matlab-instrument-control

MATLAB Instrument Control (MIC) is a collection of MATLAB classes for automated data collection on complex, multi-component custom built microscopes.

The MIC software package uses object-oriented programming where a class defines the capabilities of each instrument. Each instrument class inherits from a common MIC abstract class and therefore has a basic common interface. Common component types (lasers, camera, etc.) have their own further abstract sub-classes to provide common interfaces and to facilitate the development of control classes for specific new instruments. Use of the MATLAB environment allows immediate access to data and image analysis even during data collection. Proficient MATLAB users can also easily extend or modify any of these control classes.

Class Structure Overview

The structure of MIC is designed to ensure scalability and easy integration of new hardware.

MIC_Abstract

• Defines basic functions and properties common across all classes.
  • MIC_Abstract

MIC_LightSource_Abstract

• MIC_LightSource_Abstract is the base class for all light sources (e.g., lasers), defining common functions and properties.
  • MIC_CoherentLaser561
  • MIC_CrystaLaser561
  • MIC_CrystaLaser405
  • MIC_DHOMLaser532
  • MIC_MPB_Laser
  • MIC_RebelStarLED
  • MIC_VortranLaser488
  • MIC_TubeLaserDiode
  • MIC_TIRFLaser488
  • MIC_HSM_Laser488
  • MIC_IX71_Lamp01

MIC_Camera_Abstract

• MIC_Camera_Abstract is the base class for all camera-related classes, defining common functions and properties.
  • MIC_AndorCamera
  • MIC_HamamatsuCamera
  • MIC_IMGSourceCamera
  • MIC_ThorlabsIR

MIC_LinearStage_Abstract

• MIC_LinearStage_Abstract is the abstract class for linear stages.
  • MIC_MCLMicroDrive
  • MIC_KCubePiezo
  • MIC_TCubePiezo

MIC_3DStage_Abstract

• MIC_3DStage_Abstract is the abstract class for 3D stages.
  • MIC_MCLNanoDrive
  • MIC_NanoMaxPiezos

MIC_PowerMeter_Abstract

• MIC_PowerMeter_Abstract creates an interface with the power meter.
  • MIC_PM100D

This class structure is integral to the functioning and expansion of our imaging capabilities, facilitating easy maintenance and upgrading of the imaging system components.

Common Features

Each of the instrument components in MIC have export methods, unit tests and graphical user interfaces with a common format.

Export state method

The current state of the individual instrument can be obtained using the function exportState. The output of the exportState function is organized as Attributes, Data and Children.

Example:

[Attributes, Data, Children] = MIC_TIRFLaser488.exportState()

Attributes is a structure with fields carrying information on the current state of the instrument. In the example, Attribute is a structure with fields Power, IsOn and InstrumentName.

Data contain any data associated with the instrument.

Children contain exportState output from children instrument components (if any) called within the parent instrument class.

Unit test method

Each instrument component class in MIC comes equipped with a static method unit test. The unitTest function cycles through a series of pre-defined tests, uniquely selected for the corresponding instrument component, outputting success status. Common steps in the unit test method are creating the object, turning the instrument On/Off, change/modify state of the instrument, output exportState and deleting the object.

It is important to know the input arguments needed for calling the class on a particular instrument component before calling the unitTest. This information can be obtained by performing a doc function on the corresponding MIC class.

Example:

Success=MIC_TCubeLaserDiode.unitTest('64864827','Power',10,100,1)

Graphical user interface

Instument component classes in MIC also come equipped with graphical user interfaces (gui). Classes inheriting from the same instrument abstract class (e.g., MIC_LightSourceAbstract) share a common gui, located in the abstract class folder. For all other instrument components, the corresponding gui scripts are stored in the local folder.

Example:

MIC_DynamixelServo.gui

Installation Notes

Each instrument will be controlled by its own drivers, which must be installed on the system. In many cases, the manufacturer's software development kit (SDK) is provided to create custom applications for controlling the instrument. When installing the drivers, either a header file or dynamic-link library is installed. For example, the MIC_MCLNanoDrive class controls the Mad City Labs 3D Piezo stage and requires the madlib.h header file. During the first initialization of this class on a system, users are prompted to set the location of the madlib.h header file, typically located in C:\Program Files\Mad City Labs\NanoDrive.

Similarly, the MIC_MCLMicroDrive class controls the Mad City Labs Micro Stage and requires the MicroDrive.dll dynamic-link library. The first time this class is used on a given computer, the user will be prompted to select the location of MicroDrive.dll. On a Windows machine, this is typically placed by default in C:\Program Files\Mad City Labs\MicroDrive\MicroDrive.dll during the installation process (installation files provided by MCL).

Documentation

The detailed documentation of each MIC class can be found here: MIC Classes.

Contribution

We welcome contributions to the MIC project. Please see CONTRIBUTING for more information.