to 512M or 256M; otherwise the Pi will complain that the MaxDirectMemorySize of 1000G is too large. You can start Micro-Manager by running this modified script.

What's next?

Though Micro-Manager compiles and runs on the Pi, I have not yet tested it thoroughly acquisitions. I am currently waiting on a camera board to arrive in the mail, and when it does, I will attempt to interface with it through Micro-Manager. Though I could write my own Python library, Micro-Manager is appealing because it can save a lot of time by providing a ready-made means to annotate, process, and store imaging data.

Running Micro-Manager on the Pi also raises the possibility of a fully open, embedded biomedical imaging platform, though I am uncertain at the moment whether the hardware on the Pi is up to the task. If you manage to do anything cool with Micro-Manager and the Raspberry Pi, please let me know in the comments!


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