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ImSwitch Configuration

This section provides comprehensive guides for configuring ImSwitch with various hardware components and use cases.

Configuration Overview​

ImSwitch uses JSON configuration files to define:

  • Hardware setup: Cameras, stages, lasers, LEDs
  • Device managers: Software interfaces for hardware control
  • System settings: Paths, options, and preferences
  • Integration settings: External software connections

Configuration Structure​

Configuration Files Location​

Default Locations:

  • Windows: %USERPROFILE%\Documents\ImSwitchConfig\
  • macOS: /Users/$USERNAME/ImSwitchConfig/
  • Linux: ~/ImSwitchConfig/

Folder Structure:

ImSwitchConfig/
├── config/
│   └── imcontrol_options.json     # Main configuration
├── imcontrol_setups/
│   ├── uc2_basic.json             # Hardware configurations
│   ├── uc2_multicolor.json
│   └── custom_setup.json
├── imcontrol_slm/                  # SLM patterns
└── scripts/                       # Custom scripts

Main Configuration File​

The imcontrol_options.json file defines:

{
    "setupFileName": "uc2_basic.json",
    "recording": {
        "outputFolder": "./recordings",
        "includeDateInOutputFolder": true
    },
    "watcher": {
        "outputFolder": "./scripts"
    }
}

Hardware Configuration​

1. UC2-ESP32 Basic Setup​

File: imcontrol_setups/uc2_basic.json

{
  "rs232devices": {
    "ESP32": {
      "managerName": "ESP32Manager",
      "managerProperties": {
        "host_": "192.168.1.100",
        "serialport": "/dev/ttyUSB0",
        "serialport_windows": "COM3"
      }
    }
  },
  "positioners": {
    "ESP32Stage": {
      "managerName": "ESP32StageManager",
      "managerProperties": {
        "rs232device": "ESP32",
        "stepsizeX": -0.3125,
        "stepsizeY": -0.3125,
        "stepsizeZ": 0.3125
      },
      "axes": ["X", "Y", "Z"],
      "forScanning": true,
      "forPositioning": true
    }
  },
  "lasers": {
    "LED": {
      "managerName": "ESP32LEDLaserManager",
      "managerProperties": {
        "rs232device": "ESP32",
        "channel_index": 1
      },
      "wavelength": 635,
      "valueRangeMin": 0,
      "valueRangeMax": 100
    }
  },
  "detectors": {
    "WidefieldCamera": {
      "managerName": "OpenCVCamManager",
      "managerProperties": {
        "cameraListIndex": 0,
        "OpenCVCamera": {
          "exposure": 0,
          "gain": 0
        }
      },
      "forAcquisition": true,
      "forFocusLock": true
    }
  }
}

2. Advanced Multi-Color Setup​

File: imcontrol_setups/uc2_multicolor.json

{
  "rs232devices": {
    "ESP32": {
      "managerName": "ESP32Manager",
      "managerProperties": {
        "host_": "192.168.43.129",
        "serialport": "/dev/ttyUSB0"
      }
    }
  },
  "positioners": {
    "ESP32Stage": {
      "managerName": "ESP32StageManager",
      "managerProperties": {
        "rs232device": "ESP32"
      },
      "axes": ["X", "Y", "Z"],
      "forScanning": true,
      "forPositioning": true
    }
  },
  "lasers": {
    "Laser405": {
      "managerName": "ESP32LEDLaserManager",
      "managerProperties": {
        "rs232device": "ESP32",
        "channel_index": 1
      },
      "wavelength": 405,
      "valueRangeMin": 0,
      "valueRangeMax": 100
    },
    "Laser488": {
      "managerName": "ESP32LEDLaserManager",
      "managerProperties": {
        "rs232device": "ESP32",
        "channel_index": 2
      },
      "wavelength": 488,
      "valueRangeMin": 0,
      "valueRangeMax": 100
    },
    "Laser561": {
      "managerName": "ESP32LEDLaserManager",
      "managerProperties": {
        "rs232device": "ESP32",
        "channel_index": 3
      },
      "wavelength": 561,
      "valueRangeMin": 0,
      "valueRangeMax": 100
    }
  },
  "detectors": {
    "WidefieldCamera": {
      "managerName": "HikCamManager",
      "managerProperties": {
        "isRGB": 1,
        "hikcam": {
          "exposure": 100,
          "gain": 0,
          "blacklevel": 100
        }
      },
      "forAcquisition": true,
      "forFocusLock": true
    }
  },
  "ledMatrixes": {
    "ESP32 LEDMatrix": {
      "managerName": "ESP32LEDMatrixManager",
      "managerProperties": {
        "rs232device": "ESP32",
        "dimx": 8,
        "dimy": 8
      },
      "wavelength": 635,
      "valueRangeMin": 0,
      "valueRangeMax": 255
    }
  },
  "autofocus": {
    "camera": "WidefieldCamera",
    "positioner": "ESP32Stage",
    "updateFreq": 10,
    "frameCropx": 100,
    "frameCropy": 100
  }
}

Device Managers​

Camera Managers​

OpenCV Camera (USB/Built-in):

"WidefieldCamera": {
  "managerName": "OpenCVCamManager",
  "managerProperties": {
    "cameraListIndex": 0,
    "OpenCVCamera": {
      "exposure": 0,
      "gain": 0,
      "fps": 30
    }
  }
}

HIK/Daheng Industrial Camera:

"IndustrialCamera": {
  "managerName": "HikCamManager",
  "managerProperties": {
    "isRGB": 1,
    "hikcam": {
      "exposure": 100,
      "gain": 0,
      "blacklevel": 100,
      "gamma": 1.0
    }
  }
}

Raspberry Pi Camera:

"PiCamera": {
  "managerName": "PiCamManager",
  "managerProperties": {
    "resolution": [1920, 1080],
    "framerate": 30,
    "sensor_mode": 0
  }
}

Stage Managers​

UC2-ESP32 Stage:

"ESP32Stage": {
  "managerName": "ESP32StageManager",
  "managerProperties": {
    "rs232device": "ESP32",
    "stepsizeX": -0.3125,
    "stepsizeY": -0.3125,
    "stepsizeZ": 0.3125,
    "homeSpeedX": 15000,
    "homeSpeedY": 15000,
    "homeSpeedZ": 15000,
    "enabledAxes": ["X", "Y", "Z"]
  },
  "axes": ["X", "Y", "Z"],
  "forScanning": true,
  "forPositioning": true
}

Laser/LED Managers​

UC2-ESP32 LED Control:

"LED_White": {
  "managerName": "ESP32LEDLaserManager",
  "managerProperties": {
    "rs232device": "ESP32",
    "channel_index": 1
  },
  "wavelength": 635,
  "valueRangeMin": 0,
  "valueRangeMax": 100
}

LED Matrix Control:

"ESP32_LEDMatrix": {
  "managerName": "ESP32LEDMatrixManager",
  "managerProperties": {
    "rs232device": "ESP32",
    "dimx": 8,
    "dimy": 8
  },
  "wavelength": 635,
  "valueRangeMin": 0,
  "valueRangeMax": 255
}

Communication Settings​

Serial/USB Communication​

"ESP32": {
  "managerName": "ESP32Manager",
  "managerProperties": {
    "serialport": "/dev/ttyUSB0",        # Linux
    "serialport_windows": "COM3",        # Windows
    "serialport_mac": "/dev/cu.usbserial-1410", # macOS
    "baudrate": 115200,
    "timeout": 1.0
  }
}

WiFi/Network Communication​

"ESP32_WiFi": {
  "managerName": "ESP32Manager", 
  "managerProperties": {
    "host_": "192.168.1.100",
    "port": 31950,
    "timeout": 5.0
  }
}

Configuration Templates​

1. Basic Microscope​

Minimal setup for testing:

  • USB camera
  • Single LED
  • Basic stage control

2. Multi-Channel Fluorescence​

Advanced setup for fluorescence microscopy:

  • Industrial camera
  • Multiple lasers (405nm, 488nm, 561nm)
  • XYZ stage with autofocus
  • LED matrix for structured illumination

3. High-Content Screening​

Setup for automated plate imaging:

  • High-resolution camera
  • Fast stage movement
  • Multiple illumination options
  • Automated well scanning

4. Custom Research Setup​

Template for specialized applications:

  • Custom device managers
  • Specialized hardware interfaces
  • Research-specific workflows

Advanced Configuration​

Custom Device Managers​

Creating custom device interfaces:

from imswitch.imcontrol.model.interfaces import DeviceManager

class CustomDeviceManager(DeviceManager):
    def __init__(self, deviceInfo, name, **kwargs):
        super().__init__(deviceInfo, name, **kwargs)
        # Initialize custom hardware
        
    def custom_function(self):
        # Implement custom functionality
        pass

Widget Configuration​

Enable/disable UI components:

{
  "availableWidgets": [
    "Image",
    "Laser",
    "Positioner", 
    "Recording",
    "Settings"
  ],
  "nonAvailableWidgets": [
    "EtSTED",
    "FocusLock",
    "PixelCalibration"
  ]
}

Scripting Integration​

Configure script execution:

{
  "scripting": {
    "enabled": true,
    "scriptPaths": ["./scripts", "/custom/scripts"],
    "autoStart": ["startup_script.py"],
    "allowedModules": ["numpy", "scipy", "opencv"]
  }
}

Validation and Testing​

Configuration Validation​

# Validate configuration file
import json

def validate_config(config_file):
    try:
        with open(config_file, 'r') as f:
            config = json.load(f)
        print("Configuration is valid JSON")
        return True
    except json.JSONDecodeError as e:
        print(f"Invalid JSON: {e}")
        return False

# Test hardware connectivity
def test_hardware(config):
    # Test each device defined in configuration
    pass

Common Validation Errors​

JSON Syntax Errors:

  • Missing commas
  • Unmatched brackets
  • Invalid quotes

Device Reference Errors:

  • Incorrect device names
  • Missing manager properties
  • Invalid parameter values

Best Practices​

Organization​

  1. Use descriptive names for devices and configurations
  2. Comment your configurations (JSON doesn't support comments, use separate documentation)
  3. Version control your configurations
  4. Test incrementally when building complex setups

Performance​

  1. Optimize camera settings for your application
  2. Configure appropriate timeouts for network devices
  3. Use hardware triggering when available
  4. Minimize unnecessary polling of slow devices

Maintenance​

  1. Regular backups of working configurations
  2. Document custom settings and their purposes
  3. Test after updates to ensure compatibility
  4. Keep templates for common setups

Next Steps​