pycmm

This package is used to control the Ti2 microscopes in SIAT. The commands for controlling Nikon microscope relay on package pycromanager, a package of MMCoreJ wrap of python, and some third-party devices which have a clear documented SDK was designed python interface for efficiency reasons.

Third-party devices including:

• Prior SDK python interface
• Andor sCMOS camera
• myRIO trigger

Device

/device/NI_FPGA

We use myRIO 19000 as the signal generator. The package nifpga is used for communicating myRIO. Connector A DIO 27 is used for camera trigger signal output. Connector C DIO 0 is used for receive the camera output. Connector C DIO 1-7 are usd for triggering the light source, for convenience, 1-6 are used for spectraX, and DIO 7 is used for controlling the prior bright field source.

• Register description

  PulseNumberperLoop: int, How much trigger signals (pulse) was trigger with one cycle. When set to -1, myRIO will output pulse continuously.
  BreakinLoop: bool, default is False, if set True, it will disrupt current trigger cycle.
  Trigger: int, default is 0. It determines the trigger cycle numbers.
  OFFTime: int, Trigger pulse width (high state width) in microsecond.
  ONTime: int, Trigger pulse width (high state width) in microsecond.
  OutPutPinMap: uint8, Connector C DIO 1-7 are mapped to its bitwise value. i.e., for C:DIO 1 to be ON, when the camera output signal come, needs a decimal value of 1 (B00000001), for all pins to be ON, needs a decimal value 127 (B01111111).

  

Module

multi_t_xy_c_acquisiation/PymmAcq

This module used to control the device states and the UI

For live mode, the two methods can be called.

PymmAcq.start_streaming(step)

the step set the exposure time of camera.

PymmAcq.stop_streaming()

Dependence

This package needs python packages followed,

micromanager
pip install pycromanager --upgrade
numpy
scipy
tifffile
nifpga
pip install nifpga
napari
pip install "napari[pyside2]"

Appendix