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User Documentation:

  • User Documentation
    • Installation
    • Quickstart Guide
      • Workflows
        • EDS compositional analysis for phase identification
        • Fit and quantify EDS spectra
        • Measure particle size distribution via SEM
        • Quantify the extent of intermixing in precursor powders
    • Tutorials
      • GUI tutorials
        • Tutorial: Get started with the AutoEMX GUI
        • Tutorial: EDS compositional analysis for phase identification in the GUI
        • Tutorial: particle size statistics in the GUI
        • Tutorial: Fit and quantify individual spectra in the GUI
      • Script tutorials
        • Tutorial: EDS compositional analysis for phase identification
        • Tutorial: Fit and quantify individual spectra acquired with AutoEMX
        • Tutorial: Fit and quantify individual spectra exported by commercial EDS software
        • Tutorial: Quantify externally exported spectra in batch
        • Tutorial: Measure particle size distribution via SEM
        • Tutorial: Quantify the extent of intermixing in precursor powders
    • Topic Guides
      • Quantification flags (quant_flag)
        • Flag meanings
        • How to use them
      • Clustering modes
        • Clustering algorithms
        • Geometries
        • Zeros and trace elements (Aitchison)
        • How 'auto' chooses
        • Examples
        • Which setting to use
      • Number of clusters
        • Step 1: single-cluster check
        • Step 2: choosing k
        • Step 3: merging clusters
        • Setting k yourself
        • Reading the result
      • Mixture decomposition
        • The idea
        • Reading the results
        • Plots
        • Things to keep in mind
        • Changing the defaults
      • Particle size statistics
        • Size bands
        • Segmentation models
        • Corrections
        • Reported statistics
        • Stopping on precision
        • Output
        • References
    • AutoEMX Public API
      • autoemx.runners package
        • Submodules
      • autoemx.config package
        • Subpackages
        • Submodules

Maintainer Documentation:

  • Maintainer Documentation
    • EDS Detector Calibration
      • How it works
      • Setting up the script
      • Running the script
      • Where the calibrations are saved
    • EDS Experimental Standard Collection
      • Choosing the standards
      • Collecting the standards
      • Where the reference values are saved
      • Managing the standards
    • Calibrate a new Detector for EDS fit and quantification
      • The detector model
      • Calibration procedure
        • Peak width
        • Peak shape
        • Background
        • Fine-tuning factors
    • Add new Electron Microscope Driver
      • Start from the Phenom XL driver
      • What AutoEMX uses from the driver
      • Testing the driver
    • AutoEMX Advanced API
      • autoemx.core package
        • Subpackages
        • Submodules
      • autoemx.calibrations package
        • ensure_standards_model()
        • load_detector_model()
        • microscope_driver_name()
        • load_microscope_calibrations()
        • load_latest_detector_channel_params()
        • get_latest_detector_channel_params()
        • update_detector_channel_params()
        • load_standards_model()
        • load_standards()
      • autoemx.microscope_drivers package
        • load_microscope_driver()
        • get_active_driver_module()
        • connect_to_microscope()
        • is_microscope_connected()
        • Submodules
      • autoemx.data package
        • Subpackages
      • autoemx.utils package
        • Subpackages
        • Submodules
AutoEMX
  • User Documentation
  • AutoEMX Public API
  • View page source

AutoEMX Public API

The following modules are intended for users: the runners, called by the scripts, and the configurations and results they read and write (sample ledgers).

  • autoemx.runners package
    • Submodules
      • autoemx.runners.analyze_sample module
      • autoemx.runners.annotate_particle_images module
      • autoemx.runners.batch_acquire_and_analyze module
      • autoemx.runners.batch_acquire_experimental_stds module
      • autoemx.runners.batch_fit_experimental_stds module
      • autoemx.runners.batch_fit_spectra module
      • autoemx.runners.batch_quantify_and_analyze module
      • autoemx.runners.calibrate_detector_model module
      • autoemx.runners.calibrate_peak_sigma_params module
      • autoemx.runners.calibrate_peak_weights_experimental_standard module
      • autoemx.runners.collect_particle_statistics module
      • autoemx.runners.extract_experimental_standards_details module
      • autoemx.runners.fit_and_quantify_spectrum module
      • autoemx.runners.fit_and_quantify_spectrum_from_ledger module
      • autoemx.runners.modify_standards_file module
      • autoemx.runners.process_particle_statistics module
      • autoemx.runners.publish_standards module
      • autoemx.runners.reanalyze_particle_statistics module
      • autoemx.runners.quantify_external_spectra module
      • autoemx.runners.reinitialize_ledger module
      • autoemx.runners.set_active_analysis module
  • autoemx.config package
    • Subpackages
      • autoemx.config.schema_models package
    • Submodules
      • autoemx.config.defaults module
      • autoemx.config.ledger_io module
      • autoemx.config.ledger_schemas module
      • autoemx.config.runtime_configs module
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