Filter Wheels

Filter wheels can be used in both illumination and detection paths. The user is expected to change the names of available filters to match what is in the filter wheel or turret. If more than one filter wheel is present, the user should add additional filter_wheel instances in the configuration.yaml file as follows:

Configuration File

microscopes:
  microscope_name:
    -
      filter_wheel:
        hardware:
          name: Lower Filter Wheel
          type: SutterFilterWheel
          wheel_number: 1
          port: COM1
          baudrate: 9600
        filter_wheel_delay: 0.03
        available_filters:
          Empty-Alignment: 0
          GFP: 1
          RFP: 2
          Far-Red: 3
    -
      filter_wheel:
        hardware:
          name: Upper Filter Wheel
          type: SutterFilterWheel
          wheel_number: 2
          port: COM1
          baudrate: 9600
        filter_wheel_delay: 0.03
        available_filters:
          CFP: 0
          YFP: 1
          RFP: 2
          Far-Red: 3

Note

The name parameter under hardware is optional. If not provided, the name of the device will be default to Filter 0, Filter 1, … Filter N in the GUI. However, if is is provided, then the GUI will automatically use the name provided as a label.

Sutter Instruments

Lambda 10-3 & 10-B

We typically communicate with Sutter Lambda 10-3 controllers via serial port. It is recommended that you first establish communication with the device using manufacturer provided software. Alternatively, one can use MicroManager. For some filter wheel types, the filter_wheel_delay is calculated according to the size of the move and model of the filter wheel. For other filter wheel types, the filter_wheel_delay is a fixed value, which is specified as the filter_wheel_delay entry in the configuration file. The number of filter wheels connected to the controller is specified as wheel_number in the configuration file. Currently, both wheels are moved to the same position, but future implementations will enable control of both filter wheels independently.

Configuration File

microscopes:
  microscope_name:
    -
      filter_wheel:
        hardware:
          type: SutterFilterWheel
          wheel_number: 1
          port: COM1
          baudrate: 9600
        filter_wheel_delay: 0.03
        available_filters:
          Empty-Alignment: 0
          GFP: 1
          RFP: 2
          Far-Red: 3

ASI

FW-1000

The ASI filter wheel is controlled by the ASI Tiger Controller. Thus, you should provide the same comport entry as you did for the stage. A single communication instance is used for both the stage and filter wheel.

Configuration File

microscopes:
  microscope_name:
    -
      filter_wheel:
        hardware:
          type: ASI
          wheel_number: 1
          port: COM1
          baudrate: 115200
        filter_wheel_delay: 0.03
        available_filters:
          Empty-Alignment: 0
          GFP: 1
          RFP: 2
          Far-Red: 3

LUDL Electronic Products

MAC6000

Note

Currently, the software only supports a single filter wheel for the MAC6000 device. Should additional filter wheels be necessary, please reach out to the navigate team by placing a feature request on GitHub.

Configuration File

microscopes:
  microscope_name:
    -
      filter_wheel:
        hardware:
          type: LUDLFilterWheel
          wheel_number: 1
          port: COM1
          baudrate: 9600
        filter_wheel_delay: 0.03
        available_filters:
          Empty-Alignment: 0
          GFP: 1
          RFP: 2
          Far-Red: 3

Analog/Digital Devices

Some manufacturers provide filter wheels that are controlled by analog or digital signals. Here, each digital signal corresponds to a filter position. The user must specify the number of filters in the filter wheel and the digital signal that corresponds to each filter position.

Configuration File

microscopes:
  microscope_name:
      filter_wheel:
        hardware:
          type: NI
          wheel_number: 1
        filter_wheel_delay: 0.050
        available_filters:
          473nm: Dev2/port0/line1
          561nm: Dev2/port0/line3
          638nm: Dev2/port0/line5
          Empty: Dev2/port0/line7

Synthetic Filter Wheel

If no filter wheel is present, one must configure the software to use a synthetic filter wheel.

Configuration File

microscopes:
  microscope_name:
      filter_wheel:
        hardware:
          type: synthetic
          wheel_number: 1
          port: COM1
          baudrate: 9600
        filter_wheel_delay: 0.03
        available_filters:
          Empty-Alignment: 0
          GFP: 1
          RFP: 2
          Far-Red: 3