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.

MIC publication in the Journal of Open Source Software (JOSS) can be accessed by clicking the badge below:

Class Structure Overview

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

abstract

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

camera

• The camera namespace is the base for all camera-related classes, defining common functions and properties.
  • abstract
  • AndorCamera
  • AndorCameraZyla
  • DCam4Camera
  • HamamatsuCamera
  • Imaq
  • IMGSourceCamera
  • PyDcam
  • ThorlabsIR
  • ThorlabsSICamera
  • example

lightSource

• The lightSource namespace is the base for all light sources (e.g., lasers), defining common functions and properties.
  • abstract
  • CoherentLaser561
  • CrystaLaser405
  • CrystaLaser561
  • DHOMLaser532
  • HSMLaser488
  • IX71Lamp01
  • MPBLaser
  • RebelStarLED
  • TIRFLaser488
  • TubeLaserDiode
  • VortranLaser488
  • example

linearStage

• The linearStage abstract is the abstract class for linear stages.
  • abstract
  • KCubePiezo
  • MCLMicroDrive
  • TCubePiezo
  • example

powermeter

• The powermeter namespace creates an interface with the power meter.
  • abstract
  • PM100D
  • example

stage3D

• The stage3D is the namespace for 3D stages.
  • abstract
  • MCLNanoDrive
  • NanoMaxPiezos
  • example

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 constructor, export methods, functional tests, and graphical user interfaces with a common format.

Constructor method

The constructor method of each instrument component class is used to create an object of the class. The constructor method is called when the class is initialized. The constructor method can take input arguments. One example of the constructor method is shown below. ``` attenuator = mic.Attenuator('Dev1', 'ao1');

% Load calibration data attenuator.loadCalibration('CalibrationFile.mat');

% Set transmission to 50% attenuator.setTransmission(50);

% Shutdown the attenuator attenuator.shutdown(); ```

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: % obj = mic.lightsource.TCubeLaserDiode(SerialNo, Mode, MaxPower, WperA, TIARange); TIRFLaser642 = mic.lightsource.TCubeLaserDiode('64838719', 'Power', 80, 182.5,1); [Attributes, Data, Children] = TIRFLaser642.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.

Functional test (funcTest) method

Each instrument component class in MIC comes equipped with a static method functional test. The funcTest cycles through a series of pre-defined tests, uniquely selected for the corresponding instrument component, outputting success status. Common steps in the functional 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 funcTest. This information can be obtained by performing a doc function on the corresponding MIC class.

Example: TCubeLaserDiode = mic.lightsource.TCubeLaserDiode('64838719','Power', 80, 182.5, 1) Success = TCubeLaserDiode.funcTest()

Graphical user interface

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

Example: DynamixelServo.gui

Full example

See mic_example.m for an example of z-stack acquisition using various MIC low-level routines for a laser, camera and 3D stage. (Note: this won't run properly without the appropriate hardware and Kinesis software installed!) See also "Projects using MIC" below.

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 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 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).

To set up the correct MATLAB path for MIC in startup.m (typically located in the Documents\MATLAB folder in the user's home directory), add the line matlab run(fullfile(userpath, 'matlab-instrument-control', 'setupMIC')) (for MATLAB 2017a or more recent versions).

Testing

See tests folder for unit tests of simulated classes, which in turn tests the various abstract classes the simulated classes are based on. This is done automatically on a push or pull request to main.

Top-level files and directories

name | description ---|--- doc | miscellaneous documentation genDoc.m | generates Readme.md files for each MIC class LICENSE | MIT license mex64 | Windows executable mex files generated from those in mexsource mexsource | mex source files paper | JOSS paper README.md | this document setupMIC.m | set the MATLAB path correctly for MIC src | MATLAB code source tests | simulated functional tests

High-level implementation of MIC classes

High-level implementations of MIC classes are demonstrated through: - Custom-built Sequential microscope available on Sequential SR Microscope specifically designed for dSTORM and DNA-PAINT based super-resolution imaging. - TIRF based super-resolution microscope available on TIRF SR Microscope.

Projects using MIC

• David J. Schodt, Farzin Farzam, Sheng Liu, and Keith A. Lidke, "Automated multi-target super-resolution microscopy with trust regions," Biomed. Opt. Express 14, 429-440 (2023). https://doi.org/10.1364/BOE.477501
• Fazel, M., Wester, M.J., Schodt, D.J. et al. High-precision estimation of emitter positions using Bayesian grouping of localizations. Nat Commun 13, 7152 (2022). https://doi.org/10.1038/s41467-022-34894-2

Related software

• Micro-Manager is a customizable platform for controlling microscopy systems, supporting a wide range of hardware devices, and is primarily built on Java. This software can be obtained from: https://micro-manager.org/
• PYME (PYthon Microscopy Environment) is a Python based environment designed to facilitate image acquisition and data analysis in microscopy, with a focus on super-resolution techniques like PALM, STORM, and PAINT. This software can be obtained from GitHub: https://github.com/python-microscopy/python-microscopy
• LSMAQ is a lightweight and flexible laser scanning microscope acquisition software written in MATLAB. It supports National Instruments hardware for galvo-based scanning. This software can be obtained from GitHub: https://github.com/danionella/lsmaq

Documentation

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

Contributions

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