openUC2 FiveD v3

Design Files

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https://github.com/openUC2/openUC2_XYZ_Stagescanning_Microscope/

Version 3

This is a novel version of the XYZ microscope that also includes fluorescence imaging. It is not based on the UC2 cubes anymore but featues a monolithic body that is still 3D printed.

More information are comming soon!

Introduction

A first video explains the basic operation of the device

Software

The device runs using ImSwitch with the following Configuration. Find the ImSwitch Installer here: https://github.com/openUC2/ImSwitchInstaller/releases/tag/v0.0.2 (go to latest release)

Config

{
  "positioners": {
    "ESP32Stage": {
      "managerName": "ESP32StageManager",
      "managerProperties": {
        "rs232device": "ESP32",
        "isEnable": true,
        "enableauto": false,
        "stepsizeX": -0.3125,
        "stepsizeY": -0.3125,
        "stepsizeZ": 0.3125,
        "homeSpeedX": 15000,
        "homeSpeedY": 15000,
        "homeSpeedZ": 15000,
        "isDualaxis": true,
        "homeDirectionX": 1,
        "backlashXOld": 15,
        "backlashYOld": 40,
        "backlashX": 0,
        "backlashY": 0,
        "homeEndstoppolarityY": 0,
        "homeDirectionY": -1,
        "homeDirectionZ": 0,
        "homeXenabled": 1,
        "homeYenabled": 1,
        "homeZenabled": 0,
        "initialSpeed": {
          "X": 15000,
          "Y": 15000,
          "Z": 15000
        }
      },
      "axes": [
        "X",
        "Y",
        "Z"
      ],
      "forScanning": true,
      "forPositioning": true
    }
  },
  "rs232devices": {
    "ESP32": {
      "managerName": "ESP32Manager",
      "managerProperties": {
        "host_": "192.168.43.129",
        "serialport": "COM5",
        "baudrate":115200,
        "debug":1
      }
    }
  },
  "lasers": {
    "LED": {
        "analogChannel": null,
        "digitalLine": null,
        "managerName": "ESP32LEDLaserManager",
        "managerProperties": {
          "rs232device": "ESP32",
          "channel_index": 1
        },
        "wavelength": 0,
        "valueRangeMin": 0,
        "valueRangeMax": 1023
      },
      "Laser 488": {
        "analogChannel": null,
        "digitalLine": null,
        "managerName": "ESP32LEDLaserManager",
        "managerProperties": {
          "rs232device": "ESP32",
          "channel_index": 2
        },
        "wavelength": 635,
        "valueRangeMin": 0,
        "valueRangeMax": 1023
      },
      "Laser 635": {
        "analogChannel": null,
        "digitalLine": null,
        "managerName": "ESP32LEDLaserManager",
        "managerProperties": {
          "rs232device": "ESP32",
          "channel_index": 3
        },
        "wavelength": 488,
        "valueRangeMin": 0,
        "valueRangeMax": 1023
      }

    },
  "detectors": {
    "WidefieldCamera": {
      "analogChannel": null,
      "digitalLine": null,
      "managerName": "HikCamManager",
      "managerProperties": {
        "isRGB": 1,
        "cameraListIndex": 0,
        "cameraEffPixelsize": 0.2257,
        "hikcam": {
          "exposure": 0,
          "gain": 0,
          "blacklevel": 100,
          "image_width": 1000,
          "image_height": 1000
        }
      },
      "forAcquisition": true,
      "forFocusLock": true
    },
    "Observer": {
      "analogChannel": null,
      "digitalLine": null,
      "managerName": "OpenCVCamManager",
      "managerProperties": {
        "cameraListIndex": 1,
        "cameraListIndexWIN": 0,
        "isRGB":1,
        "opencvcam": {
          "exposure": 10
        }
      },
      "forAcquisition": true
    }
  },
  "autofocus": {
    "camera": "WidefieldCamera",
    "positioner": "ESP32Stage",
    "updateFreq": 10,
    "frameCropx": 780,
    "frameCropy": 400,
    "frameCropw": 500,
    "frameCroph": 100
  },
  "mct": {
    "monitorIdx": 2,
    "width": 1080,
    "height": 1920,
    "wavelength": 0,
    "pixelSize": 0,
    "angleMount": 0,
    "patternsDirWin": "C:\\Users\\wanghaoran\\Documents\\ImSwitchConfig\\imcontrol_slm\\488\\",
    "patternsDir": "/users/bene/ImSwitchConfig/imcontrol_sim/488"
  },
  "PixelCalibration": {},
  "focusLock": {
    "camera": "WidefieldCamera",
    "positioner": "ESP32StageManager",
    "updateFreq": 4,
    "frameCropx": 0,
    "frameCropy": 0,
    "frameCropw": 0,
    "frameCroph": 0
  },
  "availableWidgets": [
    "Settings",
    "View",
    "Recording",
    "Image",
    "Laser",
    "Positioner",
    "Autofocus",
    "MCT",
    "UC2Config",
    "ImSwitchServer",
    "PixelCalibration",
    "HistoScan",
    "ROIScan"
  ],
  "nonAvailableWidgets": [
    "STORMRecon",
    "DPC",
    "Hypha",
    "FocusLock",
    "HistoScan",
    "FocusLock",
    "FOVLock"
  ]
}

Assembly Instructions

Assembly of the Optics Cube

To begin the assembly of the microscope, the following components are needed:

The "ESP32 DEV-based UC2 standalone board V3"
Screws
Housing parts

Electronic components including a development board

Mount the middle plate with M3x12 screws:

Mounting the middle plate with screws

Ensure the screws are fixed properly on both sides. Also, cover the screws with non-conductive tape to prevent any shorts on the ESP32-based board side:

Covering screws with non-conductive tape

The top plate is attached with 8 screws on the red edges. Then, flip the microscope and attach the bottom plate with adhesive feet. For better stability, it is recommended to use 4 adhesive feet. Then the microscope can be placed upright again.

Attaching the top plate with screws Adhesive feet on the bottom plate

Assembly of the Optics Module (e.g., Camera)

Next, you will need the following parts:

Camera
Mirror
Parts for the camera module

The mirror is placed in the module.

Placing the mirror in the module Securing the mirror in the module

Apply double-sided tape around the camera for additional adhesion and assemble the camera housing parts.

Applying double-sided tape to the camera Assembled camera module

Insert the camera module into the microscope as shown:

Inserting the camera module into the microscope Securing the camera module

Mounting the Stage on Top of the Optics Cube

The stage is attached to the top plate with 4 screws and nuts. Rotate the threaded spindles to access the screw holes.

Attaching the stage to the top plate Securing the stage with screws and nuts

Now the objective can be installed:

Installing the objective Securing the objective

Wiring Up the Motors and Endstops

Next, connect the stepper motors to the board:

Connecting the stepper motors Stepper motors connected to the board

If the zero point is incorrect after installing the firmware, you can reverse the connections accordingly:

Reversing the connections if necessary

To connect the endstops, first rewire them and then connect them to the board.

Rewiring the endstops Connecting the endstops to the board

Next, you need to attach additional components. If necessary, drill new holes. The placement will depend on the objective, which needs to be positioned at the bottom left corner. After that, secure the components with two screws each.

Drilling new holes if necessary Securing additional components

Finally, attach the slide holder with 8 screws.

Attaching the slide holder

This completes the assembly of the UC2 FiveD v3 microscope. Follow each step carefully to ensure proper assembly and functionality.

Troubleshoot

We learn from mistakes. So lets start learning. The system is fully open, meaning, you can adjust and change the vast majority of the parts on your own. The entire system consists of the openUC2 frame / skeleton and the 3D printed housing to shield it from dust and light. By removing all M3 cylindrical screws, you can detach the housing from the inner structure to eventually repair or alter the system.

You can find a full description of how to dissassemble the microscope here: https://openuc2.github.io/docs/PRODUCTION/INVESTIGATOR/ProductionXYZMicroscope

Connecting the microscope to the browser and controll it

We encourage you to use the UC2ified ImSwitch software to control the microscope. You can find it in this repository: https://github.com/openUC2/ImSwitch/

However, if you want to quick-start the microscope and see if it works, you can open your browser and use the WEB-Serial interface to interact with the microscope.

Go to https://youseetoo.github.io/ and connect to your board (most right option saying ESP32 DEV-based UC2 standalone board V2). Select the COM Port which is holding the ESP32 and hit the LOG option, once the dialog opens. The alternative option will help you updating the firmware on the device. An in-depth explanation on how the firmware works can be found here.

In general, you need to send JSON strings in order to control the system. The strings relevant for the Z-microscope are:

Home the XY-axis

It's important to always home the Motors in order to avoid them from getting stuck in an end position (ATTENTION!). The following string will move the motor until the endstop is hit. Afterwards it will release the switch:

{"task":"/home_act", "home": {"steppers": [{"stepperid":1, "timeout": 2000, "speed": 15000, "direction":1, "endposrelease":3000}]}}

and

{"task":"/home_act", "home": {"steppers": [{"stepperid":2, "timeout": 2000, "speed": 15000, "direction":1, "endposrelease":3000}]}}

Afterwards the internal position is set to 0. You can check that by entering:

{"task": "/motor_get"}

Move the Z-axis:

The motor (Nema12) with 200 steps/revolution runs with 16 microstepps and offers a leadscrew with 1mm/revolution. Hence, one step corresponds to 312.5nm. Running the motor can be issued with the following command:

{"task":"/motor_act",
    "motor":
    {
        "steppers": [
            { "stepperid": 3, "position": 1000, "speed": 15000, "isabs": 3, "isaccel":0}
        ]
    }
}

stepperid: 3 correpsonds to the Z-axis
position: steps to go (not physical units!)
speed: steps / minute (do not exceed 20000)
isabs: absolute or relative motion
isaccel: for now, use only non-accelerated motion!

Safety

in case of shattered glass, make sure you don't cut yourself
Make sure you don't hurt yourself
The moving parts can potentially hurt your finger
The electronics - if used in a wrong way - can harm you
edges may be sharp, make sure you don't cut yourself

openUC2 FiveD v3

Design Files​

Version 3​

Introduction​

Software​

Assembly Instructions​

Assembly of the Optics Cube​

Assembly of the Optics Module (e.g., Camera)​

Mounting the Stage on Top of the Optics Cube​

Wiring Up the Motors and Endstops​

Troubleshoot​

Connecting the microscope to the browser and controll it​

Home the XY-axis​

Move the Z-axis:​

Safety​