Setting up the laser

Multi-photon microscopy relies on the laser emitting light in short pulses rather than continuously. This pulsing, also known as "modelocking", it critical for fluorescence emission. BakingTray communicates with the laser in order to stop acquisition should it drop out of modelock. BakingTray also turns off the laser when acquisition completes. Available laser control classes are in the components/laser directory.

Let us say you have a Chameleon laser and it is connected to your motherboard serial port, COM1. The following sample session confirms we can connect to the laser and demonstrates some features of the laser control class. Substituting chameleon for maitai will allow communication with a Spectraphysics Mai Tai.

>> c=chameleon('COM1');

Setting up Chameleon laser communication on serial port COM1
Connected to Chameleon laser on serial port COM1

>> [~,status]=c.isReady
status =
    'Laser not powered on'
% So let's turn on the laser with the key switch...

% Test if laser shutter is open (0 means it's closed, 1 means it's open)
>> c.isShutterOpen
ans =
     0
>> c.openShutter; % Let's open the shutter
>> c.isShutterOpen
ans =
     1
% Yep, shutter is now open

% Let's read and then change the wavelength
>> c.readWavelength
ans =
   920

>> c.setWavelength(940);
>> c.readWavelength
Failed to read wavelength from Chameleon. Likely laser is tuning.
ans =
   NaN

% Wait 5 seconds...
>> c.readWavelength
ans =
   940
% Nice

% Close communications with the laser
>> delete(c)
Disconnecting from Chameleon laser
Closing serial communications with Chameleon laser

With BakingTray in your path confirm you can communicate with the laser as above. Make a note of the COM port you are using, you will need this later for completing the settings file.

GDD compensation

The laser GUI in BakingTray does not control any GDD compensation you may have available. If your laser has a pre-chirper, ensure that it is set up correctly across wavelength. If you have dielectric mirrors in the path, confirm that required GDD compensation values do not change drastically over small (e.g. 5 or 10 nm) changes in wavelength. If this does occur, you will need to track down the mirror or mirrors which are causing the effect and swap them out (ideally with metal-coated mirrors).

Notes on power modulation

If you are modulating power using an external EOM, such as a Conoptics Pockels cell, you should consider making it possible to automatically switch this device on and off with the laser. The laser will be turned off automatically when acquisitions complete. EOMs have limited lifetime and you will save many hours if the unit is switched off with the laser. To achieve this you will need to build or buy a mains extension lead which has a TTL-switchable relay. BakingTray can interface with such a relay. Instructions for setting this up are detailed in the instructions for filling in the settings files.

Dealing with poor modelocking behavior at specific wavelengths

Lasers will sometimes pulse poorly at a narrow range of wavelengths. The resulting images will show high-frequency stripes and tend to look dimmer than normal. Fixing this requires a service visit of some sort. Whilst waiting for the visit, you can block users from using problem wavelengths. For instance, to block users from the 770 -- 790 nm range and also the 920 -- 925 nm range you can do:

hBT.laser.bannedWavelengths = {[770,790],[920,925]};

To avoid having to type this in every time you start BakingTray, you can add this line to the startup_bt.m file in your BakingTray SETTINGS folder.

Banned wavelengths

Tunable lasers sometimes fail to modelock in particular wavelength ranges and need servicing. You can block users from accessing those ranges temporarily. To do this, create a startup_bt.m file in your BakingTray SETTINGS folder. To block 910 to 920 nm you would add to this file:

hBT.laser.bannedWavelengths={[910,920]};

If you wanted to also block 810 to 850 nm you would do:

hBT.laser.bannedWavelengths={[810,850; 910,920]};

The contents of startup_bt are run when BakingTray starts. You can also run the above lines in the terminal to confirm the blocking is working.