CODEX® Support
  • Welcome
  • CODEX® Instrument Manager (CIM)
    • Overview
    • User Instructions
      • Experiment
      • Maintenance
      • Transfer Data
      • Settings
    • Microscope Specific Settings
      • Microscope Requirements - Overview
      • Keyence BZ-X800 and BZ-X700
        • Requirements
        • BZ-X800 Image Acquisition Settings
          • Multi-Point (BZ-X800)
        • BZ-X700 Image Acquisition Settings
          • Multi-Point (BZ-X700)
        • Exposure steps
      • Leica DMi8
        • Image Acquisition Settings
      • Zeiss Axio Observer
        • Requirements
        • Image Acquisition Settings
      • Exposure Time Settings Considerations
      • Determination of Signal to Noise Ratio
    • Technical Notes
    • Installation
      • CIM Upgrades
  • CODEX® Processor
    • Overview
    • Installation
      • Install
      • Update
      • Version History
    • User Instructions
      • Quick Start
      • Processing Options
      • Segmentation Options
      • Image Analysis Report
    • Technical Notes
      • Expected Input
      • Expected Output
      • Cycle Alignment
      • Background Subtraction
      • Deconvolution
      • Extended Depth of Field
      • Shading Correction
      • Tile Registration
      • Segmentation & Spillover
      • t-SNE
      • FCS Format
    • Troubleshooting
  • CODEX® Multiplex Analysis Viewer (MAV)
    • Overview
    • Installation
      • System Requirements
      • CODEX® MAV - Download & Install
      • Release Notes
    • User Instructions
      • Quick Start
      • Open Experiment
      • Main Menu
      • Overlay Manager
      • Marker Picker
      • Region Image
      • History Panel
      • Save / Open Analysis
      • Clustering
      • Population Table
      • Cells
      • Marker Manager
      • Gating
      • Voronoi Diagram
      • Other Analysis Operations
    • Technical Notes
      • Algorithm Details
      • FCS Format
    • Public Datasets
    • Troubleshooting
  • Workflow Documents
    • CODEX and microscope setup
    • Reagents and staining
  • Appendix
    • End User License Agreement
    • Third-party Licenses
      • CIM
      • Processor
      • MAV
  • PhenoCycler Analysis
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  1. CODEX® Processor

Troubleshooting

For all issues, please contact support@akoyabio.com for additional support.

Processing computer seems to be malfunctioning.

  • CODEX® Processing computer purchased through Akoya is supplied and supported by Origin PC. Their warranty provides lifetime 24/7 U.S. based support and free labor, 1 year part replacement and 45 day shipping warranty. Please contact Origin PC support.

Processor does not open.

  • Check that Java 8 build 201 is installed in Add or Remove Programs.

  • If the processor was close recently, please try again in a few seconds. Releasing memory used by the processor can take a few seconds to complete.

No GPU is found or tile registration fails.

  • Check that CUDA Toolkit 9.2 is installed in Add or Remove Programs.

  • Check that a compatible GPU (e.g. NVIDIA RTX 2080) is detected in Windows Device Manager.

  • Memory problems may manifest as GPU errors. Windows Memory Diagnostics may detect such errors. Please contact Origin PC support.

Microvolution license is not found.

  • Check that a valid license file is located in the CODEX® Processor folder .

  • Check that the computer can reach the license server at licensing.microvolution.com.

Study cannot be loaded.

  • Root study folder should be selected.

  • Check that the input folder contains the following components:

    • Contiguous cycle-region folders named ‘cyc001_reg001’ containing images named ‘1_00001_Z001_CH1.tif’.

    • Experiment metadata (experiment.json).

    • Channel names (channelNames.txt).

    • Exposure times (exposure_times.txt).

  • Check that the metadata files were generated using the CIM Transfer feature.

Processing does not start or fails immediately.

  • Processor requires a formatted dataset with the components listed above.

  • Image files may be missing or corrupt, which can be checked using inputFileList.txt in the diagnostic output folder.

Processing does not produce stitched images.

  • Check that all necessary input image and metadata files are present.

  • Check that the Processing computer has enough memory to support the input dataset.

Processing produces uncropped stitched images.

  • Improper marker naming and missing exposure times will cause background subtraction to fail. Please check channelNames.txt for proper 'Blank' channels and exposure_times.txt for valid exposure times for all cycles.

Image artifacts are seen in stitched images or MAV.

  • This may be due to a number of reasons. Please contact CODEX® support.

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Last updated 4 years ago

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