Nanite is a Python library for loading, fitting, and rating AFM force-distance data of cells and tissues. This is the documentation of nanite version 4.2.3.

Documentation

• Getting started
  • Installation
  • What is nanite?
  • Supported file formats
  • Use cases
  • Basic usage
  • How to cite
• Command-line interface
  • nanite-setup-profile
  • nanite-fit
  • nanite-rate
  • nanite-generate-training-set
• Fitting guide
  • Preprocessors
  • Models
  • Parameters
  • Geometrical correction factor
  • Workflow
    • Command-line usage
    • Scripting usage
• Rating workflow
  • Rating experimental data manually
  • Generating the training set
  • Applying the training set
• Scripting examples
  • Approximating the Hertzian model with a spherical indenter
  • Fitting and rating
• Developer guide
  • How to contribute
  • Updating the documentation
  • Writing model functions
    • Getting started
    • Ancillary parameters
• Code reference
  • Module level aliases
    • nanite.Indentation
    • nanite.IndentationGroup
    • nanite.IndentationRater
    • nanite.QMap
    • nanite.load_group()
  • Force-indentation data
    • Indentation
  • Groups
    • IndentationGroup
    • load_group()
  • Loading data
    • get_data_paths()
    • get_data_paths_enum()
    • get_load_data_modality_kwargs()
    • load_data()
    • DEFAULT_MODALITY
  • Preprocessing
    • CannotSplitWarning
    • IndentationPreprocessor
    • apply()
    • autosort()
    • available()
    • check_order()
    • find_turning_point()
    • get_func()
    • get_name()
    • get_steps_required()
    • preproc_compute_tip_position()
    • preproc_correct_force_offset()
    • preproc_correct_force_slope()
    • preproc_correct_split_approach_retract()
    • preproc_correct_tip_offset()
    • preproc_smooth_height()
    • preprocessing_step()
    • PREPROCESSORS
  • Contact point estimation
    • compute_poc()
    • compute_preproc_clip_approach()
    • poc()
    • poc_deviation_from_baseline()
    • poc_fit_constant_line()
    • poc_fit_constant_polynomial()
    • poc_fit_line_polynomial()
    • poc_frechet_direct_path()
    • poc_gradient_zero_crossing()
    • POC_METHODS
  • Modeling
    • Methods and constants
    • Modeling core class
    • Residuals and weighting
    • Models
  • Fitting
    • FitDataError
    • FitKeyError
    • FitWarning
    • FitProperties
    • IndentationFitter
    • guess_initial_parameters()
    • obj2bytes()
  • Rating
    • Features
    • Rater
    • Regressors
    • Manager
  • Quantitative maps
    • DataMissingWarning
    • QMap

• Changelog
• Bilbliography

Indices and tables

• Index

• Module Index

• Search Page