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MicroscopeControl.jl

Dev Build Status Coverage

MicroscopeControl.jl is a Julia package for control of optical microscopy hardware, providing a flexible and high-performance solution for microscope developers.

MicroscopeControl.jl utilizes three layers of code: high-level, low-level, and user-level. High-level code is generic, providing interfaces for stages, light sources, cameras, etc. Low-level code handles hardware-specific implementations, defining functions for individual microscope components. This design heavily leverages Julia’s multiple dispatch, enabling different behaviors for the same function based on argument types. The user-level code integrates these layers to control the microscope system.

Module Structure Overview

MicroscopeControl.jl is organized to ensure scalability and easy integration of new hardware:

Abstract Interfaces

  • Defines basic functions and properties common across all device types (e.g., cameras, light sources, stages).
  • Each abstract interface (e.g., CameraInterface, LightSourceInterface, StageInterface) outlines the required methods, such as initialize, shutdown, and export_state.

Hardware Implementations

  • Provides concrete modules for each hardware device model (e.g., TCubeLaserControl, DCAM4Camera, MCLStage).
  • These modules implement the abstract interfaces and add device-specific functionality.

Common Features

  1. Constructor Methods
    Each hardware component has a constructor that takes relevant parameters (like serial numbers or device addresses). After constructing the device object, you can call initialize or other methods to start interacting with the hardware.

  2. Export State
    The function export_state gives you a structured overview of the device’s current settings:

    • Attributes: Key-value pairs with the device’s configuration.
    • Data: Measurement or imaging data.
    • Children: Nested hardware components or linked instruments.

  3. Graphical User Interface
    Many modules provide a simple GUI for controlling hardware, created using GLMakie. This interface often allows for easy on/off toggling, parameter changes, and live readouts.

Supported Hardware

Cameras

  • Hamamatsu DCAM4 compatible cameras
  • Thorlabs Scientific Cameras (CSC series)
  • Simulated camera for testing

Stages

  • Mad City Labs nanopositioning stages
  • Physik Instrumente (PI) stages
  • PI N-472 linear stage
  • Simulated stage for testing

Light Sources

  • Thorlabs TCube laser diode controller
  • CrystaLaser 561nm
  • Vortran 488nm laser
  • Simulated light source for testing

Other Hardware

  • National Instruments DAQ cards
  • Opal Kelly XEM FPGA boards
  • DAQ-based transmission light control

Installation Notes

Since this package is under active development and not yet registered, install it pinned to a released tag:

using Pkg
Pkg.add(url="https://github.com/LidkeLab/MicroscopeControl.jl.git", rev="v0.1.0")

Advance the pinned tag deliberately when you want a newer release. Pkg.develop (tracking main directly, no tag) is for contributors working on the package itself, not for rig code that depends on it.

This package follows a 0.x versioning policy: every merge to main is tagged (.github/workflows/TagOnMerge.yml), a minor bump (0.x.0) means an interface change, and a patch bump (0.0.x) is everything else. Hardware verification is not tracked here; it is recorded by the downstream rig repo that pins to a given tag.

Contributions

Contributions are welcome! We encourage pull requests that add support for new hardware or improve existing modules.