User Manual : Si-Through-HR Wafer Microscope

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Last updated: July 6, 2026

 

1 Disclaimer

Read this document carefully before installing, configuring, operating, or maintaining this product. Users must familiarize themselves with the installation instructions and all applicable codes, laws, and standards. Installation, adjustment, commissioning, operation, assembly, disassembly, and maintenance must be performed by qualified personnel in accordance with applicable codes and accepted practices. If the product is installed, operated, or used in a manner not specified by Jay Photonics, the protection and warranty provided by the product may be impaired. 

All information in this manual is believed to be accurate at the time of publication. Jay Photonics reserves the right to make changes to the product or documentation at any time as part of its policy of continual product improvement. All specifications are therefore subject to change without notice. 

This manual may describe optional features or accessories that are not included with your specific product configuration. 

2 Introducing the SI-Through-HR Wafer Microscope

The Jay Photonics Si-Through-HR Wafer microscope is the second generation of our Si-Through-HR microscope platform, developed to meet customer application requirements and improve flexibility for a wide range of inspection tasks. 

The Si-Through-HR Wafer microscope is designed for infrared inspection of silicon chips and wafers up to 8 inches in diameter. Using proprietary transmitted infrared illumination, the system provides clear, high-resolution imaging of structures located beneath the silicon surface, making it well suited for semiconductor analysis, failure inspection, and research applications. 

To support different workflows and applications, the microscope features a modular design that allows a variety of accessories and add-ons to be integrated into the system. Depending on the configuration, the Si-Through-HR Wafer microscope can be adapted with different optical components, illumination options, stages, and imaging accessories. 

The microscope is equipped with our proprietary USB camera compatible with many open-source and proprietary imaging software platforms, allowing easy integration into existing laboratory or industrial environments. 

The following sections introduce the main components of the microscope and provide guidance for setup and operation. 

2.1 Package contents

Depending on the system configuration purchased, the package may include the following components: 

  • Si-Through-HR Wafer microscope body 
  • USB camera  
  • Illumination control unit and power adapter 
  • Microscope calibration slide with 10 µm divisions 
  • Glass stage plate  
  • One or more microscope objectives
  • Bright-field condenser    
  • Two mounted SWIR polarizers (optional)
  • Dark-field condenser (optional) 

Inspect all components upon receipt and report any shipping damage or missing items before operating the microscope. 

 2.2 Name of Each Part

 

 

3 Setup and Assembly

This section describes the basic setup procedure for the Si-Through-HR Wafer microscope. Before beginning, place the microscope on a stable surface and ensure that all components are clean and free of dust or debris. 

 

3.1 Installing the camera

Attach the USB camera to the top of the optical tube assembly and secure it in place. Once installed, connect the camera to the computer using the USB cable. Plastic adhesive cable clips are included to secure the camera USB cable. 

 

3.1.1 Software Setup 

The USB camera included with the Si-Through-HR Wafer microscope is compatible with a wide range of open-source and proprietary imaging software platforms. 

To begin operation: 

  1. Launch your preferred imaging software. 
  2. Select the USB camera from the list of available imaging devices.  
  3. Adjust exposure, gain, and image settings as required.  

Additional software recommendations and download information are available on the Jay Photonics website: https://jayphotonics.com/pages/recommended-software 

Depending on the selected software platform, compatibility may be available for Windows, macOS, and Linux operating systems. 

3.2 Installing the Objective

Carefully thread the microscope objective onto the bottom of the optical tube assembly. Tighten the objective gently until secure. Avoid over-tightening and avoid touching the optical surfaces during installation. 

When changing objectives, always support the objective with one hand during installation or removal. 

3.3 Installing the Condenser

Mount the condenser onto the condenser arm located beneath the sample stage. Make sure the condenser is fully seated and aligned with the locating notch before tightening any retaining screws. 

Connect the condenser illumination cable to the power supply. The illumination intensity can later be adjusted using the illumination control knob. 

3.4 Installing the Glass Stage Plate

Place the glass stage plate to the sample stage and secure it using the four spring-loaded stage clips. Ensure that the plate is positioned evenly and fully supported before placing samples on the stage. 

For small samples, the glass stage plate should remain installed during operation. However, for standard 4-inch, 6-inch, and 8-inch wafers the glass can be removed. 

 

4 Operation of Each Part

 

4.1 Illumination 

The illumination control unit is shown below. 

    4.1.1 Turning on/off the Lamp 

    The illumination can be turned on and off by the switch on the LED controller. The LED is on when the red light of the switch is on. 

    ⚠️ Caution: Always turn off the microscope illumination after use. Since infrared light is invisible to the naked eye, the microscope can easily be left on unintentionally. 

     

    4.1.2 Light control 

    When the light is on using the switch on the LED controller, the intensity can be controlled with the knob on the illumination control unit. Start with the minimum intensity and increase it if necessary. 

    4.2 Coarse/Fine Focus Knob 

    4.2.1 Relation between the focus knob and optical tube vertical movements 

    The optical tube moves approximately 40 mm per one complete rotation of the coarse focus knob. The optical tube moves 225 µm per one complete rotation of the fine focus knob. 

    The maximum range of the vertical movements of the optical tube using the coarse and fine movements is 30 mm. 

    If height adjustment is required, the position of the optical tube can be adjusted using the four screws that mount the optical tube arm to the main body of the microscope. Slightly loosen the screws, move the optical tube to the desired height, then retighten the screws securely. 

    Since the optical tube is heavy, it must be handled carefully during this procedure. 

    Never loosen the screws while a sample, wafer, or glass plate is mounted on the microscope. If the procedure is not performed carefully, the optical tube may fall and damage the sample or the microscope. 

    4.3 Aperture Iris 

    The iris is used to improve image contrast by blocking excess light that would otherwise reduce contrast due to saturation. This saturation is often caused by the edges of the chip or by regions that are more transparent than the area of interest. 

    Semiconductor chips and wafers frequently contain materials with different optical absorption and reflection properties. As a result, some regions may transmit or reflect significantly more light than others, leading to localized image saturation. 

    When imaging through a small, highly opaque component that occupies only a portion of the field of view, the iris can be closed down to transmit light only through the component while blocking the saturated light from the surrounding transparent areas. This significantly improves image contrast. 

    When imaging across the entire sensor or field of view, the iris should be opened until it just matches the camera sensor. This improves image contrast by blocking stray light from outside the sensor's field of view. 

     The iris can be closed in the direction shown in the figure below.

     

     

    4.4 Wafer Holder Configuration 

    For wafer inspection, remove the glass stage plate and adjust the wafer holders to the appropriate wafer diameter by lifting the spring-loaded locking pins, sliding the holders to the desired positions, and releasing the pins to lock them in place. Wafer diameters of 4, 6, and 8 inches are indicated by engraved position markings on the stage. 

    Ensure that all four holders are locked into the correct position before placing the wafer onto the stage. 

    4.5 Polarizer Kit 

    The optional SWIR polarizer kit enhances the visibility of certain structures and stress-induced birefringence during infrared inspection. 

    To use the polarizer kit: 

    1. Operate the microscope in standard bright-field mode. 
    2. Mount Polarizer #1 between the objective and the optical tube assembly. 
    3. Mount Polarizer #2 above the condenser. 
    4. Rotate the polarizers as needed to achieve the desired contrast and image response.  

    Depending on the sample structure and imaging conditions, different polarizer orientations may produce different contrast levels. 

    4.6 Dark-Field Condenser 

    The optional dark-field condenser can be used to enhance the visibility of surface features, defects, edges, and scattering structures that may not be clearly visible under standard bright-field illumination. 

     

    4.6.1 Installing the Dark-Field Condenser 

    1. Remove the bright-field condenser from the condenser arm. 
    2. Install the dark-field condenser in its place.  
    3. Connect the dark-field condenser illumination cable to the power supply.  

    Ensure that the condenser is securely mounted before operation. 

     

    4.6.2 Aligning the Dark-Field Illumination 

    1. Place the sample onto the stage. 
    2. Adjust the condenser height so that the illumination is properly focused onto the sample region.  
    3. Focus the microscope objective on the sample.  
    4. Using the three condenser alignment screws, center the dark-field illumination with respect to the camera image.  

    Proper alignment is important to achieve uniform dark-field illumination and maximum image contrast. 

    5 Microscope Optimization

    This section describes the recommended procedure for optimizing illumination and image quality for silicon inspection. 

     

    5.1 Initial Alignment 

    1. Install the camera, objective, and condenser according to the setup instructions. 
    2. Turn on the condenser illumination using the lowest LED intensity setting.  
    3. Using a low-magnification objective, adjust the condenser position so that the illumination spot is centered with respect to the optical axis of the microscope.  
    4. Use the retaining screws on the condenser arm to fine-tune the condenser alignment.  

    Since the infrared illumination can easily saturate the camera, begin with the lowest exposure time and gain settings in the imaging software. 

     

    5.2 Sample Placement and Focusing 

    For silicon chips and small samples, place the sample directly on the glass stage plate. 

    For wafer inspection, remove the glass stage plate and position the wafer using the adjustable wafer holders. 

    After placing the sample: 

    1. Focus the microscope using the stage or focusing controls. 
    2. When changing objectives, carefully refocus the sample, as the focal position may vary between objectives. 

     

    5.3 Resolution Optimization 

    For high magnification imaging using 40X to 100X objectives, fully open the condenser iris and vertically adjust the condenser position until the illumination intensity reaches its maximum value. 

    This position provides the highest numerical aperture (NA) illumination and maximizes resolution. However, the LED structure itself may begin to appear faintly in the image if the condenser is positioned too close to the optimal focal position. In this case, slightly move the condenser away from this position until the image illumination becomes uniform. 

    At lower magnifications such as 4X and 10X, the condenser should typically be moved farther away to ensure uniform illumination across the full field of view. 

    Reducing the iris diameter may improve image contrast and increase depth of field, but it will also reduce optical resolution. 

     

    5.4 Image Optimization 

    High-quality images can often be achieved without complex digital processing. 

    For silicon circuit imaging, the following adjustments are generally recommended: 

    1. Use the minimum camera gain possible 
    2. Slightly increase image contrast  
    3. Slightly reduce gamma settings  

    These adjustments are commonly available in most imaging software platforms. 

     

      5.5 Illumination Control and Camera Saturation 

    Silicon surfaces can produce strong infrared reflections, which may easily saturate the camera sensor. 

    To reduce brightness: 

    • Lower the condenser vertically 
    • Reduce the LED intensity  
    • Use an optical attenuator if required 
    • Reduce the condenser iris diameter  
    • Reduce the exposure time 

    Lowering the condenser or reducing the iris diameter may decrease optical resolution. 

    The software auto-exposure function may not operate correctly when the camera is heavily saturated. 

     

    5.6 Using the 100X Oil Immersion Objective 

    The optional 100X oil immersion objective is designed for high-resolution imaging applications requiring increased numerical aperture and maximum image detail. 

    To obtain optimal performance, follow the procedure below carefully. 

     

    5.6.1 Applying the Immersion Oil 

    1. Remove the 100X objective from the microscope if it is already installed. 
    2. Place the objective upside down on a clean, flat surface.  
    3. Using the supplied oil container, apply a single small drop of immersion oil directly onto the tip of the objective lens.  

    Apply the oil to the objective rather than to the sample surface. This helps minimize the formation of trapped air bubbles between the objective and the sample. 

    ⚠️ Caution: Use only a small amount of oil. Excess oil may spread to surrounding optical or mechanical components. 

     

    5.6.2 Installing and Focusing the Objective 

    1. Raise the microscope tube before installing the 100X objective.
    2. Carefully thread the objective into place.
    3. Lower the objective tube slowly while observing the live camera image to achieve focus. 

    As the objective approaches the sample, the immersion oil will fill the gap between the objective and the sample surface. 

    If the sample is small or lightweight, secure it properly before focusing. In some cases, the sample may adhere to the oil on the objective, making inspection difficult. A simple method is to secure the sample edges to a microscope slide using adhesive tape. 

    ⚠️ Caution: Lower the tube slowly to avoid accidental contact between the objective and the sample. 

    5.6.3 Cleaning the Objective After Use 

    The 100X oil immersion objective must always be cleaned immediately after use. Residual oil is one of the most common causes of reduced image quality and optical contamination. 

    To clean the objective: 

    1. Use a clean lint-free cloth or a cotton swab lightly moistened with isopropyl alcohol. 
    2. Gently wipe the objective tip to remove the immersion oil.  
    3. Immediately dry the surface using a clean dry cloth or dry cotton swab.  

    After cleaning, inspect the objective lens under reflected light or with a magnifying glass to verify that no oil residue or contamination remains. 

     

    6 Maintenance

    Proper maintenance of the Si-Through-HR Wafer microscope is essential for ensuring its longevity and continued high performance. Regular cleaning and inspection will help maintain the quality of your imaging.

     

    6.1 Periodic Inspection and Maintenance

    It is recommended to perform periodic inspections of the microscope’s components, especially the optical elements. Ensure that the lenses and objectives are free from dust and debris, and verify that all mechanical parts are functioning smoothly.

     

    6.2 Cleaning the Instrument

    After each use of the 100X oil immersion objective, it is crucial to thoroughly clean the objective to prevent oil residue from degrading image quality. Use a cloth or Q-tip moistened with isopropanol to clean the objective, and then wipe it with a clean, dry cloth or Q-tip. Verify that no residue remains by checking the lens with a magnifying glass and light reflection. 

    If any other objective or optical component is dirty, use the same method to clean and inspect them.

     

    6.3 Troubleshooting

    In the event of any issues with the Si-Through-HR Wafer microscope, such as image quality problems or difficulties with software integration, please refer to this troubleshooting section for guidance. Common issues may include:

    • USB Camera Not Recognized: Ensure the camera is securely connected to the computer and that all necessary drivers are installed.
    • Poor Image Quality: Check that the lenses and objectives are clean and free of debris. Verify that the microscope is properly focused and that the software settings, such as exposure and gain, are correctly adjusted.
    • Software Compatibility Issues: Ensure that your software is up-to-date and compatible with third-party cameras. If you need a software suggestion, please visit our dedicated software page for more information.

    If these steps do not resolve the issue, further support is available. Please contact Jay Photonics customer service for additional assistance.

     

    7 Cybersecurity

    Note: This product does not require an Internet connection for operation. It only needs to be connected to a computer running appropriate software.

    It is your responsibility to ensure that the computer to which the microscope is connected is secure and protected against any kind of security breaches. Ensure that your computer's software, operating system, and any connected devices are up-to-date with the latest security patches. Jay Photonics is not liable for damages and/or losses related to security breaches on the connected computer or network.

     

    8 Patent

    The technology used in the Si-Through-HR microscope is patent pending. All rights related to this technology are reserved. Any unauthorized use, reproduction, or distribution of this product or its technology is strictly prohibited and may result in legal action. For more information regarding the patent status, please contact Jay Photonics.

     

    9 Safety Information

    The following pages provide important safety precautions. Please read this user manual carefully and thoroughly before installing, using, or maintaining the instrument.

    9.1 Symbol Definitions

    Here are some examples commonly used in the industry from recognized standards. You can use those related to your product.

    This user manual uses the following symbols to bring attention to key technical and safety-related information.

    Indicates a hazardous situation. When this symbol is encountered on the product, refer to the documentation for important safety information.
    Indicates the presence of electrical energy at voltages high enough to inflict harm on living organisms. (Potential electrical shock hazard.)
    Indicates the presence of direct current.
    Indicates that the main switch is ON.
    Indicates that the main switch is OFF.

     

    9.2 Intended Use

    Using the Si-through-HR Wafer in a manner that does not fall within the scope of its intended use, disregarding this user manual, using under-qualified personnel, or making unauthorized alterations, releases the manufacturer from any liability for any resulting damage. Also, if the equipment is used in a manner not specified by the manufacturer, it may impair the protection provided by the equipment.

    9.3 Handling Safety

    The Si-Through-HR microscope is designed to be easily transported by one person. However, it is important to handle the microscope with care due to its precision components.

    Always use proper lifting techniques to avoid injury, even when handling lighter objects. Ensure that the microscope is securely held and avoid any sudden movements that could cause damage to the device or personal injury.

    9.4 Electrical Safety

    Ensure all cables are securely connected before powering on the microscope. Keep the equipment dry and avoid exposure to water or other liquids during operation.

    Only use the provided power adapter.

     

    10 End of life Disposal

    Product or parts of the product should be handled and disposed of in accordance with federal, state, regional, and local laws. Use the appropriate take-back systems whenever possible.

    Parts of used processing kits should be handled and disposed of in accordance with federal, state, regional, and local laws for biohazard disposal. Use the appropriate take-back systems whenever possible.

    Do not put the product, parts of the product or processing kit products in unsorted municipal waste.

     

    11 Technical Specifications

    11.1 Electrical Specifications

    11.2 Mechanical

    Dimensions (L × W ×H) 378.5 × 645.7 × 682.8 mm 
    Weight 29.5 kg 


    11.3 Environmental

    For indoor use in a lab environment.

    Storage Temperature –40 °C to 70 °C (–40 °F to 158 °F)
    Operating Temperature –10 °C to 55 °C (–58 °F to 131 °F)
    Humidity less than 99% rH, non-condensing


    11.4 Technical specifications

    Microscope type Infrared brightfield
    Optical System Finite-conjugate
    Tube Length 200 mm
    Camera Jay Photonics patent pending infrared technology
    Spatial resolution Sub-micron - limited by the microscope objective NA
    Objective magnifications 4X, 10X, 20X, 40X, 50X, 100X oil (works with all infinity corrected objectives) 
    Objective Mounting Thread M26x0.75 
    Objective Turret Optional
    Focusing System coaxial coarse and fine focus
    Focus Range 30mm
    Stage Wafers (4, 6, 8 inches) and silicon chips 
    Stage Dimensions 300 mm x 370 mm 
    Stage X-Y Travel Range 200mm x 200mm 
    Transmitted Illumination Jay Photonics patent pending infrared technology
    Condenser Doublet condenser, high NA, long working distance 


     

    12 Limited Warranty

    For limited warranty, please refer to the general terms and conditions of Jay Photonics or any specific terms of the proposal, quotation, or agreement when you purchase the product.

     


    13 Contact Information

    For questions regarding the operation of this product, please contact Jay Photonics:

    Jay Photonics

    Email : info@jayphotonics.com

    Adress: 633 ave des Oblats, Quebec, Quebec, Canada, G1N 1W1

    Telephone: +1-514-560-7966

    Web: https://jayphotonics.com