Aplo Scope

The Aplo Scope User Manual is a guide to the operations and maintenance of the device. This guide should be used as a reference for everyday use of the microscope.

This user manual will give guidance on the installation, operation and general maintenance.

The Aplo Scope is designed to be completely safe during proper use, but if equipment is used in a manner not specified by ONI, the protection provided by the equipment may be impaired. Incorrect use may result in personal injury or property damage. Please read these safety precautions and keep this manual for reference.

Disassembling the Microscope Module or Light Engine may result in malfunction, damage to the product, or injury. If you think disassembly may be necessary, please contact an ONI representative. Disassembly of the instrument from unauthorized personnel will result in a void warranty. Do not try to disconnect the Light Engine from the Microscope Module as both are attached to each other through the light link.

The Aplo Scope is a Class 1 laser product. Due to its inherent closed-form design, the interlock does not allow the lid to be opened without the lasers switching off. Do not attempt to modify the interlock in any way and attempt at doing so could expose users and people in the general area to class 4 lasers and may result in serious injury.

Avoid bringing water into contact with the product. If water is spilled on the Light Engine, turn off the power switches and remove the power cord. Wipe the liquid from the product. If water enters the Light Engine or Aplo Scope body at any point, please contact an ONI representative.

Do not store any object on top of any part of the Aplo Scope.

While the Aplo Scope and associated packaging is designed for portability, the complete Aplo Scope system weighs approximately 55 kg. Handle with care. Two persons are needed to lift the system.

Do not place weight heavier than 200 g on the stage. Sample chambers / coverslips must be less than 97 mm long, 35 mm wide and 13 mm in height to avoid contact with the side of the lid, which might result in excess force on the stage and/or objective.

The Aplo Scope is not designed to hold corrosive or radioactive substances. All legal regulations and local safety recommendations should be observed when handling hazardous substances.

The Aplo Scope is a high-performance super-resolution and live-cell imaging platform designed for advanced biological research. It enables precise visualization and quantification of single-molecule and subcellular structures across a range of applications.

• Super-Resolution Microscopy (SMLM): Single-molecule localization imaging for high-precision spatial analysis.
• Live-Cell Imaging: Dynamic observation of cellular processes with minimal phototoxicity.
• Multicolor Imaging: Simultaneous detection of multiple targets for colocalization studies.
• Quantitative Imaging: Reliable measurement of molecular interactions, densities, and distributions.
• Automated Workflows: Streamlined acquisition with minimal user intervention.

The Aplo platform revolutionizes the world of super-resolution microscopy through the combination of application specific kits and chemistry with fully automated fluidic control via Aplo Flow, class leading SMLM hardware with Aplo Scope, and innovative, user centric, and automated CODI software capable of delivering true end-to-end sample to answer experimentation of both fixed and dynamic molecular interactions.

• Stable acquisition on any standard lab bench without an isolation table or dark room
• Large, homogenous 110 µm by 110 µm field of view
• Superb resolution of ≤15 nm
• Laser light engine with four discrete laser lines capable of consistent illumination from 0.01 kW/cm² to 3.325 kW/cm²
• Ten (10) expertly chosen emission filters in a turret wheel designed for rapid switching
• Advanced piezo stage driven in X, Y, and Z with 1 nm steps
• sCMOS Teledyne Prime BSI Express, with high quantum efficiency of 95% and high full well capacity
• Frame acquisition rate as high as 43 fps
• Class 1 laser safe device
• Class-leading minimal footprint of less than 95 cm² for both the Aplo Scope and gen2 light engine

• Width: 220 mm
• Depth: 420.5 mm
• Height (lid closed): 242 mm incl. feet
• Height (lid open): 406 mm incl. feet

• Width: 215 mm
• Depth: 420 mm
• Height: 457 mm incl. feet

• Input Voltage: 100 / 240 Volts AC
• Input Frequency: 50/60 Hertz
• Max. Power: 720W
• Max. Input Current: 7.2A @ 100VAC input

• Temperature: 18 – 30° Celsius or 64 – 86° Fahrenheit
• Humidity: 20% – 60% Relative Humidity

The Aplo Scope contains a Microscope Module and Light Engine which are permanently connected by the Light Link cord housing optical fibers, cooling, and electronic cables.

It is supplied with a PC to control the instrument. The cables include a USB-C cable to connect the Light Engine and the PC, the power cord for the Light Engine and the power supply for the PC. 

Since the Light Link cord houses the optical fibers and the electronics cables, the Light Link should not be bent tighter than a radius of 75 mm. Due to heat dissipation, we also recommend 15 cm on each side of the computer free.

The Aplo Scope can be used on almost any platform, including a standard laboratory bench or a solid desk. It is critical that the following installation conditions are fulfilled:

• The Light Engine can only be used in the orientation shown above.
• Place the Light Engine on a clean, dust-free, and flat surface. Do not use it on a carpet.
• Keep objects and obstructions at least 15 cm from the air vents on the back of the Aplo Scope and Light Engine.
• Position the instrument in a manner that allows easy and convenient access.
• Avoid locations that are directly exposed to direct sunlight.
• Avoid installation locations which suffer from severe temperature fluctuations, particularly directly in or near the path of air handler vents.
• Avoid locations close to water sources (sink etc.).

Fire Hazard – Improper fuses or high-voltage supply can damage the instrument wiring system and cause a fire. Before turning on the instrument, verify that the fuses are properly installed and that the instrument voltage matches the power supply in the laboratory.

Electrical Hazard – Grounding circuit continuity is vital for the safe operation of equipment. Never operate equipment with the grounding conductor disconnected. Use properly configured and approved line cords for the voltage supply in your facility.

The Aplo Scope is shipped to customers with up to three power connectors. These connectors require standard 15A wall receptacles with proper grounding. Do not replace any mains supply cords with inadequately rated cords as this could become hazardous. Do not use extension cords.

The Aplo Scope can be used in any country with mains voltage from 100V to 240V, 50 to 60hz. The system is equipped with a universal power supply. In areas where the supplied power is subject to voltage fluctuations exceeding ±10% of the nominal value, a power line regulator may be required. High or low voltages can adversely affect the electronic components of the instrument.

The instrument will arrive in 1 box labelled ONI. The box is large and requires two people to handle. The box has been designed with lifting holes at each end. 

The instrument will be accompanied by a desktop PC and monitor in separate boxes.

The scope and all the associated accessories will be packed in the boxes and will include the following items:

• Microscope
• Light Engine
• Desktop PC
• Light engine power cord
• Lens tissue
• Bead slide
• Magnets

The installation and the setup of Aplo Scope will be completed by a trained ONI technician.

There are two layers to the packaging. The top ‘Accessory Layer” that holds the accessories + cables and the bottom layer containing the system itself.

This layer contains items which should be unpacked and placed aside for use later during setup.

Once the top accessory layer has been removed, you will be able to access the system below to complete installation.

The installation of the Aplo Scope should take approximately 2.5 hours. Removing the system from the packaging and setting up on the bench top will take 15-30 minutes. After the initial set up, a customer success engineer will run tests to verify that the system is working properly. These verification tests will take 1-2 hours to complete.

After the system has arrived at the facilities, the boxes should be moved to the site of the unpacking. If the installation is being done remotely, we recommend that 2 people from the lab are present to remove the system from the packaging. The following are the steps that should be followed for unpacking and installation of the scope:

1. 1. Cut the tape to gain access to the box, care should be taken when performing this action.
   2. Remove the foam around the Light Link. As this is done, verify the connection points to the Light Engine and scope are visible. The image below shows the Aplo Scope with the excess foam removed.
   3. Two people should carefully place the Light Engine and the Aplo Scope on the bench top. Continue to ensure there is not a strained or tight bend on the Light Link. Ensure the light engine is on the left-hand side of the Aplo Scope.
   4. Remove any remaining foam to reveal the other components located in the box. These components include:
      • Light Engine power cable
      • Bead slide
      • Lens cleaning tissue
      • Magnets
      • Torx 6 screwdriver
      • Sample stage chip holder
      • Mouse and keyboard
      • Mousemat
   5. Connect the desktop PC power supply into the wall outlet. 
   6. Connect the Light Engine power cord to the back of the Light Engine and the other end of the power cord to the wall outlet.
   7. The next portion of these instructions will involve handling the objective lens and sample stage. If not done already, please put on gloves and proceed with caution. 
   8. Lift up the front lid to check the sample stage.
   9. Begin the process of removing the stage stabiliser (image below).

10. Lift the internal hollow part (1) of the stage stabilizer carefully to remove it (image below).

11. Using the provided TX6 screwdriver, remove the 2 screws holding the sample plate to the stages, taking care not to drop them into the system.
12. Once the sample plate is fully loose, lift it out of the system and place to the side with the screws.
13. Remove the lower part (2) of the stage stabiliser from the system.
14. Both parts of the stage stabiliser can be stored to one side as they will be used in the case that the system needs to be transported.
15. Refit the sample plate using the screws that were previously removed. These screws should be tightened so that they are finger tight, without applying excessive torque.
16. Close the front lid.
17. Turn on the Light Engine by toggling the switch to the “I” position on the back.
18. Turn on the desktop PC. When prompted to log in, use the Windows credentials provided for the system during the installation process.

The front of the Aplo Scope system has a LED indicator that will illuminate solid blue to indicate the machine is powered on.

See the ONI Aplo Scope Control User Guide for detailed instructions and information on operation of the Aplo Scope software and interface.

If used properly, the Aplo Scope should require minimal maintenance. However, an annual preventative maintenance is recommended for all systems:

The objective lens will need to be cleaned, when there is no sample in the microscope and/or if the system is not in use for a long period of time. Take extra care when cleaning the objective lens and always use lens cleaning paper to remove larger amounts of oil from the objective. To clean the traces of oil from the objective lens, use lens cleaning paper dipped in absolute ethanol.

If you spill some liquid on the system or need to clean the system for any reason, switch off the system and use a soft cotton cloth with 70% ethanol to wipe the outside of the Aplo Scope.

Possible cause
-The power on the Light Engine is off (‘O’ position)
-The Light Engine is not plugged in

Solution
Check all the connections and the power switch

Possible cause
The interlock is engaged

Solution
Check the lid is fully closed before imaging

Possible cause
-Incorrect TIRF or HILO angle
-Phenol-red media used for cell culture

Solution
-Adjust the TIRF angle using the ONI software
-Use phenol-red free media for cell culture

Possible cause
-The slide is not flat on the stage
-The sample is not flat

Solution
-Ensure the slide is directly in contact with the stage on both sides and not resting on glue, nail polish, or the objective lens.
-Find the most suitable position to image the sample.

Possible cause
-Objective or sample is dirty
-There are bubbles in the immersion oil

Solution
Try removing bubbles by gently raising the sample without losing contact with the immersion oil several times. Clean the objective with lens paper and absolute alcohol

Possible cause
-Unsuitable or thick cover glass
-No oil on the objective

Solution
Apply oil on the objective and use No. 1.5 coverslips (0.17 mm thickness).

Possible cause
-Sample holder is too high
-Something is on the course of the lid

Solution

Check that your sample is not more than 13 mm in height.
Check for any object that can obstruct the lid.

• ONI resource library
• Aplo Scope Webinar
• Service Desk

At ONI, supporting our users is a priority. For the latest services and support information for all locations, go to https://desk.zoho.eu/portal/onidesk/en/home or email us at support@oni.bio. All new equipment purchases will be covered by a one year warranty.

• For general inquiries and questions please follow this link
• To contact a sales representative please follow this link