This is dclab, a Python library for the post-measurement analysis of real-time deformability cytometry (RT-DC) datasets. This is the documentation of dclab version 0.62.0.post1+gdb17590.

Documentation

Contents:

• Getting started
  • Installation
  • Use cases
  • Basic usage
  • How to cite
• Command-line interface
  • dclab-compress
  • dclab-condense
  • dclab-join
  • dclab-repack
  • dclab-split
  • dclab-tdms2rtdc
  • dclab-verify-dataset
• Examples
  • Dataset overview plot
  • Young’s modulus computation from data on DCOR
  • Viscosity models for Young’s modulus estimation
  • lme4: Linear mixed-effects models
  • lme4: Generalized linear mixed-effects models with differential deformation
  • Plotting isoelastics
  • Plotting custom isoelastics
  • Working with plugin features
• Advanced Usage
  • Notation
    • Events
    • Features
    • Ancillary features
    • Filters
    • Experiment metadata
    • Analysis metadata
    • User-defined metadata
    • Basins
  • Using DC data
    • Opening a file
    • Creating an in-memory dataset
    • Filtering (Gating)
    • Creating hierarchies
    • Computing feature statistics
    • Commonly used scripting examples
  • DC data I/O
    • Exporting data
    • Writing to an .rtdc file
    • Copying (parts of) a dataset
  • Basins
    • Motivation
    • Definitions
    • Defining Basins
    • Examples
    • Accessing private basin data
    • Basin internals
  • Plugin features
    • Using plugin feature recipes
    • Auto-loading multiple plugin feature recipes
    • Writing a plugin feature recipe
    • Reloading plugin features stored in data files
  • Temporary features
    • Setting a temporary feature in a dataset
    • Accessing temporary features stored in data files
  • Scatter plots
    • KDE scatter plot
    • KDE scatter plot with event-density-based downsampling
    • KDE estimate on a log-scale
    • Isoelasticity lines
    • Contour plot with percentiles
    • Polygon filters / Shape-Out
  • Fluorescence traces
  • Young’s modulus computation
    • Background
    • Viscosity
    • LUT selection
    • Usage
  • Linear mixed-effects models
    • Computing p-values with lme4 in dclab
    • Differential feature analysis with reservoir data
  • DCOR access
    • Public data
    • Private data
    • Managing API Tokens
    • Accessing data on a different DCOR instance
    • Bypassing DCOR and using S3 directly
  • S3 access
    • Public data
    • Private data
• Code reference
  • Module-level methods
    • new_dataset()
  • Global definitions
    • Metadata
    • Metadata parsers
    • Features
  • RT-DC dataset manipulation
    • Base class
    • HDF5 (.rtdc) format
    • DCOR (online) format
    • HTTP (online) file format
    • S3 (online) file format
    • Dictionary format
    • Hierarchy format
    • TDMS format
    • Basin features
    • Ancillaries
    • Plugin features
    • Temporary features
    • Config
    • Export
    • Filter
  • Low-level functionalities
    • downsampling
    • features
    • isoelastics
    • kde_contours
    • kde_methods
    • polygon_filter
    • statistics
  • HDF5 manipulation
    • h5ds_copy()
    • is_properly_compressed()
    • rtdc_copy()
  • Writing RT-DC files
    • RTDCWriter
    • CHUNK_SIZE
    • CHUNK_SIZE_BYTES
    • FEATURES_UINT32
    • FEATURES_UINT64
  • Command-line interface methods
    • compress()
    • condense()
    • condense_dataset()
    • get_command_log()
    • get_job_info()
    • join()
    • repack()
    • split()
    • tdms2rtdc()
    • verify_dataset()
  • R and lme4
    • RNotFoundError
    • get_r_path()
    • get_r_script_path()
    • get_r_version()
    • has_lme4()
    • has_r()
    • require_lme4()
    • require_r()
    • run_command()
    • set_r_path()
    • Rlme4
    • arr2str()
    • bootstrapped_median_distributions()

• Changelog
• Bilbliography

Indices and tables

• Index

• Module Index

• Search Page