Ziath Scanner setup - LabCollector

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Ziath Scanner setup

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SUMMARY:

LabCollector offers integration of rack scanners to increase the automation process in labs thereby reducing data entry errors. LabCollector scanserver uses TCP/IP server that can send results over local/remote networks. Thus, data can be imported from rack scanners & a file can be generated that is then integrated into LabCollector LIMS. Our add-ons like tube sorter can work hand-in-hand with rack scanners to ensure automated efficient sample tracking.

Scanners always work with their own software. Ziath rack scanners work with DataPaq™ software.

However, AgileBio’s ScanServer allows for the conversion of scan results into a rack/tray map file comprehensible by LabCollector using Samples Batch Tools add-on.

To set up the scan server follow the below steps:-

1. AgileBio ScanServer Installation & LabCollector set up

2. Ziath scanner setup & configuration

  • Configure AgileBio Scan Server with Ziath

3. Scanning the Racks

1. AgileBio ScanServer installation & LabCollector set up

  • LabCollector offers integration of rack scanners to increase the automation process in labs thereby reducing data entry errors.
  • LabCollector scan server uses TCP/IP server that can send results over local/remote networks.
  • Please read further our KB to know how to setup Scanserver with LabCollector Batch generator (Rack Scanner).

2. Ziath scanner setup & configuration

  • For the Ziath scanner, you can read its manual which comes with the scanner or you can find it here.
  • Download and install the appropriate driver before connecting the scanner and installing the DataPaq™ software.
    * The DataPaq software decodes 2D barcodes using an algorithm by Ziath. DataPaq™ displays the results of the scan and can identify the difference between a correctly scanned tube (green), a damaged tube (red), and a missing tube (grey). Also, any tube image can be clicked on and the individual scan is shown (on the right-hand side) with the tube location and barcode.
  • Connect the scanner to the computer and switch on using the button at the back.
  • Install DataPaq™.
  • Configure your scanner in DataPaq™, and note the unique ID used for remote interaction (Image source: Ziath).
  • For DataPaq™ v3.15 or later, in order to activate remote communication, you should run the file “C:\Program Files (x86)\Ziath\DataPaq\server.exe” -s inside the installation folder. A black command prompt window in which you should keep it open like the below image.
  • The server can be started up using the server mode. (Read the manual which comes with the scanner or you can find it here or read this PDF)
  • The server mode starts DataPaq and listens on a specified port for incoming commands. You can confirm the scan like below.
  • 1. The DataPaq™ installation will create a shortcut icon on the desktop as shown in the image. You need to first start the server by clicking the icon.
    – Once the server is on you need to scan the server.
    – NOTE: Shortcut of Server is referring to “Server.exe” file inside DataPaq™ installation folder with this command: “[install folder]\server.exe” -s
  • 2. Click on the start in Scan Server by AgileBio.
    – Use the LabCollector page for scanning.

  • Configure AgileBio Scan Server with Ziath

    • Under the AgileBio Scan Server, click on the Options.

       

    • When you click on the OPTIONS the below box will pop-up.
    • 1. The server port is the same as in section 2 (Port 5151).
    • 2. Check the box Autostart if you want to start scanning using Batch generator (Rack Scanner) tool.
    • Click on the ZIATH option in the AgileBio scanner and you will see the below options.
    • 3. In the Ziath section, the IP address, scanner port, and notification port are by default.
    • 4. You have to choose the unique ID corresponding to your rack that you define in DataPaq™ (see just above) from the list.

    • NOTE: Check your firewall about the Ports security.
    • Now, you are ready to scan your rack!
      NOTE: Tracxer software needs to be open in the background.

3. Scanning the Racks

  • Start your scanner and open AgileBio ScanServer (DataPaq™ will be open in the background)
    NOTE: Be aware that Ziath scanners usually have an automatic sleeping mode which can be removed. If the scanner is sleeping, it will not react to scan requests.



  • Start the AgileBio Scan Server process.
  • In the LabCollector go to TOOLS -> Batch generator (Rack Scanner) tool. Below the Batch generator options are explained in detail.

  • A. 1. Direct Scanner trigger input

    • This tool allows direct imports of scanned well rack/trays from several manufacturers (Micronic, BioMicroLab, FluidX, Thermo, Ziath, Biotillion…). 
    • The scanner generates a rack/tray map file that is loaded into LabCollector.
    • This accelerates sample registration with direct storage definition.
    • LabCollector recognizes scanner file formats automatically.

    • 1. Choose the rack that you set up in LabCollector from the list,
    • 2. Then click on Scan! button, the rack/box map preview will appear.
    • NOTE: JAVA has to be updated to allow the Scan! button to be active.
    • NOTE: If you have problems after the Process step, such as the list of positions not loading fully, please ensure that your php.ini file has a sufficient memory limit. The php.ini file can be found via the LabCollector -> Server Manager -> Configure Servers -> PHP Search for “memory_limit” in this file and increase the figure as needed e.g. 512M. Check the KB for more information on LabCollector server manager.

  • B. 2. Scanner Output or File Import

    • This mode allows you to import a file produced by a rack scanner and you can choose the correct format of the file.

    • 3. Here you can select the output file for the rack scanner.
    • 4. You can choose the file format from the options if you want the position, RackID, tube code, etc.

  • C. 3. Generic

    • The External Data Source part can be used together with the Direct scanner trigger mode if you want to import additional information about the samples at the same time.

    • 5. You can do generic settings like rack or box (which rows and columns) you don’t want to scan.
    • 6. You can choose the options depending upon if it’s a storage box or microplate.
    • 7. Here you can choose to automatically name the record.
      – You can assign an automatic name or add a prefix and suffix according to your requirement.

  • D. Processing options.

    • 8. Processing options allow you to process the box or plate by either forcing the specific position by row and column or labels.
    • 9. You can choose a field separator that you want in your CSV.
    • 10. If you want to add and merge more data together with scanned vials you can choose the format of the CSV.
    • 11. You can choose the file that you want to upload.

  • E. Rack origin and template

    • 12. Based on the template [choose a template to apply].
      NOTE: You can create this template by going to ADMIN -> SETUP -> RACK SCANNERS. Check section 2 of this linked KB.
    • 13. You can choose if you want to create a new tube/rack existing rack with a direct barcode read.
    • 14. This option allows you to choose the existing tube rack, enter the rack ID/barcode corresponding, which is already in LabCollector.
    • 15. Here you can replicate the existing rack, select tube rack/box in the list. In this case, the box will be saved as secondary storage of existing samples.
    • 16. This option allows you to derive to a new record from the existing rack.
    • 17. Here you can select the master tube or rack from the below options.
      NOTE: You can create the storage by going to ADMIN -> STORAGE -> MANAGE STORAGE. Check this linked KB.
    • 18. Once you have entered all the details you can click on process.

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