Page 1 September 2024 ® QIAcuity User Manual 911000, 911020, 911040, 911050 QIAGEN GmbH, QIAGEN Strasse 1, 40724 Hilden, GERMANY Sample to Insight...
Page 2: Table Of Contents
Table of Contents 1. Introduction 1.1. About this user manual 1.2. General information 1.3. Intended use of the QIAcuity 1.4. Requirements for QIAcuity users 2. Safety Information 2.1. Proper use 2.2. Electrical safety 2.3. Environment 2.4. Biological safety 2.5. Chemicals 2.6.
Page 3 8.7. Regular maintenance procedure for QIAcuity Software Suite 9. Troubleshooting 9.1. General information 9.2. Contacting QIAGEN Technical Services 9.3. Performing a self-check on the QIAcuity instrument 9.4. Creating a support package with the QIAcuity instrument software 9.5. Software support package 9.6.
Page 4 Appendix D – Sicherheitshinweise Sachgemäße Handhabung Schutz vor Stromschlag Umgebung Biologische Sicherheit Chemikalien Wartungssicherheit Strahlensicherheit Symbole auf dem QIAcuity Appendix E – User Management Permissions Document Revision History QIAcuity User Manual | 09/2024...
Page 5: Introduction
1. Introduction Thank you for choosing QIAcuity. We are confident it will become an integral part of your laboratory. Before using QIAcuity, it is essential that you read this user manual carefully and pay attention to the safety information. The instructions and safety information in the user manual must be followed to ensure safe operation of the instrument and to maintain the instrument in a safe condition.
Page 6: General Information
QIAGEN customers are a major source of information regarding advanced or specialized uses of our products. This information is helpful to other scientists as well as to the researchers at QIAGEN. We therefore encourage you to contact us if you have any suggestions about product performance or new applications and techniques.
Page 7: Requirements For Qiacuity Users
If QIAcuity is used with products other than QIAGEN kits or QIAGEN assays designed for dPCR, it is the user’s responsibility to validate the performance of such product combinations for any particular application. The QIAcuity system is intended for use by professional users trained in molecular biological techniques and the operation of the QIAcuity system.
Page 8: Safety Information
Servicing of the QIAcuity must only be performed by a QIAGEN field service specialist. Perform the maintenance as described in the “Maintenance Procedures” section. QIAGEN charges for repairs that are required due to incorrect maintenance.
Page 9: Electrical Safety
WARNING Risk of explosion The QIAcuity is intended for use with reagents and substances supplied with QIAGEN kits or others that are outlined in respective Information for Use. Use of other reagents and substances may lead to fire or explosion.
Page 10: Environment
If liquid has spilled inside the instrument, power OFF the instrument, disconnect it from the power outlet, and contact QIAGEN Technical Services. If the instrument becomes electrically unsafe, prevent other personnel from operating it, and contact QIAGEN Technical Services. The instrument may be electrically unsafe when: It or the line power cord appears to be damaged.
Page 11: Biological Safety
2.4. Biological safety Specimens and reagents containing materials from humans should be treated as potentially infectious. Use safe laboratory procedures as outlined in publications such as Biosafety in Microbiological and Biomedical Laboratories, HHS (www.cdc.gov/labs/BMBL.html). 2.4.1. Samples Samples may contain infectious agents. You should be aware of the health hazard presented by such agents and should use, store, and dispose of such samples according to the required safety regulations.
Page 12: Maintenance Safety
2.6. Maintenance safety WARNING/ Risk of personal injury and material damage CAUTION Only perform maintenance that is specifically described in this user manual. WARNING Risk of fire Do not allow cleaning fluid or decontamination agents to come into contact with the electrical parts of the QIAcuity.
Page 13: Symbols On The Qiacuity
2.8. Symbols on the QIAcuity Symbol Location Description Type plate on the back of the instrument CE mark for European Conformity Type plate on the back of the instrument UKCA mark for UK Conformity Type plate at the back of the instrument CSA listing mark for Canada and the USA Type plate on the back of the instrument RCM mark for Australia and New Zealand...
Page 14: General Description
3. General Description After manually loading and sealing the QIAcuity Nanoplate, the QIAcuity performs a fully automated processing of the QIAcuity Nanoplates, including all necessary steps of plate priming, sealing of partitions, thermocycling, and image analysis. Depending on the plate type, up to 8, 24, or 96 samples per plate can be analyzed. For high sensitivity applications, the QIAcuity Nanoplate 26K 8- or 24-well is available.
Page 15 Principle of priming and rolling to allow partitioning of the wells. Thermocycling: The second step and module is a high-accuracy plate thermocycler that performs the polymerase chain reaction. The cycling profile can be set in the QIAcuity Software Suite or the instrument software. For more details on the thermal cycler specification, see the “Technical Specifications”...
Page 16: External Features Of Qiacuity
3.2. External features of QIAcuity 3.2.1. Touchscreen The QIAcuity is controlled using a swivel-mounted touchscreen. To adjust the angle of the touchscreen, pull gently at the bottom edge. The touchscreen enables the user to see an overview of all plate slots and the corresponding process steps and remaining times.
Page 17 USB port from the QIAcuity to the USB stick. The USB ports can also be used to plug in an external bar code reader or a keyboard. Important: We recommend using QIAGEN USB sticks only to ensure full compatibility. If QIAGEN USB stick is not available, use a FAT32 or exFAT-formatted USB stick.
Page 18: Thermal Cycler
Cooling air outlet Cooling air outlets are located at the rear side of the QIAcuity and allow cooling of the internal components of the QIAcuity. CAUTION Risk of overheating To ensure proper ventilation, maintain a minimum clearance of 10 cm at the sides and rear of the QIAcuity. Slits and openings that ensure the ventilation of the QIAcuity must not be covered.
Page 19: Optical System
3.4. Optical system The optical system of the QIAcuity is a camera- based fluorescence microscopy system. The excitation source for the fluorescence dyes is a high-power white LED. This source in combination with a specific excitation filter is used to illuminate a whole well at a time.
Page 20: Installation Procedures
This section provides instructions on unpacking, packing, and installing the QIAcuity. The installation procedure of the product is recommended to be carried out by a certified QIAGEN field service specialist. A person who is familiar with the laboratory and computer equipment should be present during the installation.
Page 21: Power Requirements
4.0.2. Power requirements The QIAcuity operates at 100–240 V AC, 50/60 Hz, 1500 VA (max.) Ensure that the voltage rating of the QIAcuity is compatible with the AC voltage available at the installation site. Main supply voltage fluctuations should not exceed 10% of nominal supply voltages. WARNING Damage to electronics Before powering ON the instrument, make sure that the correct supply voltage is used.
Page 22: Unpacking The Qiacuity
7. Read the packing list to check that you have received all items. If anything is missing, contact QIAGEN Technical Services. 8. Check that the QIAcuity is not damaged and that there are no loose parts. If anything is damaged, contact QIAGEN Technical Services. Make sure that the QIAcuity has equilibrated to ambient temperature before operating it.
Page 23: Installing The Qiacuity
WARNING Risk of personal injury and material damage The QIAcuity is too heavy to be lifted by one person. To avoid personal injury or damage to the instrument, do not lift the instrument alone. The bottom plane shall be used for lifting. Do not lift at the touchscreen.
Page 24 5. If there is an initialization error, retry the initialization process by turning the instrument off and on again using the front power switch. If the problem persists, see “Troubleshooting the instrument and software“ section or contact QIAGEN Technical Services.
Page 25 4.4.6. Installing a fresh copy of the QIAcuity Software Suite Visit www.qiagen.com and go to the Software section of the QIAcuity product page to check if an updated software version is available for download. ® The QIAcuity Software Suite is designed to work with Windows 10 and Windows 11 operating systems.
Page 26 Before starting the installation process and after an update of the Windows operating system using the QIAcuity Setup Wizard, note the following important setup information: 1. Ensure that the system data and time of the laptop to be used are up to date. 2.
Page 27 To install the QIAcuity Software Suite on the notebook, follow the steps below. 1. Locate the QIAcuitySoftwareSuite.exe file on the hard drive and double-click it. The installation process starts. 2. Read the license terms and conditions. These needs to be agreed to by checking the box in the End- User License Agreement window and clicking Install.
Page 28 4. When the installation is completed, click Close. 5. In the local host site that says the site is not secure, click Advanced. Note: If the localhost is not accessible after the software installation, wait for 2−3 min and open it again. 6.
Page 29: Upgrading The Qiacuity Software Suite To A Newer Version
4.5. Upgrading the QIAcuity Software Suite to a newer version Note the following important information, which is valid for all Software Suite version upgrades: 1. Before updating the QIAcuity Software Suite, ensure that no run activity is in progress. 2. The installation of the QIAcuity Software Suite shall be performed by a Windows administrator user. 3.
Page 30 Note: In case user is trying to upgrade the software directly to version 3.0 and the upgrade scenario is not supported (e.g., from version 1.2.18), user is informed in the following way: 4.5.1. Upgrading QIAcuity Software Suite from version 2.5 or 2.2 (direct upgrade) To upgrade the QIAcuity Software Suite from version 2.5 or version 2.2, follow the steps below.
Page 31 5. When the installation is completed, click Finish. 6. Note that the computer must be restarted after a successful QIAcuity Software Suite upgrade. You will receive the following message: 7. Click OK. 8. Then click Restart, and the computer will begin to restart. QIAcuity User Manual | 09/2024...
Page 32 4.5.2. Upgrading QIAcuity Software Suite from version 2.0 to version 2.2 This section describes the QIAcuity Software Suite upgrade from version 2.0. The Software Suite version 2.0 cannot be updated directly to version 3.0 but must be updated to version 2.2 first. To upgrade the QIAcuity Software Suite version 2.0 to version 2.2 follow the steps below.
Page 33 4.5.3. Upgrading QIAcuity Software Suite from version 1.2.18 to version 2.0 This section describes the QIAcuity Software Suite upgrade from version 1.2.18 to 2.5. The Software Suite version 1.2.18 cannot be updated directly to version 3.0, but has to be updated to version 2.0 first, followed by updating to version 2.2. To upgrade the QIAcuity Software Suite version 1.2.18 to version 2.0 follow the steps below.
Page 34 3. Click Next in the Destination Folder window. 4. Click Install to start the installation. 5. In the prompt window asking you if you want to allow changes to your device, click Yes. QIAcuity User Manual | 09/2024...
Page 35 Note: During installation, some command line windows may appear in the foreground. Do not close any of them. 6. When the installation is completed, click Finish. 7. Note that the computer must be restarted after a successful QIAcuity Software Suite upgrade. You will receive the following message: QIAcuity User Manual | 09/2024...
Page 36 8. Click OK. Then, click Restart and the computer will begin to restart. 9. Your QIAcuity Software Suite is now upgraded to version 2.0. Next, continue with “Upgrading QIAcuity Software Suite from version 2.0 to version 2.2” section to finally be able to upgrade to 3.0. 4.5.4.
Page 37 3. Locate the QIAcuitySuite.msi file on the hard drive and double-click it. The installation process starts. Click Next. 4. Check the “I accept the terms in the License Agreement” box in the End-User License Agreement window and click Next. QIAcuity User Manual | 09/2024...
Page 38 5. Make sure that the Destination Folder points to the existing installation of the QIAcuity Software Suite. Click Next in the Destination Folder window. 6. Click Install to start the installation. QIAcuity User Manual | 09/2024...
Page 39 7. In the prompt window asking if you want to allow changes to the device, click Yes. The system will then automatically upgrade the existing installation. 8. When the installation is completed, click Finish. 9. Continue with the QIAcuity Software Suite upgrade from version 1.2.18 to version 2.0. Refer to “Upgrading QIAcuity Software Suite from version 2.0 to version 2.2“...
Page 40 In case a backup is required after the installation or upgrade of the software, an offline script for QIAcuity Software Suite version 3.0 can be downloaded from www.qiagen.com. This script may be used manually or automatically as part of a regular task.
Page 41 Software Suite” section). 2. Manually remove folders C:\ProgramData\Qiagen, C:\Program Files (x86)\QIAcuity Software Suite, and C:\Program Files\Qiagen.CommonInterfaces.QIAidentity if these folders exist. Be aware that \ProgramData might be hidden and you might need to change the view settings of Windows Explorer to view it.
Page 42: Uninstalling The Qiacuity Software Suite
4.6. Uninstalling the QIAcuity Software Suite To uninstall the QIAcuity Software Suite from your system, follow the steps below. Note that this will lead to loss of all data including plate runs. 1. Go to the Control Panel app. 2. Select Uninstall a program from the Programs menu. 3.
Page 43 4. In the prompt window asking you if you want to allow changes to your device, click Yes. 5. In the uninstallation wizard, read the description for each action. Note: The uninstall process will result in database deletion; all plate data will be lost. 6.
Page 44: Updating The Instrument Software
Note: After uninstalling the Software Suite, check the following locations and, if they exist, remove them manually: C:\ProgramData\Qiagen — be aware that folder ProgramData might be hidden, and you may need to change the view settings in Windows Explorer in order to see it C:\Program Files (x86)\QIAcuity Software Suite C:\Program Files\Qiagen.CommonInterfaces.QIAidentity...
Page 45 Software section of the QIAcuity product page to check if an updated software version is available for download. On a computer running Microsoft Windows, download the software update from www.qiagen.com. Insert the USB drive provided with the QIAcuity, create a new folder named update, and extract the update software into this folder.
Page 46: Establishing A Connection Between The Qiacuity Instrument And The Qiacuity Software Suite
4.8. Establishing a connection between the QIAcuity instrument and the QIAcuity Software Suite The QIAcuity instrument needs to be connected to the QIAcuity Software Suite to enable the exchange of data for the analysis and configuration of the instrument. An established connection enables the QIAcuity Software Suite to set up plates, analyze results, and monitor the status of runs in real time.
Page 47 Windows Time Service (NTP) is used. Please make sure that above service is enabled on the notebook or contact your administrator. Note: Make sure that the QIAcuity instrument is connected to the LAN. Any other configurations are not supported by QIAGEN. QIAcuity User Manual | 09/2024...
Page 48 For communication with the QIAcuity Software Suite, the following ports are used and should be always opened in the correct direction: The inbound TCP port 44321 The inbound TCP port 8080 The inbound TCP port 8687 The inbound UDP port 123 After any changes are applied to the ports above, the QIAcuity instrument must be restarted.
Page 49 4. On the left pane, click Change adapter settings. 5. Right-click the ethernet network adapter and select Properties. 6. Select Internet Protocol Version 4 (TCP/Ipv4) and click Properties. QIAcuity User Manual | 09/2024...
Page 50 7. Select Obtain an IP address automatically. If your organization does not provide DNS details, select Obtain DNS server address automatically as well. Click OK, then Close. Optional: You can check if the addresses have been assigned properly by following the steps below. 8.
Page 51 3. Select the Ethernet tab. 4. Check the “DHCP Enabled” box. If you check this box, the “IP address” and “MAC address” fields are disabled. The assigned IP and MAC addresses of device are displayed in the “IP address” and “MAC address” fields. Alternatively, the customer’s IT may configure a fixed IP address for the instrument.
Page 52 4.8.6. Configuring a direct cable connection between the QIAcuity instrument and the QIAcuity Software Suite Note: Before you start, ensure that the QIAcuity instrument and the notebook are connected with an Ethernet cable. Follow the steps below to configure the notebook running the QIAcuity Software Suite in Windows 10. 1.
Page 53 6. Select Internet Protocol Version 4 (TCP/Ipv4), and click Properties: 7. Select Use the following IP address. Enter the following information: IP address: Enter “192.168.1.1”. Subnet mask: Enter “255.255.255.0”. Default gateway: Enter “192.168.1.254”. Preferred DNS server: Enter the DNS server address. Alternative DNS server: Enter the alternative DNS server address.
Page 54 8. Click OK, then click Close. Optional: You can check if the addresses have been assigned properly by following the steps below. 9. From your Home screen, click the Search icon. Enter ”cmd” and press the Enter key. 10. Wait for the command line window to open. Enter ”ipconfig”. The address should be visible under the ethernet interface name for which modifications were made.
Page 55 3. Ensure that the ”DHCP Enabled” box is not checked. Enter the following information: IP address: Enter “192.168.1.2”. Subnet mask: Enter “255.255.255.0”. Gateway: Enter ”192.168.1.1”. 4. Tap Save. 4.8.7. Configuring the connection to the QIAcuity Software Suite in the QIAcuity instrument software The QIAcuity instrument needs to be connected to the QIAcuity Software Suite to enable the exchange of data.
Page 56 4. Tap the Software Suite tab. 5. Enter the IP address in the address field of the Software Suite URL section. Note: To obtain the IP address of the Suite Server, the instrument must be connected to the Suite Server. From the home screen on the Suite PC, click the Windows icon and navigate to Command Prompt, or enter “cmd”...
Page 57 Due to technical limitations, Suite Server IP address shall not contain the full IP of the instrument (e.g., instrument IP set to xxx.xxx.xxx.12 will not work correctly with Suite Server IP xxx.xxx.xxx.123; in that case the latter value should be changed, e.g., to xxx.xxx.xxx.13).
Page 58: Getting Started With The Qiacuity
4.9. Getting started with the QIAcuity 4.9.1. Configuration of the QIAcuity If you are using QIAcuity for the first time, we recommend that you define the required settings. Other settings can be changed later, when needed. For more information about using the touchscreen and software, refer to the “Operating the QIAcuity Instrument ” section. 4.9.2.
Page 59 5. The Home screen appears. Note: To return to the Home screen from another screen, tap Running Status. 4.9.3. Setting basic system data This section describes how to set your preferred name for the instrument. To set your preferred QIAcuity name 1.
Page 60: Managing Users
4.9.4. Managing users The QIAcuity requires users to log in before accessing instrument functionalities. Each user must have a user account with an appropriate role assigned to it. The QIAcuity supports various pre-‍ d esigned user roles and customer-created user roles. Each role has different access rights to QIAcuity functions described in section “Log-in screen”.
Page 61 Automatic log-off and blocking user account QIAcuity Software Suite automatic log-off and user account blocking: After three unsuccessful login attempts, a user is temporarily blocked and needs to wait 10 minutes to unblock the account. In case of 15 minutes of inactivity, users are automatically logged off. Activity consists of mouse clicks, mouse scrolling, and pressing buttons on the keyboard (mouse movement without clicks nor scrolling is not considered as activity).
Page 62 To download labware information from the Software Suite, follow the steps below. 1. On the toolbar, tap Tools and then proceed to the Labware Synchronization tab. 2. Tap Labware sync. The Labware synchronization dialog box appears. 3. The progress of the download is shown in the dialog box. Once the synchronization is complete, tap OK to finish the process.
Page 63: Operating Plates
In the QIAcuity plate-based system, one reaction mix per well is partitioned into a large number of individual partitions prior to the amplification step, resulting in one or very few templates being present in each partition. QIAGEN offers different plate types according to specific user needs.
Page 64: Qiacuity Nanoplate 26K 8-Well
5.2. QIAcuity Nanoplate 26K 8-well For applications requiring high sensitivity, QIAGEN offers the 26K nanoplate. In this plate, one reaction mix is distributed over 4 wells and separated into approximately 26,000 partitions. The plate may be used for up to 8 samples and has a light blue frame as distinction from the other plates.
Page 65: Reaction Setup
For better handling of the Nanoplate, you can place it into the Nanoplate tray that can be ordered as an accessory, see Appendix B — QIAcuity Accessories or the QIAcuity webpage on www.qiagen.com To set up a plate, follow these steps: 1.
Page 66 Note: It is recommended to cover the plate with the top seal within 30 minutes after pipetting to prevent subsequent filling issues. Note: Keep the plate seals stored in a dry, darkened, and air-free environment by always completely closing them inside the provided storage bag in which they came, and storing them in the Nanoplate box.
Page 67: Operating The Qiacuity Instrument
6. Operating the QIAcuity Instrument The QIAcuity is operated through a touchscreen. Elements of the QIAcuity user interface are shown in the following table. Table 5. QIAcuity interface elements Button/Icon Function Starts the run Stops the run Starts runs on all loaded plates Stops all runs Closes an open tray Ejects selected tray...
Page 68: Entering Text And Numbers
6.1. Entering text and numbers To enter text or numbers, tap the corresponding field. An on-screen keyboard is displayed on the touchscreen. In some cases, the value required in a text field must meet a specific criterion. If required, the criteria are specified in the corresponding input window.
Page 69: Turning On The Instrument And Logging In
6.2. Turning on the instrument and logging in To turn on the instrument and log into the software, follow these steps: 1. Press the Power button to turn on the QIAcuity. 2. The startup screen appears on the touchscreen and the instrument automatically performs initialization tests. After the initialization setup, the Login window appears.
Page 70: Setting Up An Experiment
6.4. Setting up an experiment Note: A plate run can only be performed if the instrument is connected to the QIAcuity Software Suite either through a network or a direct cable connection to the QIAcuity Software Suite server. Note: It is recommended to cover the plate with the top seal within 30 minutes after pipetting to prevent subsequent filling issues.
Page 71 2. Place a plate in one of the slots of the ejected tray. Ensure that the plate is placed in the correct orientation, facing the barcode toward the instrument and the QIAGEN lettering toward you. Also, ensure that the plate seal of the plate is intact and not overlapping any of the sides more than 1 mm.
Page 72 6. When all plates are correctly labelled and the corresponding data is received from the QIAcuity Software Suite, start the run. To start the run on all plates simultaneously without making any changes, tap Run all. To start the run of an individual plate without making any changes, tap the Run icon on the plate’s pane.
Page 73 3. Proceed to “Plate configuration procedure”. To start the configuration of a plate that has not been loaded into the instrument, follow these steps: 1. On the Home (Running status) screen, tap New Plate. Note: The New Plate button is not available for single-plate instruments. 2.
Page 74 Note: If you are creating a plate, you are automatically assigned as an owner of a plate. Owners are displayed under plate name on running status page. Modifying owners of the plate is only possible by editing the plate in the Software Suite.
Page 75 4. Perform the following steps in the Cycling tab: a. Enter your desired temperature in the “Temperature” field. b. In the “Duration” field, enter the cycling duration for the plate. c. Tap Add temperature step. Note: The gradient cycling option can only be defined in the Software Suite. 5.
Page 76 c. To include more steps in the run, tap the Add icon, then select the applicable step. Provide the required information for the step. Repeat this step if more steps are needed for the run. In total, 9 steps can be performed per plate.
Page 77: Tracking The Run Status
To link the barcode to a defined plate in the Software Suite, that has no barcode defined, follow these steps: 1. Tap the Link icon. 2. In the “Select Plate” dialog box, select the plate that you want to link to the barcode of the loaded plate. Note: Only plates with a “Defined”...
Page 78 The panel also shows all the steps within the run. The font color of the steps that are completed is black. When a step is in progress, its font color is blue. Pending steps are shown in light gray. To view more details about the run, tap Show details. The dialog box appears containing information about the plate (in the General Data tab), as well as each step of the run (in the dPCR Parameters tab).
Page 79: Continuous Loading And Unloading Of Plates
Table 7 shows the meaning of each status icon that is shown in the dPCR parameters step. Table 7. dPCR step status icon Icon Status The step is successfully finished. The step is being executed. The step is pending, and its execution will start after the current step is done. The step failed.
Page 80: Aborting A Run
Note: Depending on the time frame for unloading/loading of plates, the drawer opening might be delayed some time to finalize current movement steps. 6.7. Aborting a run If needed, a run can be stopped at any time. You can either abort all running plates or only a single running plate. To abort all runs on all plates, tap Stop all.
Page 81: Error Clearing
6.8. Error clearing The Control Software provides an error-handling functionality to ensure that the software is in a defined state It is designed to provide a streamlined and efficient way to manage potential system faults. If an error appears on a specific module during the run, a notification will display under the “Alarm” notification box, for logged in users with appropriate permissions.
Page 82 Confirmation is required after pressing the Clear errors button, as the process requires the affected modules to be reinitialized and the control software is blocked while this task occurs. While the error clearing process occurs, information about the clearing status is displayed: QIAcuity User Manual | 09/2024...
Page 83: Rerunning A Plate
After the errors are cleared an information message appears at the top of the screen, informing the user that the errors have cleared successfully. The errors no longer appear on the System status tab and under the “Alarm” notification box. 6.9.
Page 84 In QIAcuity Four, the run starts with slot number 1, and ends with slot number 4. The slot numbers are presented in Table 9. Table 9. Slot numbers of the QIAcuity Four Slot numbers To edit the run schedule, follow these steps: Note: Only runs that are not started yet (with Pending Run status) can be rearranged.
Page 85: Viewing Notifications
6.11. Viewing notifications If the QIAcuity detects an error that affects the workflow of the instrument that the user can resolve, a notification displays on the screen. To view a list of all notifications and possible solutions to the errors, tap the Alarm icon.
Page 86: Logging Out
Yellow – When the usage of the disk occupation rises above 75% Red – when the remaining free disk space is less than 4 GB (approx. 14%) In case of Yellow and Red scenarios, additional information is shown to inform user about the actions that should be taken to regain disk space: forcing the clearing of images which have not been transferred to the Software Suite or setting up a connection with the Software Suite.
Page 87: Automatic Logout
2. In the Confirmation dialog box, tap OK to confirm or tap Cancel to go back. 6.13.1. Automatic logout Users are automatically logged off after a default setting of a 15 minute period of inactivity. Time delay between user inactivity and log off can be configured manually or disabled under Configuration > Automatic log off. The maximum value that can be applied is 7 hours 59 minutes.
Page 88 6.13.2. Accessing the run status when you are logged out After you log out, the Login screen is displayed on the QIAcuity display. To view the run status of an ongoing run, tap Running status. The Running status screen is displayed in view-only mode. All functions are disabled. To perform any actions related to the run and the plates that are being processed, log into the instrument.
Page 89: Operating The Qiacuity Software Suite
7. Operating the QIAcuity Software Suite 7.1. Getting started This section describes the workspace within the QIAcuity Software Suite, its basic concepts, and the general software use. Note: If the network connection was set up, the Software Suite can be accessed via another laptop using the IP address of the Software Suite server.
Page 90 To archive plates on an external drive, user can configure the archive. See section “Archive” for more information. The Tools tab contains the Troubleshooting sub-page that allows user to generate a password-protected software support package described in section “Problem during the Software Suite runtime”. In the Configuration tab, user can access configuration features such as Instrument name, Archive Management, User Management, and Audit Trail.
Page 91: Concepts Of The Qiacuity Software Suite
7.2. Concepts of the QIAcuity Software Suite 7.2.1. Log-in screen The main toolbar shows which user is currently logged in. To view more information about the user, click the icon. The user can change the password, edit the user profile, and log out. Note: Log-in on QIAcuity Software Suite is independent from log-in on the instrument.
Page 92: User Management
(except the initial administrator user with login name “admin” provided by QIAGEN during the initial installation). When working with Good Manufacturing Practice (GMP)/Good Laboratory (GLP) regulations, deactivate this initial admin user (for which the password does not expire) once at least one additional user with administrator rights has been created.
Page 93: New User Creation
The centralized user management enables independent use of instrument Control Software and Software Suite. Regardless of which user is logged in with which role on the Software Suite, another user can log in with a different role on the instrument. Both log-ins are completely independent from each other.
Page 94 2. Fill out the form: user name (first name), surname, login, and password. Note: There is an already existing login “System” that is reserved for special users. It cannot be selected by the Administrator when the new user is created. A warning message is shown when the Administrator tries to create a user with a reserved login.
Page 95 4. In the Permissions (second) step, one role is chosen and assigned to the user. Description of all Roles can be found below. For detailed information about roles and permissions, refer to the table “Default role permissions” or the descriptions displayed on screen in the Software Suite during the user creation process. 5.
Page 96 7. Show/hide descriptions of the permissions related to particular permissions group or for all permissions at once by using the show/hide all descriptions button. 8. To go back and check or change user information, click the Back to User Information button or the User information step in the navigation on the top of screen.
Page 97 It is possible to start with the user creation process from the Permissions step, but entries in the User information step are mandatory and will be highlighted by the software (see next screenshot). 1. If Permissions are defined prior to User information, a yellow warning icon displays and the new User cannot be created until all mandatory information is entered.
Page 98 4. To create the user, click the Save button. At any time during user creation it is possible to return to the Users List section by clicking the Back to Users List button, but all data entered will be lost. 7.2.5.
Page 99 a. User information tab Click on the input field and type in the new name/surname. User login name cannot be changed. b. User permissions tab Click on the new desired role and click the Save button. c. User password tab Change the user’s password.
Page 100 d. In the “New password” field, enter the new password. In the “Confirm password” field, re-enter the same password as in the “New password” field. Those passwords should be the same. If the passwords entered matched, click the Save button. e.
Page 101 4. Click the Activate user icon. 5. When the Activate button is clicked, the user is moved to the “Active” and “All” Users list. 7.2.7. User deactivation Users with Administrator role are able to deactivate other users to restrict access to the system. Note: It is not possible to delete users.
Page 102 7.2.8. Log in (Instrument and PC software) 1. Instrument — User can log in to the instrument (login and password is needed). Log into the Instrument by providing credentials. 2. Software Suite — User can log in to the Software Suite (PC software) (login and password is needed). Log into the Software Suite by providing credentials Change own password Modify own user data...
Page 103 3. Edit Analysis Data — User can change the threshold and use the polygon selection on the Analysis page of all Plates to verify the accuracy of the results. Note: The “Read all Plate” permission is required to have the fully available permissions. 4.
Page 104 Unlock plate When a Plate is in locked status, then the Unlock Plate button is visible in the Plate details. Note: Avoid use of the Unlock Plate button. If the Unlock Plate button is tapped during a run, the run will stop and the data will be lost.
Page 105 8. Create Report for Analysis — User can create and generate a report using the charts and data from the Analysis of the Plate. Note: The “Read owned Plate“ or “Read all Plate“ permission is required to have the fully available permissions. Add charts to a report Check selected items for a report Create a report (add report name, select or change report elements)
Page 106 See all created Templates Search Templates (and sort them) Create a Plate from a Template If the user also has the “create plate” permission Import a Template while creating a new Plate or Reaction mix If the user also has the “create plate” permission Import a Template while editing a Plate or Reaction mix If the user also has the “edit plate”...
Page 107 Note: The “Archive Overview“ permission is required to have the fully available permissions. a. Go to the Archive and the Disk Monitor. If the user does not have the “Archive overview” permission, then the following information is displayed: In order to view archived plates, you need to have “Archive overview“ permission. Please contact administrator to get access rights.
Page 108 c. Go to the Users tab in the User Management and create new users or edit exiting users. d. Go to the Roles tab in the User Management and create new roles, see permissions list or see users list that are assigned to role and edit existing roles.
Page 109 a. View Audit Trail — The user can see the list of the Audit Trail events, search for specific events, check details of an event, and export it to PDF. Go to the Configuration panel. Go to the Audit trail tab in the configuration panel. Go to the events list.
Page 110 4. Technician The technician has limited access to the QIAcuity Control Software and QIAcuity Software Suite. Users with this role can process (create, run) their own plates and use existing templates to run an experiment. 5. Quality Assurance The quality assurance role has the rights to check all information about the plate, can import plates, and create and sign reports.
Page 111 Table 10. Default role permissions (continued) Group Quality Administrator Supervisor leader Technician Assurance Lab leader Operator Delete Plate Other permissions Import Plate Export Plate Unlock Plate Set Plate Ownership Upload VPF Upgrade Plate Create Support Package Create Report for Analysis Sign Report Delete Report Templates...
Page 112 This section describes how the functionalities in the application are impacted by permissions, which are assigned to user roles. Pay special attention to notes, because some permissions require other ones to work – Notes become visible after checking checkbox. 7.2.16. New role creation All activities related to creating/editing/deleting roles and a list of existing roles can be found within the User Management tab in the Roles view.
Page 113 5. If you want to go back and check or change the role name, click the Back to Role name button or click the Role name step in the stepper. 6. Click the Save button to confirm and create the role. Note: All entries need to be completed under Role name before moving to the Permissions step.
Page 114 Pressing the Users list button will bring you to the list of all users and their status. 7.2.17. Editing existing role Note: Editing a Role requires the “Create and Edit Roles” permissions. Only roles created by users can be edited. Predefined roles cannot be edited.
Page 115 3. On the left-hand side are two tabs related to role information and role permissions. a. Role information tab Change role name and description. To edit a user name or surname, click on the input field and type the new value. b.
Page 116 d. To confirm changes, click the Yes, edit role button. If no users are assigned to the role being modified, the confirmation window will not appear. 7.2.18. Role deletion Note: Deleting a Role requires the “Delete role” permission. Only roles created by users with no users assigned can be deleted.
Page 117: Setting Up An Experiment
7.3. Setting up an experiment This section provides information about the steps required to set up a new experiment. 7.3.1. Creating a new plate 1. Click Plates in the main toolbar to enter the plates environment. 2. Click New Plate. 3.
Page 118 Table 11. Required steps in creating a plate Steps General data Enter the basic information about the plate: Plate name Plate type Description Labels Plate ownership Barcode dPCR parameters Specify the following information: Priming profile Cycling Imaging Reaction mixes Provide the following information for a new reaction mixes: Reaction mix name Color Target Name...
Page 119: Plate Configurator
7.4. Plate configurator 7.4.1. Defining general data In the General Data tab, specify the basic information about the plate. Mandatory input fields are marked with an asterisk. The plate name is required to save a plate. Note: Make sure that the selected plate type corresponds with the entered barcode, if manually entered. If they do not match, it will lead to an error on the instrument (error 205).
Page 120 7.4.3. Assigning the owner of the plate 1. On the Plates tab (Plates Overview), find the plate to which ownership must be assigned. 2. In the General Data tab, the “Plate Ownership” field is displayed (below “Labels”). 3. Click on the “Plate Ownership” input field. 4.
Page 121 7.4.4. Removing an owner of the plate 1. To remove one owner of a plate, click the close icon placed within the user name tag. 2. To remove all owners, click the clear icon on the end of the input field. 3.
Page 122 Priming tab Select the priming profile applicable for the plate and your type of experiment in the Priming tab . Cycling tab Define the temperature profile of each experiment in the Cycling tab. To do this, follow these steps: 1. In the “Temperature” field, specify the temperature of the step, then specify the duration of the temperature step in the “Duration”...
Page 123 6. In the first column of the grouped temperature steps, add the number of cycles. Note: To separate the grouped temperature steps, check the box corresponding to the group, then click Ungroup. To delete a temperature step, check the box corresponding to the step, then click Delete. The three-dotted icon in each temperature step enables you to edit or delete the step.
Page 124 Selection of optimum temperature can be based on multiple criteria. The most common criteria are the signal-to-noise ratio (S/N), the presence or absence of rain, and concentration results. The selected optimum temperature should allow the highest signal-to-noise ratio, minor to no rain and that the obtained concentration reflects the expected results. Finding the optimum temperature is also important to minimize primer mismatch, which could lead to cross-hybridization issues in a multiplex reaction mix.
Page 125 Imaging tab The Imaging tab enables you to set the respective exposure duration and gain value for each channel. The channel options depend on the connected instrument. QIAcuity multiplex instruments support dPCR assays up to 8-plex by using six optical channels for six standard dyes and the additional use of two channel combinations for LSS (Long Stoke Shift), which can be selected from five different channel combinations.
Page 126 Table 13. QIAcuity instruments and their available channels Instrument Available channels QIAcuity One, 2plex Green Yellow QIAcuity One Green Yellow Orange Crimson Far red + two combinations from Green/Yellow, Yellow/Orange, Orange/Red, Red/Crimson, Crimson/Far red QIAcuity Four Green Yellow Orange Crimson Far red + two combinations from Green/Yellow, Yellow/Orange, Orange/Red, Red/Crimson, Crimson/Far red QIAcuity Eight...
Page 127 The following actions can be performed when each run is finished: 1. To reimage the plate with different settings, click +, then select Imaging. 2. To rerun the plate with additional cycles, click +, then select Cycling + Imaging. a. Important: After a run is finished, remove the plate from the instrument before adding a new imaging or cycling + imaging step.
Page 128 7.4.6. Reaction mixes tab Create a new reaction mix or import a reaction mix from a template for each experiment (plate) on the Reaction mixes tab. The General View tab displays the name of all reaction mixes used in the plate. To edit, delete, or save the reaction mix as template, click the three-dotted icon.
Page 129 Creating new reaction mix To create a new reaction mix: 1. Click New Reaction Mix. 2. The New Reaction Mix window appears. 3. Enter the name of the reaction mix in the “Reaction mix name” field. The name must be unique and must not contain any special characters.
Page 130 7.4.7. Saving reaction mixes as templates From QIAcuity Software Suite version 3.0 onwards, existing reaction mixes can be saved as Reaction mix templates for later usage in other experiments. To save an existing reaction mix as Reaction mix template: 1. Click the three-dotted icon of the reaction mix and select the Save as template option. 2.
Page 131 2. Import reaction mix template window appears. 3. Select which reaction mix template should be imported. Note: Reaction mix templates defined in the system can be searched by their names or reaction mix names defined inside the templates using the search field and sorted by template name, reaction mix name, modification and creation dates using the drop-down menu.
Page 132 7.4.8. Defining samples & controls Samples To add a new sample: 1. In the Samples & control tab, click New Samples. 2. The New Samples window appears. 3. Enter the following information in the required fields: a. Sample Name: Enter the sample name. The name must be unique and must not contain any special characters. Up to 100 characters can be entered in this field.
Page 133 5. The sample(s) is/are added to the plate and can be used for each experiment. Note: A user can change the sample dilution or the conversion parameters for several samples at once by selecting the samples with the checkbox and using the buttons Set sample dilution and Set Conversion factor. QIAcuity User Manual | 09/2024...
Page 134 7.4.9. Adding controls and non-template controls You can add positive or negative controls to your experiments. Controls To add controls: 1. Click the Controls tab. 2. Enter the name of your control in the “Control Name” field. 3. Click Add Control. 4.
Page 135 4. The non template control is added to the plate and can be used in the experiment. Note: For Non Template Controls, no dilution nor conversion information can be defined. 7.4.10. Defining plate layouts Plate view To define the plate layout, you must add reaction mix, samples, and controls to your plate. Adding a reaction mix to the plate QIAcuity User Manual | 09/2024...
Page 136 1. Left-click the desired well. 2. Left-click the + icon, then select Add reaction mix or Mark as blank. The Add reaction mix window appears. 3. Select the reaction mix you want to add to the plate. To create a new reaction mix, click the Create new tab. See the “Creating new reaction mix ”...
Page 137 Adding samples to the plate 1. On a marked well, click the … icon in the bottom right corner of a well or right-click the well. Note: You can also mark more than one well if you want to assign a sample to multiple wells. 2.
Page 138 Adding controls to the plate 1. On a marked well, click … icon in bottom right corner of well or right-click the well. Note: You can also mark more than one well if you want to assign a control to multiple wells. 2.
Page 139 Adding NTCs to the plate 1. On a marked well, click the … icon in bottom right corner of the well or right-click the well. Note: You can also mark more than one well if you want to assign a non template control to multiple wells. 2.
Page 140 Legend User can click the Help icon in the upper right corner of plate layout area to display a legend and check the meaning of all icons and descriptions used on a plate layout. Plate layout with defined gradient cycling In case a gradient cycling is defined, the plate layout looks slightly different: 1.
Page 141 3. With the help of the View details button, a temperature map is presented. By clicking on Download PNG, the temperature map can be downloaded in *.png format. List view The list view in the Plate layout tab displays a detailed overview of your plate setup. You can modify this view by sorting and filtering: 1.
Page 142 7.4.11. Plate layout: CSV import/export It is possible to export plate data as CSV file. Click CSV import/export, then click Export to CSV to export the data. An import of the whole plate data from a CSV file is possible to define the plate layout. The file structure for import and export is identical.
Page 143 CSV structure 1. The import and export CSV file looks the same and includes the following columns. Well – identifier of the well (A1, B1, etc.). This is a mandatory field. 2. Sample name – name of the sample. 3. Type (Sample/NTC/Control) – sample type – one of Sample/NTC/Control. Note: Please pay attention to the exact notation of Sample, NTC, and Control.
Page 144 Important: In case the reaction mix with CXTM is used in a plate layout CSV a user should not fill the following field manually: Channel Internal Control These fields are automatically filled in based on the aforementioned CXTM Reaction mix template ID. Filling them in manually will cause the import to fail.
Page 145 In case of successful CSV import (there are no errors nor warnings in file), all data from the CSV file will be imported to the plate and the user will be notified by a message “CSV successfully imported” in bottom right corner: When will the CSV import function fail? If there some errors in the CSV file, there are two possible scenarios: 1.
Page 146 2. Data will not be imported, current data will not be overwritten, and the user will receive a notification with the error: Possible errors and warnings Possible errors and warning related to reaction mixes, samples, and control in the CSV file are listed below: 1.
Page 147 b. Errors: Sample name exceeds the limit of 80 characters. The same sample has different: c. Type d. Concentration factor e. Template volume f. Labels g. Description The labels exceed the amount of 10 characters. The description exceeds the limit of 1000 characters. The sample has a non-existing type assigned (the allowed types are sample, control, and non_template_control).
Page 148 7.4.12. Managing your plates To enter the Plates environment, click Plates in the main toolbar. Existing plates are shown in the Plates Overview window. Plates can be presented in grid view and list view accordingly. Plate Overview – grid view. Plate Overview –...
Page 149 4. Plates created in the current QIAcuity Software Suite version do not display any of above icons and tooltip: On the bar, information about the last update of a plate is shown. When a plate was updated less than an hour ago, minutes, or seconds are shown.
Page 150 Example of read-only date plate without VPF. Sorting You can sort the Plates Overview window by Last updated, Plate name, or Plate status. 1. Click the symbol for tile or list view to switch views within the Plates Overview window. Note: Both views provide information regarding the plate name, plate status, modified date, type of plate, and used disk space.
Page 151 Filtering Click the calendar symbol beside Time Frame to limit the overview results to plates modified within a specific time period. A window appears and enables selection or entry of a specific time frame. Click Apply to filter the results. Export and import plate data To archive data and free-up disk space, plates can be exported as password-protected zip files.
Page 152: Setting Up Templates
Note: If a plate from a previous version is imported to a newer QIAcuity Software Suite version, it will be visible in read-‍ o nly mode and must be upgraded before it can be edited. There is no possibility to import a plate from QIAcuity Software Suite versions earlier then 1.2.18.
Page 153 7.5.2. Saving existing plate as a plate template Follow the steps to set up a new plate as described in section “Setting up an experiment”. After you have entered all required information, you can save the information as a template to use for future plates. 1.
Page 154 2. Click Plate templates, then click Import template. 3. The Import Plate Template window appears with all existing templates. 4. Select an existing template, then click Import. 5. All information in the selected template is automatically transferred to the new plate setup. QIAcuity User Manual | 09/2024...
Page 155 To use a plate template from the Templates level: 1. Go to Templates, then select the Plates tab. 2. Find the template you want to use on the list then click the three-dot icon and select the option Use in a new plate. 3.
Page 156 Example: 3. Enter the name for the template in the “Template name” field. Up to 100 characters are possible. 4. Follow the steps as described in the section “Defining reaction mixes”. 5. After you have entered all required information, click the Create button. 6.
Page 157 Note: Creating reaction mix templates from an existing reaction mix or from reaction mix templates is described in sections “Saving reaction mixes as templates” and “Importing reaction mixes from templates”, accordingly. 7.5.5. Managing your templates To enter the Templates environment, click Templates from the Main toolbar. The overview screen lists all existing templates for plates and reaction mixes on separate tabs.
Page 158: Analysis
7.6. Analysis The QIAcuity Software Suite analysis of plates that have been processed by the instrument. The following analysis options are available in the software: 1. Absolute Quantification 2. Mutation Detection 3. Genome Editing 4. Copy Number Variation 5. Gene Expression 7.6.1.
Page 159 3. Select Analyze from the context menu. 7.6.2. Plates after QIAcuity Software Suite version upgrade After upgrading the QIAcuity Software Suite (see “Installation Procedure” and “Upgrading the QIAcuity Software Suite to a newer version” sections), the status of all plates will be changed to Read-only until the plates are upgraded to the new software version.
Page 160 During the plate upgrade, a blue pulse indicator is shown on the plate tiles, indicating the upgrade process is taking place. During the upgrade process, both plates are blocked and cannot be accessed and changed to avoid inconsistent data or loss of data.
Page 161 VPF is imported. The microstructure molding form is defined by the first two digits of the plate barcode. Note: Multiple plate batches can come from one microstructure molding form. New sets of VPFs will be published during production of the Nanoplate batches and can be downloaded from the QIAGEN website.
Page 162 In addition, information about missing VPF is available on: 1. Plates Overview screen 2. Analysis screen 3. Plate Configuration screen 4. Report QIAcuity User Manual | 09/2024...
Page 163 Loading VPF All existing VPFs to all used microstructure negative forms are bundled together in one zip file to allow the user to always download the most recent version. After uploading the file, the QIAcuity Software Suite automatically chooses which VPFs are missing and applies them.
Page 164 7.6.4. Custom cross talk matrix To compensate the spectral overlap between the fluorescent dyes called cross talk, a correction algorithm is usedimplemented for the six standard channels (Green, Yellow, Orange, Red, Crimson, Far red) in the QIAcuity Software Suite. This standard cross talk matrix is automatically applied to experiments using above mentioned standard channels and no additional actions are required from the users.
Page 165 Preparing custom cross talk matrix (CXTM) For creation of a custom cross talk matrix (CXTM), a dedicated plate needs to be created. This plate must exhibit all targets of interest (from one up to eight targets) as individual simplexes. For example, if a custom cross talk matrix is desired for a triplex reaction mix, all three individual targets must be available as simplexes on one dedicated plate.
Page 166 To finally prepare custom cross talk matrix user should follow below procedure: 1. The CXTM configurator can be triggered from any dedicated plate in the plate overview or during analysis. In the plates overview environment, plates that fulfil the pre-requisites for CXTM creation, exhibit the “create CXTM” function under the three dot menu: To start the CXTM creation during analysis, click on More and use the “Create CXTM”...
Page 167 After selecting wells with the proper reference channel type, click on the Add to CXTM button. After adding wells to the custom cross talk matrix, an information table containing Channel, Target, wells and reference type selected is presented. In case of wrong selection, user can remove it using the trash icon. After reference channel is added correctly to CXTM, click on the Next button at the bottom of screen.
Page 168 When all desired targets/channel of interest are added, click on Next to continue. QIAcuity User Manual | 09/2024...
Page 169 c. Review & correction – In this step, user saves the created custom cross talk matrix along with new reaction mix template. Enter a Template and Reaction mix name (see further detail under Creating a new reaction mix template “ section).
Page 170 d. Create new reaction mix – In this step user save created custom cross talk matrix along with new reaction mix template. Similarly like for regular Reaction mix template user needs to input Template name and Reaction mix name as mandatory. Optionally user can define Total volume parameter and change the color. In section below there is a list of targets that user defined in step 2 of configurator.
Page 171 Usage of Custom cross talk matrix All available reaction mixes templates are listed template list: After user with sufficient permission, click three-dot icon and select Details/Edit option. Edit reaction mix template modal is presented. If reaction mix template consists custom cross talk matrix: User cannot modify Dyes, Channels, and check options Internal control for particular targets/channels.
Page 172 During plate creation, user can import Reaction mix template along with CXTM, like already described in section “Importing reaction mixes from templates”. To ease identification, they have special CXTM icon. QIAcuity User Manual | 09/2024...
Page 173 After importing, user can review reaction mix and CXTM parameters in the same way, like on Templates tab, and edit the Reaction mix name, the Target name, or the Total volume. CXTM icon ( ), informing that reaction mix consists CXTM, is presented on Reaction mix General View and Detailed List, during assigning Reaction mix to wells and on well information modal.
Page 174 Similar warnings (exclamation mark) are presented on Detailed List. And later on Analysis: 1. Channel cross talk notice (3rd on warning list above) warns which reaction mixes are missing CXTM. (If no reaction mixes are assigned to plate layout warning is very similar but does not point reaction mixes names.) 2.
Page 175 Note: Errors affecting single wells or empty wells are indicated by a symbol in the affected well. Try reimaging the plate with different exposure and/or gain settings. If the error persists, create a support package and contact QIAGEN Technical Services. QIAcuity User Manual | 09/2024...
Page 176 Image quality control The fluorescence signal in the reference channel is measured to determine the number of valid partitions in a well. Differences in the signal intensities between partitions are normalized and the fluorescence signals in the target channels are corrected accordingly.
Page 177 In case more than one imaging step has been done, the imaging step where the low signal quality occurred is marked in red and the message is shown when moving the mouse over the camera icon. Reasons for the invalidation of an image are: 1.
Page 178 7.6.8. Dust and other particles Dust and other particles like hairs or strands are detected by the QIAcuity Software Suite and are removed from the images. This figure shows an example of a well before and after dust/other particles correction. Raw image of a well showing dust particles (marked with red circles).
Page 179 In case the images still show dust particles or other particles after the correction, the recommendation is to unload the plate, wipe the plate with a lint-free tissue and to re-image the plate. Note: For QIAcuity Software Suite v2.0 or higher, dust detected in one channel is used for finding dust in other channels as well.
Page 180 7.6.10. Areas of bad filling Incorrect pipetting or sealing can lead to areas of the well which are not filled with reaction mix. Those areas affect the reference channel as well as the target channels and reduce the number of valid partitions. See “Operating Plates” for instructions on how to pipet and seal the Nanoplates properly.
Page 181 Note: In case insufficient compensation or overcompensation is seen (e.g., as double negative bands), check the RFU level of positive signals of neighbor channels if saturated or very bright. By lowering the RFU level of positive signals, the insufficient compensation or overcompensation might be reduced. 7.6.12.
Page 182 In such case, user is warned about discrepancy in: Plate layout – Indicator is presented if discrepancy exists on any of Imaging step. Analysis Warning – User can go back to plate configurator and do needed adjustments. Exclamation mark on List view next to wells with reference discrepancies. CSV export –...
Page 183 7.6.13. General analysis options Selecting wells for analysis 1. To select multiple wells at the same time, click the individual wells or click one well then drag your mouse until all wells are selected. 2. To select all wells, click Select all. 3.
Page 184 Hyperwells To achieve higher accuracy, multiple wells can be grouped together and analyzed as a single well. To define a hyperwell, select multiple wells with the same reaction mix and same sample name. By clicking on Group as hyperwells, the software automatically groups all selected samples exhibiting the identical reaction mix and sample to hyperwells.
Page 185 Details about CI calculation and concentration determination in hyperwells are described in the QIAcuity User Manual Extension: QIAcuity Application Guide available at www.qiagen.com. Hyperwells can be selected for Absolute Quantification, Mutation Detection, and Genome Editing, Copy Number Variation, and Gene Expression analysis.
Page 186 2. Then, enter the number of copies/genome. You can choose the value between 1 and 99. 3. Select target of interest from the drop-down list. 4. Reference selection is now unavailable because you have not selected the wells/hyperwells with the same sample ID for the chosen reference sample.
Page 187 1. First select reference sample. In this case, the user has selected sample ID 01 “patient 01”. 2. Enter the copies/genome. You can choose the value between 1 to 99. In this case, the user enters “10”. 3. Then, select the target of interest. In the example below, the user has chosen SARS-COV-2 with channel Green. 4.
Page 188 Multiple imaging steps If the plate was configured with multiple imaging steps, you can select the one used for analysis. To select the imaging step, click one of the available boxes indicated by camera icon. The channels along with the duration and gain settings, that were activated in the selected imaging step are shown after expanding Imaging info section.
Page 189 Diagram options There are several tools related to the diagrams and charts that enable you to adjust the view and download the chart you want to view. To access the tools, point to a diagram. Table 14 shows the toolbar buttons and their corresponding functions. Table 14.
Page 190 Dilution calculation option From QIAcuity Software Suite version 2.5 onwards, there is the possibility to calculate the concentration of the undiluted sample. Dilution calculations can be used in all type of analysis: Absolute quantification as well as in all second-level analysis (Mutation detection, Genome editing, Copy number variation, and Gene expression).
Page 191 Usage of dilution calculation feature in analysis Before using dilution calculation for data analysis, make sure all needed samples have dilution factor parameters filled accordingly (described in sections “Defining samples and controls” and “Defining reaction mixes”). You can use drop icons on plate layout for it.
Page 192 Results visualization 1. List View The list view column with results of concentration is divided into two sub-columns: dPCR reaction and undiluted sample (based on provided dilution information). When user enables the option to show the mean values for replicates, columns mean concentration and standard deviation (SD) are additionally presented and divided in similar manner.
Page 193 3. Concentration diagram On the concentration diagram, user needs to check the checkbox to display concentration for undiluted sample: Note: Results visualization works the same on for absolute quantification and all second- level analysis (Mutation Detection, Genome Expression, Copy Number Variation, and Gene Expression). Conversion factor From QIAcuity Software Suite version 2.5 onwards, there is possibility to convert concentration result by default given in copies per microliter, into another unit defined by the user.
Page 194 Conversion from copies/µL into cell equivalents: 2. The 16S rRNA gene has been detected in genomic DNA isolated from E. coli cells. The copy number of the 16S rRNA gene is 7 per one E. coli cell. The weight of one E. coli genome is approximately 5.1 fg. A total of 1000 copies of the target corresponds to (a) 729 fg of DNA and (b) to approximately 1423 cell equivalents.
Page 195 Results visualization 1. List View To display converted results on list view user needs to select wells for analysis exhibiting an identical conversion factor unit and enable checkbox ”Use conversion factor”. Otherwise, checkbox is disabled and following information is presented on tooltip: When all selected wells for analysis exhibit identical conversion unit, the converted result concentration is displayed in addition the default sample result concentration (copies/µL) When all parameters were filled correctly, Concentration column is divided in following way:...
Page 196 Note: Sample name and assigned reaction mix must be identical to enable the replication calculation option. 2. Heatmap To display converted result concentration, user needs to enable checkbox ”Use conversion factor”. Results are displayed in custom unit. In addition, the result presentation of both diluted and converted concentration results can be selected by use of ”Use sample dilution”...
Page 197 3. Concentration diagram On the concentration diagram, user needs to check the same checkbox to display converted concentration that also can be combined with dilution factor. Note: Results visualization for all second-level analysis (Mutation Detection, Genome Editing, Copy Number Variation and Gene Expression), works the same as for the Absolute Quantification.
Page 198: Absolute Quantification
7.6.14. Absolute quantification The Absolute Quantification tab is the first tab in the Analysis environment. After selecting the wells to be analyzed, you can view lists, signal maps, heatmaps, histograms, 1D scatterplots, 2D scatterplots, and concentration diagrams in this tab. The total number of copies of the target molecule in all valid partitions of a well is calculated by multiplying the copies of the target molecule per partition with the number of valid partitions.
Page 199 The CI range is equal to This range is used to determine how many digits of the result are significant. The result is based on detecting 4000 positive partitions out of 8000 total valid, the parameter is distributed with around a value and there is 95% certainty that the true value lays between .
Page 200 Replicates Replicates are analyzed as separate wells but in addition the mean concentration value and the CI value of the mean concentration are provided on demand. On the right side above the table there is a checkbox, which allows the user to show mean values for replicates in addition. By default, the button is unchecked and results are displayed without mean values.
Page 201 Standard deviation Coefficient of variation Coefficient of variance is a ratio of Standard deviation to Mean concentration for replicates, expressed in %: Setting up an absolute quantification analysis 1. Click the applicable wells in the plate layout. For more information, refer to “Selecting wells for analysis”. 2.
Page 202 3. To analyze the plate by targets, select the targets from the Select Targets list. You can select one or more targets from the list. To select all targets, click Select all. 4. Select Horizontal or Vertical wells results presentation. 5.
Page 203 List tab for absolute quantification The List tab contains a table with an overview of the analyzed wells. The following columns are available in the table: 1. Well ID – Like A1, B2, when gradient cycling was selected, there is also temperature in the well (temperature range instead of single one, if hyperwells were selected) 2.
Page 204 Note: Reaction mixes without advised custom cross talk matrix are marked with symbol in the list view. Furthermore, a dedicated information message is shown above the diagram. For more information refer to section “Custom cross talk matrix”. Export to CSV Besides displaying the table with results, there is additional option in List tab, to export results of analysis to CSV file that can be saved on hard drive.
Page 205 Current results If you want to export current results of analysis, follow the instruction below. 1. Select wells that you want to get results for. 2. Choose if you want to analyze per target or per channel by clicking the proper tab, and select targets or channels you are interested in.
Page 206 SD [ng/µL] (dPCR reaction) – converted standard deviation of concentration for replicates in dPCR reaction in custom unit SD [cp/µL] (undiluted sample) – calculated standard deviation of concentration for replicates in undiluted sample SD [ng/µL] (undiluted sample) – converted standard deviation of concentration for replicates in undiluted sample in user-defined unit CV% –...
Page 207 Plate name – name of the plate Plate ID – unique identifier of the plate Plate type – type of the plate Well – identifier of well Hyperwell – identifier of hyperwell if wells were grouped Reaction Mix name – name of reaction mix Sample name –...
Page 208 Conv. Undiluted Conc. Per group error – standard error of the Conv. Undiluted Conc. Per group % intact – % ratio of the concentration of target molecules for full positive group divided by concentration of all molecules from all groups % intact error –...
Page 209 Channel – first letter of channel on which picture was taken Cycled volume (µL) – well volume corrected by VPF Threshold – threshold value Partition – number by which a partition can be identified Is Invalid – code for invalidation reason (check mapping table code statuses, there can be a maximum three codes separated by a comma) Status Code...
Page 210 It is strongly recommended to check/adapt the column type for the result data to Decimal Number. Signalmap tab for absolute quantification The Signalmap tab provides positive partitions for target channels and valid partitions for the reference channel of selected wells. For each channel included in target or channel selection, one signal map view is created. The signal map views are sorted by channel position in imaging, separated by a horizontal line.
Page 211 Signal map for a target channel. On mouse-click, a modal window opens containing the well image providing following tool options on top of the right side. 1. Zoom In 2. Zoom out 3. Download signal map of this well as picture 4.
Page 212 Heatmap tab for absolute quantification The Heatmap tab shows the concentration of the selected targets or channels in each well. The values of all selected wells are also displayed in this tab. Values for disabled wells are not displayed. One heatmap view is created for each selected target or channel.
Page 213 The partitions view for heatmap of a selected target. To add any of the heatmaps to the report, click Add to report next to the relevant diagram. For more information on reports, see section “Reports”. Heatmap for hyperwells Histogram tab for absolute quantification The Histogram tab displays graphs that visualize the fluorescence values of selected wells for the selected target or channel.
Page 214 To view an additional toolbar that enables actions related to the diagram, such as downloading the plot, zoom, and pan, hold the pointer over the diagram. For more details about the toolbar, refer to section “Diagram options”. The Threshold field shows the threshold value of the fluorescence intensity that is used to distinguish between positive and negative calls.
Page 215 Thus, a 1D Scatterplot view has two axes. The x-axis represents the analyzed partitions, while the y-axis represents the relative fluorescence intensity of each partition. A 1D Scatterplot view concentrates the diagrams for each selected well in a horizontal way separated by a vertical line (column indicator).
Page 216 To open an individual plot, click on the appropriate header of the 1D Scatterplot. The user can change the range of the y-axis by adjusting the value in the field Max value for the y-‍ a xis (RFU) and clicking Save.
Page 217 Changing the threshold individually per well 1. To change the threshold individually per well, click on the appropriate header of the well in the 1D Scatterplot view. A window opens and the threshold can be changed by pointing over the chart, which triggers the appearance of a dotted line.
Page 218 Changing the thresholds for all selected wells (Common threshold) The 1D Scatterplot view provides an option to set a common threshold value for all associated wells, using the “Common threshold” input field. Click the Recalculate button to trigger the re-analysis of data. Use the Auto-threshold button to reset the threshold to the values, which is calculated by the analysis algorithm for each well.
Page 219 2D Scatterplot tab for absolute quantification The 2D Scatterplot tab shows a 2D Scatterplot view, that displays the fluorescence intensity from two selected channels or targets, allowing for a comparison and evaluation of the fluorescence from two sources. To create a 2D Scatterplot, assign targets or channels to the x-axis and y-axis using the drop-down menus. When two of the selected sources for analysis are assigned, the 2D Scatterplot view is displayed.
Page 220 Setting the common thresholds for all selected wells and each axis (channel) The 2D Scatterplot view provides an option to set a common threshold value for the x-axis and y-axis for all associated wells. There are two ways to change the threshold. The first one involves pointing to the chart, which triggers the appearance of two perpendicular dotted lines.
Page 221 Assigning partitions to a group using free hand (Polygon mode) The user can select Polygon partitions measurement dots with a free-hand mode, so that he can use a more precise way to assign partitions to the group they should belong to. The polygon selection is available in menu above the diagram on hover. 1.
Page 222 3. User need to create polygon by placing its vertex on by one, until polygon become the closed area. After placing each vertex, there is possibility to undo last move (remove last vertex) using icon or totally clear the polygon using icon.
Page 223 7. After pressing the Recalculate button, user gets the results – legend is filled with results. Polygon selection in 2D Scatterplot also affects histogram and 1D Scatterplots views. For details, refer to “Histogram tab for absolute quantification” and “1D Scatterplot tab for absolute quantification” sections. To adjust axis to ease drawing user can change values of X and Y axis using panel below the plot: To add the 2D scatterplot to the report, click Add to report.
Page 224 Each mini 2D Scatterplot tittle bar contains following information: Well ID Hyperwell ID (if wells has been grouped into hyperwell on source selection) Sample name (if assigned to well) detected reference channel (Std-Ref or HM-Ref) temperature in well (if gradient was applied) Each mini 2D Scatterplot can be enlarged by clicking the gray title bar with above information.
Page 225 2. Mode Samples In mode Samples user additionally selects Samples that will be presented: Note: If no samples are assigned to selected wells mode Samples will be inactive. After selecting samples, the overview of Custom analysis is divided into horizontal sections – each section represents replicates of particular Samples of one reaction mix.
Page 226 Any change, for example, threshold change introduced on mini 2D Scatterplot of particular sample, will affect grouped 2D Scatterplot of that sample and main 2D Scatterplot. Each individual mini plot can be enlarged by clicking gray bar, but here Replicate details window appears and user navigates between particular replicates (mini 2D Scatterplots from particular sections).
Page 227 Clicking on the bar enlarge the particular mini 2D Scatterplot. Hyperwell details is presented. This modal represents merged 2D Scatterplot of all wells being part of selected hyperwell – user operates on group of wells instead of single one. Concentration diagram tab for absolute quantification The Concentration Diagram tab shows the diagrams that display the distribution of concentration values and confidence intervals.
Page 228 Each diagram presents two values for each well – the concentration value, displayed as a bar, and the confidence interval, displayed as an error bar. To view the exact values, point to one of the bars. After a concentration diagram loads, the first 32 wells are shown in the diagram.
Page 229 Setting up a mutation detection analysis 1. Click the relevant wells in the Select wells pane. For more information, see “Selecting wells for analysis”. 2. Select the applicable wild-type target from the Wild type target list. 3. Select the applicable mutant target from the Mutant target list. 4.
Page 230 Note: Columns related to Concentration and Mean concentration can provide additionally sub-columns, depending if dilution factor and/or conversion factor (described in sections “Dilution calculation option” and “Conversion factor” accordingly) have been selected. 7. Mutation fraction – This column shows the Mutant fraction value in %. 8.
Page 231 Heatmap tab for mutation detection The Heatmap tab contains a heatmap that shows the mutant fraction as percentage in each of the wells. If a well is not selected as a source for the analysis, the value is not displayed on the heatmap and its background color is gray. To view detailed information about a well, point the cursor over the well.
Page 232 The y-axis scale can be modified from linear to logarithmic scale using the buttons located on the left below the diagram. The buttons are visible when you hold the pointer over a graph. To view the values on a linear scale, click lin. To view the values on a logarithmic scale, click log10.
Page 233 replicates within selected wells for mutant target the bars do not change. The corresponding well IDs of the replicates are shown on the x-axis. This is also applied in same way by default to the view where targets are in different reaction mixes. In this case individual replicate results are not available. Mean values are calculated and shown over all replicates that are included in the well selection only.
Page 234 2. Select the applicable wild-type target from the Wild type target list. 3. Select the applicable edited target from the Edited target list. 4. To view the results of the analysis, click Show results. 5. The results are divided into several tabs. To view the contents of the tab, click the tab title. List tab for genome editing The List tab contains a table with an overview of the analyzed wells.
Page 235 Replicates are treated different for multiplex and simplex test setup: 1. Multiplex test (configured wildtype and edited targets are part of the same reaction mix): a. Replicates are analyzed as separate wells but in addition the mean concentration and mean edited fraction values together with the corresponding mean CI are provided on demand.
Page 236 To add the heatmap to the report, click Add to report. For more information on reports, see section “Reports”. Point diagram tab for genome editing The Point diagram tab shows a diagram that displays the percentage of edited fractions in each analyzed well. A point diagram has two axes.
Page 237 To add the point diagram to the report, click Add to report. For more information on reports, see section “Reports”. Concentration diagram tab for genome editing The Concentration diagram tab shows a diagram that displays the distribution of concentration values in the wells together with their confidence intervals A concentration diagram has two axes.
Page 238 To add the Concentration diagram to the report, click Add to report. For more information on reports, see section “Reports”. 7.6.17. Copy number variation The Copy number variation tab contains diagrams that visualize the data related to copied genes in targets of interest comparing to reference targets or reference sample.
Page 239 Setting up a copy number variation analysis with reference sample 1. Click the applicable wells in the plate layout. For more information, see section “Selecting wells for analysis”. 2. Select the applicable reference sample from the Reference sample list. 3. Enter the number of copies per genome in the “Copies/genome” field for the target of interest in reference sample. The value should be between 1 and 99.
Page 240 Note: Targets that were selected as target of interest (TOI) or reference target (Ref) are marked accordingly depending if you selected CNV with reference target or sample. 6. CI (95%) – This column shows the value of the confidence interval at a 95% confidence level. a.
Page 241 indicating following mean values: Mean conc. [copies/µL] – mean concentration value CI (95%) – CI of mean concentration as percentage Mean copies/genome CI (95%) – CI of mean mutation fraction as percentage 2. Simplex test (configured target of interest and reference targets are part of different reaction mixes): 3.
Page 242 To add the heatmap to the report, click Add to report. For more information on reports, see section “Reports”. Point diagram tab for copy number variation The Point diagram tab shows the diagram that displays the number of copies per genome of the configured copy number variation test and the confidence intervals related to every value.
Page 243 Note: If the selected analysis source contains replicates of the reference sample, your results can be calculated only by using mean results for replicates. In this case the “Show mean values for replicates” checkbox is marked and cannot be changed. In this case there is a warning message above the diagram title and when the user hover on the checkbox, a tooltip appears to inform the user that selected analysis source contains replicates of the reference sample and result is calculated only by using mean results for replicates.
Page 244 The Bar size is fixed if: 1. The reference targets and target of interests are situated on one well there is one well label for all that belongs to the same well. 2. The reference targets and target of interests are situated on two wells or more wells there are one well label per targets that are within this well.
Page 245 7.6.18. Gene expression The Software Suite analyzes the gene expression of the samples. The analysis results are put into list views, heatmaps, point diagrams, and concentration diagrams. Note: Saving gene expression tests is not yet provided. Setting up a gene expression analysis 1.
Page 246 a. When checkbox “Show mean values for replicates” is checked additionally two columns are displayed: Mean conc. [copies/µL] – This column shows the mean concentration assigned to each target or channel per well for replicates. CI (95%) – This column shows the value of the confidence interval at a 95% confidence level for the mean concentration.
Page 247 Mean conc. [copies/µL] – mean concentration value CI (95%) – CI of mean concentration as percentage Mean fold change CI (95%) – CI of mean fold change as percentage Mean fold regulation Note: If the selected analysis source contains replicates of the reference sample, your results can be calculated only by using mean results for replicates.
Page 248 Point diagram for gene expression The Point diagram tab shows a point diagram view that displays the fold change values of configured gene expression test and the confidence intervals related to every value. A point diagram has two axes. The x-axis shows the analyzed wells and samples, and the y-axis represents the fold change.
Page 249 To add any of the point diagrams to the report, click Add to report next to the corresponding diagram. For more information on reports, see section “Reports”. Concentration diagram for gene expression The concentration diagram tab shows the diagram that displays the concentration values of the configured gene expression test and the confidence intervals related to every value.
Page 250 The bar size is fixed if: 1. The reference targets and target of interests are situated on one well there is one well label for all that belongs to the same well. 2. The reference targets and target of interests are situated on two wells or more wells there are one well label per targets that are within this well.
Page 251: Reports
7.7. Reports In the QIAcuity Software Suite, you can create reports about your analysis results of a plate. All created reports remain accessible in the Software Suite and can be downloaded. Only unsigned reports can be deleted. 7.7.1. Creating a new report for a plate from the analysis environment To create a new report from your analysis results, follow these steps: 1.
Page 252 3. To remove the pre-selection of diagram, clear the Add to report box. 4. Click on the arrow icon next to the number of selected graphs in the footer to open a preview window of all your preselected diagrams and use the icon to delete a diagram from the list of your diagrams to be included in the report.
Page 253 Table 15. Report elements Element Description Report name Every Report needs a specific name, without special characters ~ ‘ “ ! @ ^( ) = [ ] { } : ; , < > | \ . Run details Author, Start and end time, Run steps, Run status, Software & Instrument version Plate general data Plate name, type, description, plate owners, labels, barcode Plate layout...
Page 254 7.7.2. Managing reports of a plate in the report environment The report environment of a plate provides an overview of all created reports for this plate. You can use this environment to manage your created reports. To enter the report environment of a plate, go to the plate tile in the plates overview. Click the three-dotted icon, then click Reports.
Page 255 7.7.3. Sign report To support GMP/GLP requirements, the QIAcuity system provides an option to electronically sign existing reports. To do so, the user has to follow the steps given below. 1. Go to report list view. 2. Select the Add signature button. 3.
Page 256 If wrong password will be typed user will be presented with following information: After three incorrect attempts in adding password, user will be automatically logged out and a corresponding event is tracked in the audit trail. 1. When the report is signed, an appropriate message will be presented on the report list and the Add signature button will be disabled.
Page 257 d. Reason (of signing) Moreover, during PDF export of the signed report, an additional page with information about signers (same as the list above) is added at the end of the document: name and surname [login name], role, and date of signature. QIAcuity User Manual | 09/2024...
Page 258 7.7.4. Run details in report On first page of report in section Run details all information about particular run steps are listed in table: Where Instrument ID is the name if Instrument connected to Software Suite: QIAcuity User Manual | 09/2024...
Page 259 While some plate general data are now presented on second page of the report: Note: For plates from older Software Suite versions, information in columns: Software Suite version, Instrument ID, CSW version are not available – only run steps and date and time are presented: QIAcuity User Manual | 09/2024...
Page 260: Archive
7.8. Archive In the QIAcuity Software Suite, you can set up an archive on an external drive. This will allow you to store your old plates and save disk space on the laptop. Only the user with Administrator role can set up an archive; to do so, go to Configuration and select the Archive tab: When Add archive is clicked, the user can provide a path to the external drive and click Save.
Page 261 Configuring network drive as archive User can set network as archive location. It is required to make several changes in operating system first: 1. On the PC where the archive folder will be stored, right-click on the shared folder and go to Properties, then go to Sharing tab and update in following way: It is required to create new user and add it to permissions.
Page 262 b. Press Add. In the new popup window, enter the Windows User that will be used to run the Software Suite and click Check names to make sure the name is correct and then press OK. c. Back in the “Security” window, check “Full control” permission for the added user and press OK. QIAcuity User Manual | 09/2024...
Page 263 d. Open the “Services” application: press the windows key, type “Services” and press ”Enter” key. Locate “QIAcuitySuite Service”, right click, and choose Properties: e. In the new window, go to Log On tab and click on Browse button: QIAcuity User Manual | 09/2024...
Page 264 f. In the new pop-up window, select the same user as in step 2b, click Check names and click OK. Provide password and confirm password in the inputs and click OK. g. Restart the service, by right clicking on the QIAcuity Software Suite service in the Services window and click Restart (if the services window is not present, press CTRL + SHIFT + ESC on the keyboard).
Page 265 3. On the QIAcuity Software Suite server machine (where Software Suite is installed), press the windows button on keyboard, type credential manager and press enter. In the newly opened window, choose Windows Credentials and click Add a Windows Credential. 4. In the newly opened window, provide server UNC (Universal Naming Convection) address and reuse credentials user name and password given above.
Page 266 7.8.1. Automatic archiving When the archive is set up, the administrator can turn on automatic plate archiving. It will automatically move plates older than selected time duration to the archive. The default value is 6 months. When automatic archiving is turned on, suitable information is displayed on the Archive Configuration screen.
Page 267 7.8.3. Bulk plate archiving From Software Suite version 2.5 onwards, there is possibility to bulk archive plates. To bulk archive plates, user needs to select plates: 1. One by one, using checkboxes in upper left corner of each plate: 2. Using checkbox “Select all plates” selects all plates on plate overview and then adjust selection using checkboxes on plates: 3.
Page 268 7.8.4. Archive and recovering a plate from the archive You can browse and search plates in the archive. Go to Archive on the navigation bar. You can then see all your archived plates. On plate tile there is option to check who (user login) archived the plate: To restore plates from the archive, go to the Archive screen and click on the three dots (…) on any of the plates on the Archive screen and select Restore.
Page 269: Audit Trail
User should confirm decision on pop-up and restoring process will start, what will be indicated with blue pulse indicator: Note: All imported and restored plates will automatically receive the VPF assignment, if a VPF is loaded in the system. 7.9. Audit trail The Audit trail is a functionality in the QIAcuity Software Suite, which supports users meeting Good Manufacturing Practice (GMP)/Good Laboratory (GLP) regulations.
Page 270 7.9.1. Audit trail tracker settings 1. To turn the Audit trail tracker ON/OFF, on the main toolbar, click the Configuration tab. 2. On the left-hand side, you can see the tabs menu. Click on the Audit Trail tab. On the center of the page is the second tabs menu panel, click the Audit trail tracker settings tab.
Page 271 7.9.2. Events List Events list table The events list shows all events (logs) that happened in the system. There is no possibility to remove an event from the system by the User or Administrator. To display the Events list, on the main toolbar, click the Configuration tab. From the left-hand side menu, you can see the tabs menu.
Page 272 7.9.3. Search Search for Instrument ID, affected Plate ID, user login, and role name You can search for Instrument ID number, affected Plate ID, affected user login, or affected role name. Click on the search field: “Search for”. Input your query. After a few seconds, the records on the events list will be updated automatically (example of Plate ID number: b0bd01c1-0c6d-4377-b030-677f12711831, example of instrument ID number: QIAcuity-00617).
Page 273 Filter: Category You need to use the “Category” filter to check all data related to one specific category (Instrument, Suite, or Plate). Category refers to device/tool: Instrument, Suite (PC Software), or Plate, on which the action has been taken. 1. Instrument – all events related to the instrument 2.
Page 274 Filter: Event type Event type refers to the action that happened in the system on the Instrument, Suite (PC software), or Plate. If you do not choose any option from the category, the filter displays a list of all event types (a sum of events type from all the three categories).
Page 275 Filter: Initiated by The filter “Initiated by” is related to a person (search for user login) that performed actions in the system. Login is unique and cannot be duplicated, so filtering for it will provide the user specific results. This filter allows you to even search for multiple users. 7.9.5.
Page 276 The check details option allows you to see all detailed changes that happened in the system. Changes are displayed as a table. Tracked differences in detailed audit trail events For the following event types, the difference between existing and newly changed parameters (old to new value) is supported: ...
Page 277 To see the difference, user has to go to the “check details” page of the given Audit Trail event. 1. Created — This section contains all the information that was newly added and was not previously present in the event. 2.
Page 278 3. Deleted — This section contains all information that was previously available but was removed from the entity. 7.9.6. AT part of plate From QIAcuity Software Suite version 2.5 onwards, all dedicated plate-related audit trail events became part of the plate and are preserved during plate archiving and exporting.
Page 279 After clicking on Plate Audit Trail, you are automatically redirected to the audit trail environment and plate dedicated events are filtered by plate ID. To check the plate-related audit trail events from a plate originated in another Software Suite instance, click check details in one of the following events: Import plate or Restore plate.
Page 280 7.9.7. Exporting to PDF All event details can be exported to a PDF file. Note: Depending on the data throughput, the audit trail PDF export of all existing entries can take several minutes. Therefore, it is recommended to filter for the desired events first and then performing a PDF report export. 1.
Page 281: Entering Data
7.10. General software use 7.10.1. Entering data These shortcut functions are available in QIAcuity Software Suite: Table 17. Shortcut functions in QIAcuity Software Suite Shortcut Function Ctrl + C Copy Ctrl + V Paste Tab and arrow keys Navigate from one field to another 7.10.2.
Page 282: Warning Message
7.10.4. Warning message A warning message is displayed in yellow in case further optimization of the experimental setup is recommended. A user interaction is not required to proceed with this step. 7.10.5. Information message At certain fields in the experiment, you can view additional information regarding the required data to be entered on a field. Fields with information messages are marked with icon.
Page 283: Maintenance Procedures
8. Maintenance Procedures WARNING/ Risk of personal injury and material damage CAUTION Only perform maintenance that is specifically described in this user manual. The following maintenance procedures must be carried out to ensure reliable operation of the QIAcuity: 1. Regular maintenance 2.
Page 284 Removal of RNase contamination ® RnaseZap RNase Decontamination Solution (Ambion, Inc., cat. no AM9780) can be used for cleaning surfaces. RnaseZap can also be used to perform decontamination by spraying the respective items. Removal of nucleic acid contamination DNA-ExitusPlus™ (AppliChem, cat. no. A7089,0100) can be used for cleaning surfaces. DNA-ExitusPlus can also be used to perform decontamination by spraying the respective items.
Page 285: Servicing
WARNING Toxic fumes Do not use bleach to disinfect used labware. 8.2. Servicing Contact QIAGEN Technical Services or your local distributor for more information about flexible Service Support Agreements from QIAGEN. WARNING/ Risk of personal injury and material damage CAUTION Improper use of the QIAcuity may cause personal injuries or damage to the instrument.
Page 286: Periodic Maintenance
8.4. Periodic maintenance 8.4.1. Air filter change We recommend that you change the air inlet filter of the instrument once per year. This will be part of an annual scheduled service visit. When operating the instrument in unusual dusty environments, a more frequent filter change might be necessary. Note: Air filters can be ordered separately.
Page 287: Decontaminating The Qiacuity
QIAcuity, the user is responsible for carrying out appropriate decontamination. If damaged plates were used and the inside of the instrument is contaminated, contact QIAGEN Technical Services. The QIAcuity should also be decontaminated before shipping (e.g., back to QIAcuity). In this case, a decontamination certificate must be completed to confirm that the decontamination procedure has been carried out.
Page 288 1. Tap the Tools icon. 2. Tap Data Management. 3. To clear the data, tap Force clear images. Click OK in the confirmation dialog box to delete the data. Images from the system and database will be removed. QIAcuity User Manual | 09/2024...
Page 289: Regular Maintenance Procedure For Qiacuity Software Suite
8.7. Regular maintenance procedure for QIAcuity Software Suite To monitor the space of your disk, click Disk monitor in the main toolbar. This shows an overview about the state of the disk, disk name, and disk path. It also shows the remaining free space and total space of your disk. Disk monitor overview.
Page 290: Troubleshooting
4. Serial number of the instrument This information will help you and your QIAGEN Technical Service Specialist to deal most efficiently with your issue. Note: For most cases, to allow proper analysis of an error situation, the support package either from the instrument and/or the Software Suite is required.
Page 291 To start a self-check, follow these steps: 1. Tap Tools 2. Tap Self-check. 3. Tap Quick Test or Extended Test depending on the type of test you want to perform. 4. The instrument starts the test. The ongoing actions and their statuses are shown in the Log File Preview pane. The log from the test can be downloaded as part of a support package.
Page 292: Creating A Support Package With The Qiacuity Instrument Software
9.4. Creating a support package with the QIAcuity instrument software You can create a support package in case of an error. The support package can be uploaded to the Software Suite or saved to a USB drive. To create a support package and upload it to the Software Suite, follow the steps below. The QIAcuity Software Suite will combine the support package from the instrument and the Software Suite.
Page 293 6. Tap Apply to save the changes. Set Support Package Timeframe dialog box. 7. Tap Create & Download. 8. A progress bar is shown. To cancel the download, tap the progress bar. Once the download is complete, a notification is displayed.
Page 294 3. Connect a USB drive to the instrument. Wait for the device to detect the USB drive. A notification is displayed once the drive is connected. 4. In the Support Package pane, select Download to USB drive. 5. To set the timeframe of the support package, tap Set timeframe .
Page 295: Software Support Package
9.5. Software support package Since version 2.5, QIAcuity Software Suite offers possibility to automatically generate Software support package that can automatically collect required logs from Software Suite and Instrument as well. Software support package can be generated in following scenarios: 1.
Page 296 1. On above window, user should select package type: a. Software Suite package — all available logs for the Software Suite will be automatically collected b. Software Suite and Instrument — all available logs for the Software Suite and logs for connected instrument will be automatically collected: Note: User needs to trigger collecting and sending logs to the Software Suite on instrument first according following screenshot:...
Page 297 User needs to point the Instrument from which logs should be collected by selecting it from instrument drop-down list shown on window below: 2. User needs to select appropriate time period using one of: a. Time frame buttons b. From/To selectors 3.
Page 298 9.5.3. Problem during the Software Suite runtime When there is a problem during application runtime, user can navigate to Tools on top bar and then click Generate software support package button from Troubleshooting menu: After clicking the above button, a similar window as described in previous sections will be presented and user needs to follow the same procedure.
Page 299: Creating A Support Package With The Qiacuity Software Suite
9.6. Creating a support package with the QIAcuity Software Suite 1. Select a plate in the plates overview. 2. Click the left side of the screen on Support Package. A new window pops up, where you can specify what kind of support package you want to generate and from which time frame.
Page 300: Troubleshooting The Instrument And Software
A missing Plate Seal is detected by the instrument. Ensure that always a closed plate with Plate Seal is loaded into the Plate Seal presence instrument. A run cannot be started if a plate seal is not detected by the instrument. Only use QIAGEN products for closing the plates.
Page 301 Poor or no amplification Check if correct restriction enzyme was used when using gDNA as template material. Check the starting quality and quantity of the template. We recommend that you use QIAGEN kits for sample preparation. Check if the correct protocols and reagents have been used.
Page 302: Accessing The System Status And Clearing Errors
This error occurs when the data received from the instrument does not conform to the expected pattern. Communication error between QIAcuity instrument Further investigations are required by a QIAGEN Field Service Specialist to diagnose the problem with the instrument. and software Contact your distributor or QIAGEN Technical Service.
Page 303 QIAcuity One, the More details button is located in the Tray pane. 6. Restart the instrument. The instrument initializes and all modules are returned to their home positions. Note: If the affected module is not working after you cleared the error and restarted the instrument, contact QIAGEN Technical Services.
Page 304: Technical Specifications
10. Technical Specifications QIAGEN reserves the right to change specifications at any time. 10.1. Operating conditions 100–240 V AC, 50/60 Hz, Mains supply voltage fluctuations are not to exceed 10% of nominal supply Power voltages. Maximum power consumption: QIAcuity One, 2plex: 1000 VA...
Page 305: Mechanical Data And Hardware Features
10.4. Mechanical data and hardware features Width: 60 cm (23.6 in.) Dimensions Four/Eight Height: 58 cm (22.8 in.) Depth: 65 cm (25.6 in.) Width: 38 cm (15.0 in.) Dimensions Height: 45 cm (17.7 in.) Depth: 65 cm (25.6 in.) QIAcuity One: 36.0 kg (79.4 lb.) Mass QIAcuity Four: 43.0 kg (94.8 lb.) QIAcuity Eight: 55.0 kg (121.3 lb.)
Page 306: Glossary
Separation of the single partitions filled with the reaction volume Support Package Information wrapped up in a *.zip file to be sent via an email program to QIAGEN Technical Services to inform QIAGEN what went wrong at the customer's site and how to help the customer...
Page 307: Declaration Of Conformity
Recycling can be provided by QIAGEN upon request at additional cost. In the European Union, in accordance with the specific WEEE recycling requirements and where a replacement product is being supplied by QIAGEN, free recycling of its WEEE-marked electronic equipment is provided.
Page 308: California Proposition
Liability Clause QIAGEN shall be released from all obligations under its warranty in the event repairs or modifications are made by persons other than its own personnel, except in cases where the Company has given its written consent to perform such repairs or modifications.
Page 309 Table 20. Marking for the restricted use of hazardous substances in electronic and electrical products (SJ/T 11364-2014) (continued) Toxic or Hazardous Substances and Element 有毒或有害的物质成分 Polybrominated Hexavalent Polybrominated diphenyl ethers Part Name Lead (Pb) Mercury (Hg) Cadmium (Cd)
Page 310: Appendix B - Qiacuity Accessories
QIAcuity, IQ/OQ product 9245414 manufacturer’s specifications. IQ/OQ Service is an on-site qualification service provided by a certified QIAGEN Service Specialist. This includes labor and travel Separate 2D barcode scanner for reading of QIAcuity Barcode Hand Scanner, QIAcuity...
Page 311 For up-to-date licensing information and product-specific disclaimers, see the respective QIAGEN kit handbook or user manual. QIAGEN kit handbooks and user manuals are available at www.qiagen.com or can be requested from QIAGEN Technical Services or your local distributor.
Page 312: Appendix C - Informations De Sécurité
Le QIAcuity ne doit être utilisé que par du personnel qualifié ayant été convenablement formé. L’entretien du QIAcuity ne doit être effectué que par un spécialiste de l’entretien sur site QIAGEN. Procéder à la maintenance comme décrit dans la section Procédures de maintenance. QIAGEN facture les réparations dues à...
Page 313: Sécurité Électrique
AVERTISSEMENT Risque d’explosion Le QIAcuity est conçu pour être utilisé avec les réactifs et les substances fournis avec les kits QIAGEN ou autrement que de la façon décrite dans le mode d’emploi correspondant. L’utilisation d’autres réactifs et d’autres substances peut provoquer un incendie ou une explosion.
Page 314: Conditions De Fonctionnement
4. Si un liquide s’est répandu à l’intérieur de l’appareil, l’éteindre, le déconnecter de la prise secteusr et prendre contact avec les services techniques de QIAGEN. Si l’appareil présente un danger électrique, empêcher le reste du personnel de s’en servir et contacter les services techniques de QIAGEN.
Page 315: Sécurité Biologique
Sécurité biologique Les prélèvements et les réactifs contenant des matières provenant d’êtres humains doivent être considérés comme potentiellement infectieux. Utiliser des procédures de laboratoire sûres, comme décrites dans des publications telles que Biosafety in Microbiological and Biomedical Laboratories, HHS (www.cdc.gov/labs/BMBL.html). 11.0.1.
Page 316: Sécurité De Maintenance
Sécurité de maintenance AVERTISSEMENT/ Risque de dommages corporels et matériels ATTENTION Effectuer uniquement la maintenance qui est décrite spécifiquement dans le présent manuel d’utilisation. AVERTISSEMENT Risque d’incendie Ne pas laisser le liquide de nettoyage ou les agents de décontamination entrer en contact avec les Pièce électriques du QIAcuity.
Page 317: Symboles Sur Le Qiacuity
Symboles sur le QIAcuity Symbole Emplacement Description Plaque signalétique à l’arrière de l’appareil Marquage CE pour la conformité européenne Plaque signalétique à l’arrière de l’appareil Marquage UKCA pour la conformité UK Plaque signalétique à l’arrière de l’appareil Label CSA pour le Canada et les États-Unis Plaque signalétique à...
Page 318: Appendix D - Sicherheitshinweise
Die Instandhaltung des QIAcuity darf nur durch einen Service-Spezialisten des QIAGEN Außendienstes durchgeführt werden. Führen Sie alle Wartungsarbeiten gemäß den Anweisungen im Abschnitt Wartungsarbeiten dieses Handbuchs durch. QIAGEN stellt Reparaturen, die auf nicht fachgerecht durchgeführte Wartungsmaßnahmen zurückzuführen sind, in Rechnung. WARNUNG Gefahr von Personen- und Sachschäden...
Page 319: Schutz Vor Stromschlag
Lassen Sie keine Gegenstände in das Gerät fallen, wenn das Plattentablett ausgeworfen wird. WARNUNG Explosionsgefahr Der QIAcuity darf ausschließlich mit Reagenzien und Substanzen aus den QIAGEN Kits bzw. gemäß den Angaben in der entsprechenden Gebrauchsanweisung verwendet werden. Die Verwendung anderer Reagenzien und Substanzen kann zu einem Brand oder zu einer Explosion führen.
Page 320 4. Falls Flüssigkeit auf dem Gerät verschüttet wird und hineinläuft, schalten Sie es sofort AUS, ziehen Sie den Netzstecker und setzen Sie sich mit dem Technischen Service von QIAGEN in Verbindung. Falls die elektrische Sicherheit bei der Bedienung des Geräts nicht mehr gewährleistet werden kann, muss das Gerät gegen Benutzung durch darüber nicht informiertes Personal gesichert werden.
Page 321 Umgebung Betriebsbedingungen WARNUNG Explosive Atmosphäre Der QIAcuity ist nicht für den Gebrauch in explosionsfähiger Atmosphäre vorgesehen. VORSICHT Beschädigung des Geräts Direktes Sonnenlicht kann zum Ausbleichen von Teilen des Geräts führen und Schäden an Kunststoffteilen verursachen. Der QIAcuity muss an einem Ort aufgestellt werden, an dem er vor direkter Sonneneinstrahlung geschützt ist.
Page 322: Biologische Sicherheit
Biologische Sicherheit Bei Substanzen und Reagenzien, die humanes Untersuchungsmaterial enthalten, sollte immer von einer möglichen Infektionsgefahr ausgegangen werden. Wenden Sie nur sichere Laborverfahren an, wie sie z. B. in Veröffentlichungen wie Biosafety in Microbiological and Biomedical Laboratories HHS, (www.cdc.gov/labs/BMBL.html) beschrieben sind. Proben Proben können infektiöse Erreger enthalten.
Page 323 Wartungssicherheit WARNUNG/ Gefahr von Personen- und Sachschäden VORSICHT Es dürfen nur Wartungsarbeiten ausgeführt werden, die in diesem Benutzerhandbuch konkret beschrieben sind. WARNUNG Brandgefahr Achten Sie darauf, dass keine Reinigungsflüssigkeiten oder Dekontaminationsmittel in Kontakt mit den elektrischen Bauteilen des QIAcuity kommen. VORSICHT Beschädigung des Geräts Verwenden Sie keine Bleichmittel, Lösungsmittel oder Reagenzien, die Säuren, Laugen oder Abrasivstoffe enthalten, um den QIAcuity zu reinigen.
Page 324 Symbole auf dem QIAcuity Symbol Beschreibung Typenschild an der Geräterückseite CE-Markierung der EU-Konformität Typenschild an der Geräterückseite UKCA-Markierung der UK-Konformität Typenschild an der Geräterückseite Symbol der CSA-Zertifizierung in Kanada und den USA Typenschild an der Geräterückseite RCM-Zeichen für Australien und Neuseeland Typenschild an der Geräterückseite Markierung gemäß...
Page 325 Appendix E – User Management Permissions The table below shows all available permissions for the user management including short descriptions and technical names. These technical names are shown in audit trail details in case a user has made changes to any users or roles. Permission Technical name Description...
Page 326 Permission Technical name Description Other permissions Import Plate SUITE_PLATE_OTHER_IMPORT User can import the Plate as a ZIP file. Export Plate SUITE_PLATE_OTHER_EXPORT User can export the Plate as a password protected ZIP file. Unlock Plate SUITE_PLATE_OTHER_UNLOCK User can unlock locked Plate. Set Plate Ownership SUITE_PLATE_OTHER_SETPLATEOWNERSHIP User can set owners of the plate.
Page 327 Permission Technical name Description View Audit Trail SUITE_AUDITTRAIL_READ User can see the list of Audit Trail events, search for specific event, check details of the event and export it to PDF. Audit Trail Toggle SUITE_AUDITTRAIL_TURNONOFF User can turn on/off the Audit Trail (events tracker). QIAcuity User Manual | 09/2024...
Page 328: Document Revision History
Document Revision History Revision Description September 2024 Manual content adjusted to Software Release 3.0 October 2023 Manual content adjusted to Software Release 2.5 May 2023 Added description and formulas of new features such as standard deviation and coefficient of variance of mean concentration into various sections.
Page 329 Trademarks: QIAGEN ® , Sample to Insight ® , QIAcuity ® , QIAgility ® (QIAGEN Group); RNaseZap ® (Ambion, Inc.); DNA- ExitusPlus™ (AppliChem); EvaGreen ® (Biotium, Inc.); Cy ® (GE Healthcare); Alexa Fluor ® (Life Technologies Corporation); Windows ® (Microsoft Corporation); Texas Red ® (Molecular Probes, Inc.);...
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Page 332 Ordering www.qiagen.com/shop | Technical Support support.qiagen.com | Website www.qiagen.com...

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