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Configure a Flow Cytometer FLA Path

This quickstart guide shows how to configure a Tetra File-Log Agent scan path for a flow cytometer after the Agent is installed and connected to the Tetra Data Platform (TDP).

Configure a Scan Path for a Flow Cytometer

To configure a Tetra File-Log Agent scan path for a flow cytometer, do the following:

  1. Open the Agent's Details page.
  2. Select the Configuration tab. The Agent's configuration information appears.
  3. For Start Date, enter the date you want to begin using the configuration. If an End Date (optional) is specified, only files with last modified dates that are on or after the Start Date and on or before the End Date are uploaded.
  4. For File Change Interval (Seconds), enter the minimum time a file in the configured path must remain unchanged before it can be uploaded. The default is 30 seconds.
  5. For Scan Interval (seconds), enter the frequency that you want to have between when paths are rescanned for new or changed files. The default is 30 seconds.
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NOTE

For Tetra File-Log Agent v4.4.x and earlier, there's only a File Change Interval (Seconds) setting.

  1. Select New Path.

  2. For Path, enter the Flow Cytometer's output directory path. The following are example paths for common flow cytometry instruments:

    • BD FACSuite: C:\BD\FACSuite\Data\* or \\FACS-PC\FACSuite\Data\*
    • BD FACSDiva: C:\BD\FACSDiva\Data\* or \\BD-FACS\FACSDiva\Data\*
    • Beckman CytExpert: C:\CytExpert\Data\* or \\BECKMAN-FC\CytExpert\Data\*
    • Thermo Attune: C:\Attune\Data\* or \\THERMO-FC\Attune\Data\*
    • Miltenyi MACSQuantify: C:\MACSQuantify\Data\* or \\MILTENYI-FC\MACSQuantify\Data\*

  3. (Optional) For Source Type, you have the option to enter a name for the data source without spaces. However, it's recommended that you use the Labels setting to update files and trigger pipelines, since the Source Type setting can't be reconfigured after a file is uploaded. Source type Examples:

    • bd-facssuite for BD FACSuite instruments
    • bd-facsdiva for BD FACSDiva instruments
    • beckman-cytexpert for Beckman CytoFLEX instruments
    • thermo-attune for Thermo Fisher Attune instruments
    • miltenyi-macsquantify for Miltenyi MACSQuant instruments

  4. For File Watch Mode, enter File or Folder, based on your use case.

  5. For Patterns, enter a Glob pattern to filter the target file or folder. Glob patterns are a set of wildcard characters. For more information about Glob patterns, including examples, see Common Glob Patterns. The following are common Flow Cytometer file types by vendor:

  • BD (FACSuite/FACSDiva): *.fcs,*.xml,*.pdf,*.csv,*.txt
  • Beckman (CytExpert): *.fcs,*.xml,*.csv,*.txt,*.pdf
  • Thermo (Attune): *.fcs,*.xml,*.csv,*.txt,*.pdf
  • Miltenyi (MACSQuantify): *.fcs,*.xml,*.csv,*.txt,*.pdf
  • Generic FCS: *.fcs,*.xml,*.csv,*.txt
  1. For Labels, either enter new labels (name : value pairs) or select existing ones to annotate files and trigger pipelines without changing any file data. For more information and best practices, see Labels. For a list of recommended labels, see Recommended Labels. Consider adding flow cytometer-specific labels such as:
  • instrument_type: flow_cytometer
  • fc_vendor: [bd/beckman/thermo/miltenyi]
  • analysis_type: [cell_sorting/immunophenotyping/viability]
  • sample_type: [cells/beads/controls]

NOTE

(For TDP v4.3.2 and higher) Five labels are applied by default, but can be removed: vendor, software, instrument_type, and instrument_model, and instrument_serial_number. Pre-defined values for these five labels are fetched from Tetra Catalog. Users may select from those values or enter their own if the value is not present in the dropdown.

  1. For Symlink Behavior (required for Agent v4.4.1 and higher), determine how the Agent handles file symbolic links by choosing one of the following options:

    • Legacy: When the Agent scans a file symbolic link, it will record the metadata of the symbolic link itself. Then, when uploading the file, the Agent follows the link and uploads the contents of the target file.
    • Ignore: The Agent skips file symbolic links entirely during scan and event handling. The Agent doesn't record any metadata for these files and doesn't upload them. Directory symbolic links are still followed.

  2. For Fetch OS File/Folder Owner (for Agent version 4.3.1 and higher), select Yes if you want the Agent to fetch the OS file (or folder, depending on the File Watch Mode) creator and add the information as a metadata to the file during upload. Select No if you don't want the OS file or folder creator information added as metadata.

  3. For Archive Settings, configure the following options based on your use case:

    • (For FLA v4.3 and later) If File Watch Mode is set to file, then the following read-only Archive information appears:
      • Archive files to folder (toggle)—indicates if archive settings are activated or not
      • Archive to—shows the root folder where archived files are stored
      • Archive time and unit—shows the amount of time after successful file upload
      • Delete file from archive permanently (toggle)—indicates if delete settings are activated or not
      • Delete time and unit—shows the amount of time that after a file has been archived and when it becomes eligible to be deleted

    For more information, see Archive Settings.

  4. Choose Overwrite Local with Existing Cloud Configuration.

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NOTE

If a Cloud/Local Configuration is Out of Sync message displays, then the Agent's cloud and local configurations are different. To review the differences, choose the Review Cloud Configuration and Review Local Configuration buttons. Based on the differences, you can decide to push the configuration or reject it.

Test the Setup

To verify that the Agent is pulling data from the path you configured, see Step 3: Test the Setup in the Upload Instrument Data Using a Tetra File-Log Agent quickstart guide.

Documentation Feedback

Do you have questions about our documentation or suggestions for how we can improve it? Start a discussion in TetraConnect Hub. For access, see Access the TetraConnect Hub.

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NOTE

Feedback isn't part of the official TetraScience product documentation. TetraScience doesn't warrant or make any guarantees about the feedback provided, including its accuracy, relevance, or reliability. All feedback is subject to the terms set forth in the TetraConnect Hub Community Guidelines.

Updated about 11 hours ago