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10x Genomics Visium CytAssist User Manual

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User Guide | CG000542 | Rev F
Visium CytAssist
with Readiness Test
For use with:
Visium CytAssist & Accessory Kit, 12-Month Warranty, PN-1000441
Visium CytAssist Instrument Accessory Kit, PN-1000433
Visium CytAssist & Accessory Kit, 24-Month Warranty, PN-1000442
Visium CytAssist Instrument Accessory Kit, PN-1000433
10xgenomics.com

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  • Page 1 User Guide | CG000542 | Rev F Visium CytAssist with Readiness Test For use with: Visium CytAssist & Accessory Kit, 12-Month Warranty, PN-1000441 Visium CytAssist Instrument Accessory Kit, PN-1000433 Visium CytAssist & Accessory Kit, 24-Month Warranty, PN-1000442 Visium CytAssist Instrument Accessory Kit, PN-1000433...
  • Page 2 © 2024 10x Genomics, Inc. (10x Genomics). All rights reserved. Duplication and/or reproduction of all or any portion of this document without the express written consent of 10x Genomics, is strictly forbidden. Nothing contained herein shall constitute any warranty, express or implied, as to the performance of any products described herein.
  • Page 3 CG000542 | Rev F User Guide | Visium CytAssist Instrument | Document Revision Summary Document Document Number CG000542 | Rev F Revision Summary Title Visium CytAssist Instrument User Guide with Readiness Test Revision Rev E to Rev F Revision Date...

  • Page 4: Table Of Contents

    CG000542 | Rev F User Guide | Visium CytAssist Instrument | Table of Contents Table of Introduction Introduction Contents Product Identification Label Product Specifications Safety & Compliance Information Safety Regulatory System Components System Components Accessory Kits Tips & Best Practices...

  • Page 5: Introduction

    Introduction Introduction Product Identification Product Specifications...
  • Page 6 CG000542 | Rev F User Guide | CytAssist Instrument | Introduction The Visium CytAssist is a compact, bench top instrument that automates Introduction the transfer of analyte-derived molecules from standard glass slides to Visium slides, enabling spatial profiling insights from an expanded range of samples.
  • Page 7 CG000542 | Rev F User Guide | CytAssist Instrument | Introduction Visium CytAssist LBL-00042-01 Regulatory Label Image of label for reference only Product Identification Label ● Must be legible from 18 inches ● Electrical shock warning required, but included. M...

  • Page 8: Safety & Compliance Information

    Safety & Compliance Information Safety Regulatory...

  • Page 9: Safety

    Pinch risk: Ensure no obstructions or fingers present near closing lid. Warning: Avoid using the Visium CytAssist in a manner not specified by 10x Genomics. The Visium CytAssist has been designed to protect the user. If used improperly, the intended user protections can be impaired.

  • Page 10: Regulatory

    CG000542 | Rev F User Guide | CytAssist Instrument | Safety & Compliance Information The Visium CytAssist has been designed, tested, and certified to be in Regulatory compliance with the following standards: Certification Standards TUV Certification only for Visium CytAssist UL 61010-1:2012 and CAN/CSA C22.2 No.

  • Page 11: System Components

    System Components System Components Accessory Kits...
  • Page 12 CG000542 | Rev F User Guide | CytAssist Instrument | System Components System Components Exterior Handle Base USB Port Touchscreen Corner Bumper Adjustable Feet Interior Tissue Slide Clips Slide Alignment Guides Tissue Alignment Windows Tissue Slide Stage Visium Slide Lock Visium Slide Stage Visium Alignment Windows Back...

  • Page 13: Accessory Kits

    3000603 PN-1000433 (IEC 60320 C-14, with C-13 Detachable Adapters) USB, 8 GB 3000664 The Visium CytAssist instrument is compatible with VFAT, exFAT, and FAT32 formatted USBs. Visium CytAssist Quick Reference Cards – for CG000548 Accessory Kit Instruction Visium CytAssist Training Kit...

  • Page 14: Icons

    Tips & Best Practices Icons Check Tissue Placement on Slide Tissue Slide Placement on Tissue Slide Stage Visium Slide Placement on Visium Slide Stage 10x Genomics Cloud...
  • Page 15 While slides are specified as being a certain size by the manufacturer, manufacturing tolerances may lead to dimensions that are too small or large to be compatible with Visium CytAssist. Ensure that slides used on the instrument are within supported tolerances. Supported slide widths may vary from assay to assay.
  • Page 16 CG000542 | Rev F User Guide | CytAssist Instrument | Tips & Best Practices Tissue Slide Position Tissue Slide on the Tissue Slide Stage Placement on Use this section to determine if the tissue section is located in an area that results in Tissue Slide Stage successful analyte-derived molecule transfer and CytAssist-mediated imaging.
  • Page 17 CG000542 | Rev F User Guide | CytAssist Instrument | Tips & Best Practices b. Align tissue to the center of the alignment guides for 6.5 mm Tissue Slide (rectangles) or 11 mm (lines) Capture Areas on either the left or right Placement on side of the stage.
  • Page 18 CG000542 | Rev F User Guide | CytAssist Instrument | Tips & Best Practices c. If necessary, rotate the slide 180° as shown below to better place Tissue Slide off-center tissues closer to the center line. Slides should not cross/ Placement on overlap the center line.
  • Page 19 Capture Area during a successful run. Tissue outside of these guides may be captured (area in yellow in the images), but it is not ensured. 10x Genomics recommends placing high-priority areas of the tissue within the alignment guides.
  • Page 20 CG000542 | Rev F User Guide | CytAssist Instrument | Tips & Best Practices Tissue Slide Load Tissue Slides onto the Tissue Slide Stage Placement on a. Press down on the wide end of clip to lift and pivot the narrow end of Tissue Slide Stage the clip.
  • Page 21 The Visium Slide Stage holds one of the following at a time: Visium Slide Stage • Visium Slide, 6.5 mm or 11 mm • Visium CytAssist Training Slide • Visium CytAssist Calibration Slide Visium CytAssist Training Slide Visium CytAssist Calibration Slide TOC | 10xgenomics.com...
  • Page 22 CG000542 | Rev F User Guide | CytAssist Instrument | Tips & Best Practices Visium Slide Load Visium Slides onto the Visium Slide Stage Placement on Visium Slide Stage Open Visium Slide Lock Load Visium Slide Stage C, D contd. Close Lock slide in image is representative a.

  • Page 23: Barcode Scanner

    Each Visium CytAssist instrument is required to be registered to the 10x Genomics Cloud during the First Time Use (FTU) set up process. Users may register multiple instruments to their accounts, and each instrument can optionally be registered to multiple 10x Genomics accounts.

  • Page 24: System Operation

    System Operation Step 1: Installation Step 2: First-Time Use Step 3: Readiness Test Step 4: Main Operation...

  • Page 25: Step 1: Installation

    • Provides a minimum of 4” (10 cm) clearance around unit to allow free air circulation. Warning: Avoid using the Visium CytAssist in a manner not specified by 10x Genomics. The Visium CytAssist has been designed to protect the user. If used improperly, the intended user protections can be impaired. General Power Safety Grounding is required to prevent electric shock.
  • Page 26 DO NOT POWER ON until ready for First-Time Use setup Accessory Kit Visium CytAssist Lift instrument from sides Retain packaging for future transportation a. Open box according to box label “this side up.” Carefully cut or remove the tape on the top of the box and open the top flaps. Ensure that cut is not too deep as it may damage the Instrument Accessory Kit box.
  • Page 27 Within the Instrument Accessory Kit box, locate the universal power cord and plug adapters. Attach the correct country adapter to the universal adapter. h. Plug the Visium CytAssist into a properly grounded outlet of proper voltage (see Product Specifications). If using an Ethernet cable (not provided) to connect to the network, connect cable directly to the instrument.

  • Page 28: Step 2: First-Time Use

    User Guide | CytAssist Instrument | System Operation Step 2: The instrument will walk through a first-time setup protocol. Setup requires the following: First-Time Use • 10x Genomics Account Onscreen instruction will guide account setup. Alternatively, visit cloud. 1 0xgenomics. com/instruments to create an account beforehand.
  • Page 29 QR code or contd. an internet-connected device. Create or log in to a 10x Genomics account. Enter the serial number + instrument ID found on the instrument screen. Read and accept the legal agreement. e. Update the firmware.
  • Page 30 CG000542 | Rev F User Guide | CytAssist Instrument | System Operation Step 2: If either setting is turned off, the following warnings will appear: First-Time Use contd. See the Firmware Update Procedure section for more details. f. Proceed to Leveling Mode. The level status of the instrument should only be verified or adjusted in Leveling Mode during First Time Use setup or after relocation of the instrument.
  • Page 31 CG000542 | Rev F User Guide | CytAssist Instrument | System Operation Step 2: Once the instrument is leveled correctly, check the back of the instrument to confirm that the center back non-adjustable foot is resting on the table top while the two First-Time Use non-adjustable corner back bumpers are not touching the table top.

  • Page 32: Step 3: Readiness Test

    CG000542 | Rev F User Guide | CytAssist Instrument | System Operation The Readiness Test calibrates the imaging parameters and verifies that Step 3: all systems are working optimally. No reagents are used (the Readiness Readiness Test Test is the only dry run the instrument utilizes). Wear gloves when performing the Readiness Test.
  • Page 33 Store the blank slides and the calibration slide away from sunlight and extreme temperature, in the original packaging bag. Retain for future use. The Visium Slide Stage of the Visium CytAssist has been designed to catch and contain drips and a small volume of liquid spills. If lab safety guidelines permit, a soft lab towel may be used to clean these areas with a mixture of mild detergent and distilled water.

  • Page 34: Step 4: Main Operation

    This section is meant as a general overview of instrument operation and its placement within the steps of the Visium CytAssist-enabled assay. When performing the protocol, follow the steps listed in the appropriate assay kit user guide and use this section only as a reference.
  • Page 35 CG000542 | Rev F User Guide | CytAssist Instrument | System Operation • Any change from default temperature and time (37 °C for 30 min) Step 4: See the appropriate assay kit user guide for further guidance. Main Operation contd. •...
  • Page 36 CG000542 | Rev F User Guide | CytAssist Instrument | System Operation g. Press the play button to start the run. Step 4: Main Operation • Midrun progress bar will show the time remaining in the run. contd. • Yellow before a run begins indicates a user-recoverable error (see Troubleshooting).
  • Page 37 View and verify the tissue samples were accurately aligned within the Visium CytAssist Slide fiducial frame. See the relevant assay kit user guide for further guidance. The instrument requires a ~20 min cool down between runs. The warning icon will disappear once instrument is cool.

  • Page 38: Menu Options

    Menu Options Menu Options Firmware Update Procedure Network Shared Folder...
  • Page 39 • If the instrument is not performing a run, the idle time data can also be exported by navigating to Menu > System > Help and pressing “Send System Logs to Technical Support”. Share a Support Package with 10x Genomics Technical Support for troubleshooting purposes. TOC |...
  • Page 40 Export Export detailed run information in CSV format and Visium CytAssist slide images in TIFF format. Data export ranges in size from 10s to 100s of MB, depending on how many runs are selected. If Diagnostics is turned on, instrument and system data are automatically exported or uploaded after a run for use in troubleshooting.
  • Page 41 To review service data with 10x Genomics Technical Support: • Email support@10xgenomics.com with the instrument serial number and any applicable error codes. • Upload pertinent logs directly to 10x Genomics Cloud with a network connection (preferred). Support personnel can guide the user through these steps. TOC | 10xgenomics.com...
  • Page 42 10x Cloud when connected to the internet. To maximize internet stability and enable the 10x Genomics support team to quickly respond to issues, Diagnostics is enabled after software updates.
  • Page 43 Network & Security Menu Options contd. Allow outbound TCP port 443 for 10x Genomics Cloud access. As an additional (optional) level of security, the instrument can be put on its own network VLAN with Internet-only access. For connectivity to work correctly, the network should allow unrestricted outbound access to the following hosts: •...

  • Page 44: Firmware Update Procedure

    Tips & Best Practices to use a scanner instead of entering manually. b. Locate two blank slides and the Visium CytAssist Calibration Slide in the Instrument Accessory Kit. Ensure slides are clean. c. Follow onscreen instruction and see...
  • Page 45 Retain for future use. contd. g. The Visium Slide Stage of the Visium CytAssist has been designed to catch and contain drips and a small volume of liquid spills. If lab safety guidelines permit, a soft lab towel may be used to clean these areas with a mixture of mild detergent and distilled water.

  • Page 46: Network Shared Folder

    NSF function. To use Visium CytAssist’s NSF functionality, the following items are required: • The Visium CytAssist and file storage location are connected to the same network • A storage location with sharing enabled •...
  • Page 47 CG000542 | Rev F User Guide | CytAssist Instrument | Menu Overview Network Shared Windows 10 Destination Storage Location Configuration: Folder a. Right-click on the folder that will receive data from the instrument. contd. b. Select “Properties”. c. In the Properties window, select the “Sharing” tab and click on “Advanced Sharing”...
  • Page 48 CG000542 | Rev F User Guide | CytAssist Instrument | Menu Overview Network Shared e. In the Advanced Sharing window, select “Share this folder” and click on “Permissions. Folder contd. f. Add or remove users that should have access to the folder. Alternatively, add “Everyone”...
  • Page 49 CG000542 | Rev F User Guide | CytAssist Instrument | Menu Overview Network Shared MacOS Destination Storage Location Configuration: Folder a. Navigate to Menu > System Preferences > Sharing. contd. b. Turn on File Sharing. c. Click on “Options”. d. Select “Share files and folders using SMB” and the checkbox next to the account of interest.
  • Page 50 CG000542 | Rev F User Guide | CytAssist Instrument | Menu Overview Network Shared f. Click on the “+” below the Shared Folder list and select the folder that will receive data. Folder contd. g. Change the user permissions to “Read & Write” h.
  • Page 51 CG000542 | Rev F User Guide | CytAssist Instrument | Menu Overview Network Shared • Enter the password for the Username that appears. Click “Modify Configuration”. Folder contd. d. In the Directory Utiliy window, select “Active Directory”. e. The “Computer ID” contains the domain name. Consult an IT professional for naming format, as some computer IDs may contain more than one domain name.
  • Page 52 User Guide | CytAssist Instrument | Menu Overview Network Shared Requirement 3 Folder Appropriately Configured Visium CytAssist contd. The instrument currently supports connection to only one network mount. Follow the instructions below to configure the instrument. Set Up New Share: a.
  • Page 53 CG000542 | Rev F User Guide | CytAssist Instrument | Menu Overview Network Shared To determine IP address on a computer running Windows 10: Folder i. Open the Start menu and select “Settings”. contd. ii. Select “Network & Internet” iii. Determine if you are connected to the internet via ethernet or WiFI •...
  • Page 54 CG000542 | Rev F User Guide | CytAssist Instrument | Menu Overview Network Shared Edit Network Shared Folder Configuration Folder Only one folder may be set up on the instrument at a time. If there is a contd. need to change the designated folder, the configurations may be edited. a.
  • Page 55 CG000542 | Rev F User Guide | CytAssist Instrument | Menu Overview Network Shared Delete Network Shared Folder Configuration Folder a. Onscreen, navigate through the menu to Connectivity > Network contd. Shared Folder. b. If a shared folder is configured, it should appear as a button with “Connected”, as shown above.

  • Page 56: Network Shared Folder Troubleshooting

    Due to the diversity of networking setups, it is not possible to cover all operating systems and network configurations in this User Guide. Please contact an IT professional or network professional for assistance when setting up the Visium CytAssist instrument or troubleshooting network issues. TOC |...

  • Page 57: Maintenance

    Maintenance System Maintenance Moving & Shipping the Instrument...
  • Page 58 Exterior The exterior of the Visium CytAssist should always be kept clean and free of dust and debris that may affect its function and/or cooling efficiency. Generally, the exterior finish can be wiped down using a mixture of mild detergent and distilled water applied to a slightly dampened lab towel.
  • Page 59 10x Genomics service personnel. Environmental Requirements It is the design intent of the Visium CytAssist that it be used in a typical indoor laboratory environment. The instrument’s operating temperature is 18–28°C (64–82°F), humidity 80% Max (Non-Condensing) (see Product Specifications).
  • Page 60 CG000542 | Rev F User Guide | CytAssist Instrument | Maintenance Step 1: Shipping Mode a. Launch Shipping Mode (for safe instrument transportation). Menu Options > System > Alternate Modes > Shipping Mode b. Once Shipping Mode is active, follow onscreen instruction to power down the instrument.
  • Page 61 CG000542 | Rev F User Guide | CytAssist Instrument | System Operation e. Move the four Tissue Clips to their innermost positions and tape down. Moving & Shipping Ensure that the tape is placed over all four Tissue Slide Clips along the Instrument with the overlap with all four corners of the protective film.
  • Page 62 Unless directed otherwise, do not include any parts of the Accessory Kit (which includes the power cord). Coordinate with 10x Genomics Support for further return instructions (some required paperwork will be placed in the box). Place the required documents into the box.

  • Page 63: Troubleshooting

    Troubleshooting Troubleshooting Error Screens...
  • Page 64 CG000542 | Rev F User Guide | CytAssist Instrument | Troubleshooting Troubleshooting Issue • Visium slide loaded incorrectly, resulting in slide breakage. Ensure that the slide sits within the grooves of the Visium Slide Stage, with the label facing toward the right. The images below show the Visium Slide loaded correctly and incorrectly.
  • Page 65 Debris on the Slide Stage Debris The images collected with Visium CytAssist are used for tissue-to-capture area alignment and image registration. The optical paths of all CytAssist instruments are inspected by 10x Genomics for the presence of dust/debris that may interfere with image collection or the image registration process.
  • Page 66 • Instrument is not level: To ensure the successful transfer of analyte- derived molecules to the Visium slide, it is important to keep the Visium CytAssist within an acceptable level range as compared to pre-calibrated values for the system. During the Leveling Mode process, the instrument uses built-in sensors to determine the system’s...
  • Page 67 CG000542 | Rev F User Guide | CytAssist Instrument | Troubleshooting • Instrument is hot: If the Visium CytAssist overheats during an Troubleshooting experiment run, the run will fail. A warning message will appear contd. instructing users to carefully remove slides and contact support@10xgenomics.com...
  • Page 68 CG000542 | Rev F User Guide | CytAssist Instrument | Troubleshooting The Visium Slide Stage of the Visium CytAssist has been designed Troubleshooting to catch and contain drips and a small volume of liquid spills. If contd. lab safety guidelines permit, a soft lab towel may be used to clean these areas with a mixture of mild detergent and distilled water.
  • Page 69 Support will request log files for troubleshooting. Upload pertinent logs to 10x Genomics by navigating to the Logs menu option on screen. (See Run Data section). There are two types of errors: Critical Errors –...

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