FAQ: System

We recommend that the customer's ambient temperature be maintained at 22 ± 3 °C, with humidity levels between 10% and 60% R.H. (non-condensing).

The light box contains precision optical components. Please avoid touching it to prevent misalignment.

No, a service manual is not available for end-users. If you encounter any issues while using the Microscoop system, we provide online technical support via email or video call, typically responding within12 hours of your inquiry.

Our support team will assess the issue and provide tailored troubleshooting or service guidance to ensure a timely resolution.

No, opening any part of the light path can expose people to Class 4 laser hazards. Only Syncell engineers are qualified to service our proprietary system. Warranty and service agreements will be void if Syncell determines outside parties have accessed the interior of the system.

Assuming a clean environment and no accidental impact / damage to equipment, we recommend preventative maintenance by a Syncell engineer once a year. Microscoop Mint is a Research Use Only (RUO) device, so PMs do NOT include Device Master Record (DMR) / Medical Device File (MDF) documentation for FDA safety compliance.

Yes, Preventative Maintenance (PM) is required to ensure optimal performance and longevity of the Microscoop system. PM will be performed exclusively by a Syncell Field Service Engineer, following the procedures outlined in the user manual.

An official PM checklist will be used during the service, and a signed copy will be provided to the customer upon completion. This ensures all maintenance steps are documented and verified for compliance and system warranty purposes.

The Microscoop is classified as a RUO device (Research Use Only).

We recommend you generate new calibration files. If this does not resolve this issue, please contact your FSE/FAS or support@syncell.com for assistance.

The primary operating costs are related to reagents and consumables, which are purchased from Syncell. These include chemicals, reagents, and other materials listed in the consumables checklist provided with your system. Contact our support team at support@syncell.com to review this list.

All critical hardware components such as lasers and light sources are either included with the system or are covered under regular maintenance. Replacement or service of these parts is typically only required after extended use and will be handled during Preventative Maintenance if necessary.

Laser Capture Microdissection (LCM) uses a laser to physically cut out Regions of Interest (ROIs) in a single Field of View (FOV), typically at the single-cell level. This is a manual and localized process.

In contrast, the Microscoop platform can rapidly and automatically photolabel thousands of FOVs across an entire slide, enabling high-throughput, compartment-specific protein discovery. Microscoop also offers ~350 nm spatial resolution, significantly surpassing LCM’s resolution, which is limited to whole-cell capture.

Resolution of each Microscoop may vary. However, we can achieve upwards of 350 nm on the xy-axis and approximately 1.5 um on the z-axis.

We are able to achieve approximately a 1.5 um resolution in the z-axis.

We use an epi-fluorescence microscope to visualize fluorescently labeled targets. The Z-plane (focus depth) is automatically adjusted using the system’s Perfect Focus System (PFS) or autofocus functions within the software for each field of view (FOV).

This ensures accurate laser alignment without the need to manually capture images across multiple focal planes.

No. Our method uses spatial accumulation of designated ROIs to study relevant proteins localizing to these ares of the cell in an effort to obtain enough mass for downstream applications, capturing a broad range of protein expression.

A 780 nm laser was selected due to its higher excitation efficiency for the photosensitive biotin probe used in the Synlight-Rich kit. This wavelength provides optimal energy absorption for efficient photolabeling while maintaining minimal sample photodamage and allowing for precise spatial control.

Longer wavelengths may offer deeper tissue penetration but often come at the cost of reduced excitation efficiency, making 780 nm ideal for our platform’s performance and resolution requirements.

Two-photon microscopes use lasers similar to those in Microscoop systems, but use the laser to excite fluorescent molecules for imaging and can be complicated to use. Microscoop employs an easy-to-learn epi-fluorescence microscope for imaging, using the two-photon laser to precisely restrict photobiotinylation to targets in the focal plane. So while it offers comparable lateral (XY) accuracy to lasers of half its wavelength, its axial (Z) labeling accuracy is significantly improved.

The Microscoop platform uses 2-photon excitation to achieve higher spatial precision and minimize photodamage. Unlike 1-photon excitation, which can activate molecules along the entire light path, 2-photon excitation is highly localized and only occurs at the focal point, where two photons are absorbed simultaneously.

This allows us to:

• Precisely target proteins within subcellular regions.
• Reduce background labeling and photobleaching.
• Improve depth penetration, enabling imaging and photolabeling in thicker samples.

Overall, 2-photon technology enhances both resolution and specificity—critical for compartment-level proteomic discovery.

A single photon can be described by a wave function that spreads out in space. This wave function's probabilistic nature means that a single photon does not have a well-defined position, making it difficult to focus it precisely at a single point on the z-axis.

No. The accuracy of photolabeling depends on the precision of the galvo scanner and the stability of the optical system, rather than on the multi-photon system itself.

Between ROI segments, the system temporarily shuts off the laser output and jumps to the next ROI, avoiding any exposure to non-targeted areas.

This approach ensures high spatial specificity and prevents unwanted photolabeling outside the selected regions.

Microscoop Mint complies with IEC 60825-1:2014 as installed by Syncell engineers, and should not pose a hazard when used as instructed. Laser safety glasses are included and recommended to be used any time the laser shutter is open. Additionally, an opaque sample cover is provided.

Yes. The Microscoop platform uses a Class 4 laser, which can cause serious harm if a user is directly exposed. However, under normal operating conditions, the laser is fully enclosed, and the system is designed so that user exposure remains below Class 1 safety limits.

To ensure safe use, please strictly follow the provided safety instructions and always wear protective laser safety goggles when operating the system. Safety interlocks and containment features are built in, but user vigilance is essential for maintaining a safe environment.

Microscoop Mint complies with IEC 60825-1:2014 standards without requiring additional shielding. If your institution has specific laser safety requirements, please have your Laser Safety Officer contact your Syncell Field Service Engineer so we can help address your needs appropriately.

The emission indicator light on the laser controller will be solid green. The emission indicator LED on the front of the engine will be illuminated orange, as will the ring LED around the emission button on the Microscoop controller, when the shutter has been opened by pressing the emission button. However, these LEDs will remain on even if the shutter is closed by the automatic safety interlock on the microscope condenser pillar or the microscope light path selector has been set to EYE or L80 mode. Even with the laser operational and the shutter open, the Autoscoop software sets laser output to near-undetectable levels except during photolabeling or calibration protocols. Future versions will indicate emission explicitly.

No, for safety reasons, users should not open the light box under any circumstances. The light box houses components critical to laser safety and system performance, including containment of the Class 4 laser. Opening it may result in exposure to hazardous laser radiation and void the system warranty.

Only authorized Syncell service personnel are permitted to access the interior of the light box for maintenance or support.

The lifespan of a laser depends on its operating time and usage conditions. When operated continuously (24/7), the laser can typically last 3–5 years. Over time, power output may gradually decrease, affecting performance.

To ensure consistent operation, laser output is regularly monitored by a certified technician during preventive maintenance (PM) visits. This helps detect any decline in performance early and ensures timely servicing or replacement if needed.

No. Address the emergency first and shutdown the laser normally when it is safe to do so. In case of power outages, shutdown the laser normally and restart it according to the System Hardware Opoeration Procedures in the Microscoop Mint Hardware User Manual when power has been stably restored.

The Microscoop supports FITC / TRITC / Cy5 and other fluorescent dyes with similar spectra. The DAPI channel can be used for imaging, but is not suitable for use with our Synlight-Rich photolabeling reagent and photolabeling procedure. In addition, transmitted light stains can be imaged in monochrome under red illumination. We cannot provide support for usage of custom dichroic and fiter sets.

The Autoscoop system supports four fluorescent channels: DAPI, FITC, TRITC, and Cy5. These are the only available channels, and the system is currently not customizable to add additional fluorescent channels.

Yes, you may photolabel 2–3 different focal planes along the Z-axis.

Wait time for laser galvo mirrors to stabilize after jumping to a adjacent pixel, ensuring accuracy.

Dwell time refers to wait times that allow different components of the Microscoop Mint system to stabilize before proceeding to the next step. Here are the definitions for each dwell time setting:

Drift-Free Dwell Time: The maximum wait time for the focus system of the device to be stabilized as it moves in between the fields of view (FOVs).

FOV Dwell Time: Wait time after stage movement to ensure stabilization before imaging or photolabeling.

Z Dwell Time: Wait time for Z-axis (vertical) stabilization after adjustment.

Jump Move Dwell Time: Wait time for laser galvo mirrors to stabilize after jumping to a non-adjacent pixel, ensuring accuracy.

Adjacent Move Dwell Time: Wait time for laser galvo mirrors to stabilize after jumping to a adjacent pixel, ensuring accuracy.

Our Microscoop Mint system is sold as a complete package including the Nikon Ti2-E inverted microscope at this time. The reason for this is that the microscope has been modified to make it compatible with our system, including a unique dichroic mirror. Additionally, other software could interfere with the functionality of our system and software.

Yes, but it also increases the complexity of system integration.

The Microscoop includes 10x, 20x, and 40x air objectives.

A 30A receptacle is not required. The Microscoop system is compatible with a standard 15A outlet, ideally connected to a 1500VA Uninterruptible Power Supply (UPS) for protection against power fluctuations.

Regarding data connectivity, the instrument does not require a 10 Gb data line. A 1 Gb Ethernet connection using an RJ45 copper network cable is sufficient for reliable operation and data transfer.

Standard sizes of chambered coverglass, 35 mm coverglass bottom dishes, and 25 x 75 mm / 1 x 3 in slides are compatible with our system. Coverglass should be added to slides after adding photolabeling reagent, and all sample holders should use #1.5 (0.17 mm thick) coverglass.

While not strictly required, it is strongly recommended that the Microscoop system be installed on an optical table to minimize vibrations and ensure optimal imaging stability and performance. Vibrations can negatively impact data quality, especially when operating at the high spatial resolution that Microscoop provides. We can provide recommendations for optical tables which have been validated with our system.

The machine must currently be equipped with a table measuring 90 cm by 120 cm.

No, the Microscoop platform must be integrated with the provided Nikon Ti2-E inverted microscope to ensure optimal performance and data quality. Integration with any other microscope is not supported and will void the warranty. The system has been extensively validated with the Nikon Ti2-E, and using alternative microscopes may result in compatibility issues or suboptimal results.

We do not currently offer automatic sample loading or exchange capabilities.

The pattern generation tools within the Autoscoop software are designed to be sufficient for most applications. For specialized needs, AI-assisted pattern generation can be developed; however, this may require significant time for training and module creation.

For advanced customization requests, please contact support@syncell.com.

There are no universal standard parameters for image pattern generation, as it is highly case-dependent. Optimal settings will vary based on sample type, staining quality, and experimental goals.

We recommend optimizing imaging parametersbased on your specific application. For guidance, please consult your Field Application Scientist (FAS) or refer to the user manual’s imaging section.

What can be done with image processing?
Image processing capabilities include:

• Brightness and contrast adjustments
• Thresholding for defining ROIs
• Morphological operations (e.g., dilation, erosion)
• Filters and transformations (e.g., Gaussian blur, rotation)
• Binarization image processing
• Mathematical operations for combining or analyzing image data

Each marker can be individually masked, and the resulting masks can then be combined using mathematical algorithms to visualize colocalization or mutual exclusivity of the markers. This allows for precise ROI selection based on complex staining patterns.

We do not offer this feature at this time.

AI training cannot be performed directly within the Autoscoop software. We utilize TensorFlow with Python and GPU hardware for our AI model training, but other platforms and AI programming languages are also compatible. The one requirement is that the output file must be in .pb format. For detailed instructions on integrating AI models into Autoscoop, please refer to the software manual.

To start with, you will need hundred of pictures for target identification to train a specific AI model. For detailed instructions on integrating AI models into Autoscoop, please refer to the software manual.

Autoscoop allows users to import their own AI models for inference, subject to certain rules and restrictions. For detailed instructions on integrating AI models into Autoscoop, please refer to the software manual.

No. The Microscoop Mint system does not include a mass spectrometer. Mass spectrometry is performed downstream and is separate from the Microscoop Mint platform.

End users are responsible for sourcing and operating their own mass spectrometry system for protein identification and analysis. Our team can provide guidance on compatibility and best practices for integrating Microscoop Mint outputs with your existing MS workflow.

Please contact your local Territory Sales Executive or info@syncell.com for further information.

System stability is defined by the precision and consistency of photolabeling across repeated runs. To maintain this stability, we recommend performing calibration once per month, or as needed if targeting precision appears compromised.

Calibration files are generated using our Autoscoop Calibration software. For step-by-step instructions, please refer to the user manual.