# CODEX® Support ## CODEX® Support - [Welcome](https://help.codex.bio/codex/master.md): We’ve rebranded some of our products. CODEX® is now PhenoCycler™. - [Overview](https://help.codex.bio/codex/cim/overview.md) - [User Instructions](https://help.codex.bio/codex/cim/user-instructions.md) - [Experiment](https://help.codex.bio/codex/cim/user-instructions/experiment-design-and-run.md): Experiment set up and run CODEX® experiments with the CODEX® Instrument Manager (CIM) - [Maintenance](https://help.codex.bio/codex/cim/user-instructions/maintenance.md): The Maintenance tab has protocols that allow priming the instrument prior to an experiment, routine instrument maintenance, and tissue clearing. - [Transfer Data](https://help.codex.bio/codex/cim/user-instructions/transfer-data.md) - [Settings](https://help.codex.bio/codex/cim/user-instructions/settings.md): Set up options for logging, ports, updates, and notification, etc. - [Microscope Specific Settings](https://help.codex.bio/codex/cim/microscope-specific-settings.md) - [Microscope Requirements - Overview](https://help.codex.bio/codex/cim/microscope-specific-settings/microscopes.md): This section presents an overview of the microscope requirements. Specific microscope requirements are listed within each microscope section. - [Keyence BZ-X800 and BZ-X700](https://help.codex.bio/codex/cim/microscope-specific-settings/keyence.md) - [Requirements](https://help.codex.bio/codex/cim/microscope-specific-settings/keyence/requirements.md): Specific recommendations for Keyence BZ-800 - [BZ-X800 Image Acquisition Settings](https://help.codex.bio/codex/cim/microscope-specific-settings/keyence/image-acquisition-settings.md): CODEX®-specific settings for the Keyence BZ-X800. - [Multi-Point (BZ-X800)](https://help.codex.bio/codex/cim/microscope-specific-settings/keyence/image-acquisition-settings/multi-point-bz-x800.md): For imaging more than 10 regions during a CODEX Run. - [BZ-X700 Image Acquisition Settings](https://help.codex.bio/codex/cim/microscope-specific-settings/keyence/keyence-bz-x700.md): CODEX specific settings for the Keyence BZ-X700. - [Multi-Point (BZ-X700)](https://help.codex.bio/codex/cim/microscope-specific-settings/keyence/keyence-bz-x700/multipoint-bzx700.md): For imaging more than 10 regions during a CODEX Run. - [Exposure steps](https://help.codex.bio/codex/cim/microscope-specific-settings/keyence/advanced-options.md): Fractions to msecs - [Leica DMi8](https://help.codex.bio/codex/cim/microscope-specific-settings/leica-dmi8.md) - [Image Acquisition Settings](https://help.codex.bio/codex/cim/microscope-specific-settings/leica-dmi8/image-acquisition-settings.md) - [Zeiss Axio Observer](https://help.codex.bio/codex/cim/microscope-specific-settings/zeiss-axio-observer.md) - [Requirements](https://help.codex.bio/codex/cim/microscope-specific-settings/zeiss-axio-observer/requirements.md) - [Image Acquisition Settings](https://help.codex.bio/codex/cim/microscope-specific-settings/zeiss-axio-observer/image-acquisition-settings.md): Setting up Zeiss for CODEX runs. - [Exposure Time Settings Considerations](https://help.codex.bio/codex/cim/microscope-specific-settings/exposure-time-optimization.md): Guidelines on how to set up exposure times for CODEX® experiments such as CODEX® Antibody Screening & Validation and CODEX® Multicycles. - [Determination of Signal to Noise Ratio](https://help.codex.bio/codex/cim/microscope-specific-settings/determination-of-signal-to-noise-ratio.md): This section offers guidelines on how to measure the Signal to Noise Ratio (SNR) in CODEX fluorescence microscopy images. - [Technical Notes](https://help.codex.bio/codex/cim/related-documentation.md) - [Installation](https://help.codex.bio/codex/cim/preparing-for-installation.md) - [CIM Upgrades](https://help.codex.bio/codex/cim/preparing-for-installation/cim-upgrades.md): The CIM Software will have updates for bug fixes and feature request additions. This page will have the upgrade installers, release notes, and instructions for upgrading the software. - [Overview](https://help.codex.bio/codex/processor/overview.md): We’ve rebranded some of our products. CODEX® is now PhenoCycler™. - [Installation](https://help.codex.bio/codex/processor/installation.md) - [Install](https://help.codex.bio/codex/processor/installation/download-and-install.md): CODEX Processor is to be installed on Akoya-provided and validated CODEX Processing computer. - [Update](https://help.codex.bio/codex/processor/installation/update.md) - [Version History](https://help.codex.bio/codex/processor/installation/version-history.md) - [User Instructions](https://help.codex.bio/codex/processor/user-instructions.md) - [Quick Start](https://help.codex.bio/codex/processor/user-instructions/quick-start.md) - [Processing Options](https://help.codex.bio/codex/processor/user-instructions/processing-options.md) - [Segmentation Options](https://help.codex.bio/codex/processor/user-instructions/segmentation-options.md) - [Image Analysis Report](https://help.codex.bio/codex/processor/user-instructions/image-analysis-report.md) - [Technical Notes](https://help.codex.bio/codex/processor/technical-notes.md) - [Expected Input](https://help.codex.bio/codex/processor/technical-notes/expected-input.md) - [Expected Output](https://help.codex.bio/codex/processor/technical-notes/expected-output.md) - [Cycle Alignment](https://help.codex.bio/codex/processor/technical-notes/cycle-alignment.md) - [Background Subtraction](https://help.codex.bio/codex/processor/technical-notes/background-subtraction.md) - [Deconvolution](https://help.codex.bio/codex/processor/technical-notes/deconvolution.md) - [Extended Depth of Field](https://help.codex.bio/codex/processor/technical-notes/extended-depth-of-field.md) - [Shading Correction](https://help.codex.bio/codex/processor/technical-notes/shading-correction.md) - [Tile Registration](https://help.codex.bio/codex/processor/technical-notes/tile-registration.md) - [Segmentation & Spillover](https://help.codex.bio/codex/processor/technical-notes/segmentation-and-spillover.md) - [t-SNE](https://help.codex.bio/codex/processor/technical-notes/t-sne.md) - [FCS Format](https://help.codex.bio/codex/processor/technical-notes/fcs-format.md) - [Troubleshooting](https://help.codex.bio/codex/processor/troubleshooting.md) - [Overview](https://help.codex.bio/codex/mav/overview.md): We’ve rebranded some of our products. CODEX® is now PhenoCycler™. - [Installation](https://help.codex.bio/codex/mav/installation.md) - [System Requirements](https://help.codex.bio/codex/mav/installation/system-requirements.md) - [CODEX® MAV - Download & Install](https://help.codex.bio/codex/mav/installation/download-and-install.md) - [Release Notes](https://help.codex.bio/codex/mav/installation/release-notes.md) - [User Instructions](https://help.codex.bio/codex/mav/user-instructions.md) - [Quick Start](https://help.codex.bio/codex/mav/user-instructions/quick-start.md) - [Open Experiment](https://help.codex.bio/codex/mav/user-instructions/open-experiment.md) - [Main Menu](https://help.codex.bio/codex/mav/user-instructions/main-menu.md) - [Overlay Manager](https://help.codex.bio/codex/mav/user-instructions/overlay-manager.md) - [Marker Picker](https://help.codex.bio/codex/mav/user-instructions/marker-picker.md) - [Region Image](https://help.codex.bio/codex/mav/user-instructions/region-image.md) - [History Panel](https://help.codex.bio/codex/mav/user-instructions/history-panel.md) - [Save / Open Analysis](https://help.codex.bio/codex/mav/user-instructions/save-open-analysis.md) - [Clustering](https://help.codex.bio/codex/mav/user-instructions/clustering.md) - [Population Table](https://help.codex.bio/codex/mav/user-instructions/population-table.md) - [Cells](https://help.codex.bio/codex/mav/user-instructions/table-view.md) - [Marker Manager](https://help.codex.bio/codex/mav/user-instructions/marker-manager.md) - [Gating](https://help.codex.bio/codex/mav/user-instructions/gating.md) - [Voronoi Diagram](https://help.codex.bio/codex/mav/user-instructions/voronoi-diagram.md) - [Other Analysis Operations](https://help.codex.bio/codex/mav/user-instructions/other-analysis-operations.md) - [Technical Notes](https://help.codex.bio/codex/mav/technical-notes.md) - [Algorithm Details](https://help.codex.bio/codex/mav/technical-notes/algorithms.md) - [FCS Format](https://help.codex.bio/codex/mav/technical-notes/fcs-format.md) - [Public Datasets](https://help.codex.bio/codex/mav/public-datasets.md) - [Troubleshooting](https://help.codex.bio/codex/mav/troubleshooting.md) - [CODEX and microscope setup](https://help.codex.bio/codex/technical-notes/codex-and-microscope-setup.md): We’ve rebranded some of our products. CODEX® is now PhenoCycler™. - [Reagents and staining](https://help.codex.bio/codex/technical-notes/reagents-and-staining.md): We’ve rebranded some of our products. CODEX® is now PhenoCycler™. - [End User License Agreement](https://help.codex.bio/codex/appendix/end-user-license-agreement.md) - [Third-party Licenses](https://help.codex.bio/codex/appendix/codex-software-third-party-licenses.md) - [CIM](https://help.codex.bio/codex/appendix/codex-software-third-party-licenses/cim-dependencies.md) - [Processor](https://help.codex.bio/codex/appendix/codex-software-third-party-licenses/codexprocessor.md) - [MAV](https://help.codex.bio/codex/appendix/codex-software-third-party-licenses/mav-dependencies.md) - [PhenoCycler Analysis](https://help.codex.bio/codex/phenocycler-analysis.md): Resources for PhenoCycler analysis. --- # Agent Instructions This documentation is published with GitBook. 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