Setting up the microscope configuration file

At startup, mesoSPIM-control prompts users for a configuration file. The configuration file is a python file in which most parameters are represented in the form of dictonaries. Example config files can be found here. Start with demo file to make sure installation is successful and all libraries are installed.

Step-by-step guide

General configuration of National Instruments hardware

PXI6733 is responsible for the lasers, PXI6259 is responsible for the shutters, ETL waveforms and galvo waveforms. If you use up to 4 lasers, all these waveforms can be controlled with a single PXI6733 board, see example.

Configuration of a system with 6 laser lines:

acquisition_hardware = {'master_trigger_out_line' : 'PXI6259/port0/line1',
                        'camera_trigger_source' : '/PXI6259/PFI0',
                        'camera_trigger_out_line' : '/PXI6259/ctr0',
                        'galvo_etl_task_line' : 'PXI6259/ao0:3',
                        'galvo_etl_task_trigger_source' : '/PXI6259/PFI0',
                        'laser_task_line' :  'PXI6733/ao0:5',
                        'laser_task_trigger_source' : '/PXI6259/PFI0'}

Adapt this section according to your device configuration.

:warning: The device names (i.e. PXI6259 and PXI6733) have to match your device designations in NI MAX. You can rename your DAQ devices in NI MAX to match the names in the config file.

:warning: The master_trigger_out_line needs to wired to /PXI6259/PFI0 for the triggering of both camera and ETL/galvo waveforms. At time of writing that means the master trigger out is assumed PXI6259/port0/line1.

The camera trigger cable (Trigger In for camera) must be connected to the 'camera_trigger_out_line' : '/PXI6259/ctr0' terminal, which is marked as CTR 0 out or PFI 12 / PI 2.4 on your BNC-2110 connector block (depending on the block model), in TRIGGER/COUNTER section.

Joystick and laser config

sidepanel = 'Demo' # 'Demo' or 'FarmSimulator'

laser = 'NI' # 'Demo' or 'NI'

Configuration of the laser enable & intensity outputs

:warning: Laser dictionary entries must be sorted in the increasing wavelength order: 405, 488, etc. Keys are the laser designation that will be shown in the user interface. Values are DO ports used for laser ENABLE digital signal.

laserdict = {'405 nm': 'PXI6733/port0/line2',
             '488 nm': 'PXI6733/port0/line3',
             '515 nm': 'PXI6733/port0/line4',
             '561 nm': 'PXI6733/port0/line5',
             '594 nm': 'PXI6733/port0/line6',
             '647 nm': 'PXI6733/port0/line7'}