VisionMate Thermoscientific scanner set up - LabCollector

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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. Thermoscientific rack scanners work with Vision Mate™ software.

However, AgileBio’s ScanServer allows for the conversion of scan results into a rack/tray map file comprehensible by LabCollector using Batch generator (Rack Scanner) tool.

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

1. AgileBio ScanServer Installation & LabCollector set up

2. Vision Mate (Thermoscientific) scanner setup & configuration

  • Configure AgileBio Scan Server with Thermoscientific Rack scanner

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. Vision Mate (Thermoscientific)  scanner setup & configuration

  • For the Thermoscientific Scanner scanner, you can read its manual which comes with the scanner or you can find it here.
  • Thermoscientific rack scanners work with Vision Mate™  software.
  • Install your scanner and Thermoscientific Viosion Mate™  software.
  • For the later Vision Mate™ version, please follow this configuration:

    • Select TCP/IP configuration
    • The below settings parameters should be configured same as below.
Add delimiter Character to line End True
Column name uses leading Zero False
Delimiter Character Comma
Export date False
Export Time False
Export Tube Locations True
Send Data Length False
Data Structure  
Data Field Prefix (Should be empty)
Data Field Suffix (Should be empty)
Order Results By Column
Honeycom Racks  
Export Empty HoneyComb Rack Locations True
  • Configure AgileBio Scan Server with Thermoscientific Rack scanner

    • You can use the default settings of scan server.

3. Scanning the Racks

  • Start your scanner and open AgileBio ScanServer (DataPaq™ will be open in the background) 
  • 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.
  • 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.

4. How to use Batch Tool as a manual without integration

  • 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.
  • 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.
  • 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.
  • 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.

5. To add root CA certificate

  • Sometimes, you want to access LabCollector or scan server utility from a computer other than where it is initially installed (Main computer or server). Such other computers are called client computers.
    Please read the below Knowledge Base about how to set up root CA certificate.

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