TrackStim

micro-manager plugin to image moving C.Elegans

Index Of Topics

1. Requrired software
2. Required hardware
3. Building and installing TrackStim
4. Running TrackStim
5. Troubleshooting Common Behaviours
6. Development guide/documentation
7. Setting up the hardware and software from scratch

Required software

All items except Mac OS X 10.7 can be found in this repository under the required software directory. Ask the IT department for Mac OS X 10.7

• Mac OS X 10.7 Lion
• USB to UART Bridge VCP Driver Legacy Version for Mac OSX
• DCAM API for Mac OS X 10.7 v13.11.4451
• Java 6 (this should come with Mac OS X 10.7, but if its not installed, you can download it here: https://support.apple.com/kb/dl1572?locale=en_GB)
• Micro-manager 1.4.23
• Arduino drivers for whatever system you are on

Required hardware

• Hamamatsu orca R2 camera
• Hamamatsu orca R2 camera controller C10600
• Thor Labs CM1-DCH/M SM1A23
• Thor Labs M00267820
• ASI MS-2000-500 xy stage (Serial: 1004-1620-2933-2148, Model: WKU-XYB-Zs-Axioskop2+)
• A mac with a firewire ieee 1394 port/cable

Building and installing TrackStim

Building Trackstim

To build TrackStim download/git clone this folder an then open a terminal window with this folder.

Then, run the following command sequence in the terminal. Note - you need Java 1.6:

javac -source 1.5 -target 1.5 -classpath /Applications/Micro-Manager1.4/ij.jar:/Applications/Micro-Manager1.4/plugins/Micro-Manager/MMCoreJ.jar:/Applications/Micro-Manager1.4/plugins/Micro-Manager/MMJ_.jar -Xlint:unchecked TrackStimPlugin.java

jar cvf TrackStim_.jar TrackStimPlugin.class TrackStim_04.class TrackingThread11.class SignalSender01.class

This creates TrackStim_.jar.

Installing Trackstim

Take TrackStim_.jar and copy it to /Applications/Micro-Manager1.4/mmplugins/. To confirm that it is installed, open the Micro-Manager -> Plugins menu. There should be an entry called TrackStim.

Running TrackStim

1. Make sure Micro-Manager 1.4 is not already running
2. Turn on the camera controller, and asi ms 2000 xy stage
3. Open Micro-Manager 1.4
4. Choose the configuration file trackstim-mm1.4.23mac.cfg
5. Click on the group setting TrackStim
6. Click on the preset default
7. Click the "live" button on the left side of the Micro-Manager window
8. Open Micro-Manager 1.4 -> Plugins menu
9. Choose TrackStim

TODO

• more detail
• guide for calcium imaging

Development Guide/Documentation

TODO

• design diagrams
• algorithm documentation
• options documentation
• camera settings documentation

Setting up the TrackStim system from scratch

1. Install Mac OS X 10.7
2. Download the first software update (installs a new version of safari that most sites support)
3. Install Google Chrome
4. Install the rest of the required software
5. Open iChat -> Settings -> Camera -> toggle the setting off (e.g. Do not open iChat when the camera turns on) Important, camera will not be detected by Micro-Manager 1.4 if this is not done )
6. plug in all of the hardware components
   • The Thor Labs USB connector must be connected to the third USB port relative to the power button in the USB 3.0 hub.
   • The USB 3.0 hub must be connected to the right-most USB port at the back of the mac (right-most when facing the side of the mac with the power button)
7. build TrackStim
8. install TrackStim