Welcome to PERI’s documentation!

Getting Started

For an introduction to how peri works and how to use it, see the walkthrough.

Parameter Extraction from Reconstruction of Images (PERI) is a package that extracts features from microscope images by fitting a physics-based model to data. It is a set of models and components that are used to recreate the physics of image formation in order to extract desired quantities such as particle sizes and positions at the information theoretic limit. While a very general software package, right now the primary model currently implemented is that of 3D confocal microscopes, particularly of the line and point scan varieties.

In these documents you will find information about:

• Installation
• Walkthrough
• Package overview

Documentation:

• Installation
  • Installation
    • Quick install
    • Source code
  • Contributing
    • Bugs and issues
    • Contributing
• PERI Walkthrough
  • What is PERI?
  • Take a microscope image.
  • Create a mathematical model of the image formation process.
  • Fit that mathematical model to the image.
  • If the fit is not good, improve the mathematical model.
  • If the fit is good, use the extracted information from the fit.
  • Making this faster
    • …using the microscope parameters from another state
    • …using the microscope parameters and positions from another state
    • …from scratch
    • …from a guess of positions and radii
    • Using a smaller image
  • Checking your model even more
• Package architecture
  • States (Example: PolyFitState)
    • Overview
    • State class
  • Image states (Example: GaussianDiscModel)
    • Model
    • Components
    • ImageState, fitting, and properties
• Optimization and sampling
  • Initial Optimization
  • Add-subtract
  • Main Optimization
  • Achieving the best-possible state
    • Adding tough missing particles
    • Additional Optimizations
  • When is the state optimized?
    • Checking optimization with the OrthoManipulator
    • Checking optimization by running more optimization
    • Seeing if the fitted values are reasonable
    • Comparing across Images
  • Speeding this process up
    • Using a Good Initial Guess; The Runner Functions
    • Fitting a small image
    • Sacrificing Precision for Speed
    • Inventing a new algorithm for fitting in high-dimensional spaces

Reference:

• peri.comp
  • peri.comp.comp
  • peri.comp.objs
  • peri.comp.ilms
  • peri.comp.psfs
  • peri.comp.exactpsf
• peri.conf
• peri.fft
• peri.viz.interaction
• peri.interpolation
  • peri.interpolation.BarnesInterpolation1D
  • peri.interpolation.ChebyshevInterpolation1D
• peri.logger
• peri.models
• peri.opt
  • peri.opt.optimize.burn
  • peri.opt.optimize.finish
    • peri.opt.optimize
  • peri.opt.optimize functions
  • peri.opt.optimize classes
    • peri.opt.addsubtract
• peri.runner
• peri.states
  • peri.states.State
  • peri.states.ImageState
  • peri.states.{save,load}
• peri.util
  • peri.util.Tile
  • peri.util.Image
  • peri.util.RawImage
  • peri.util.{*}

Indices and tables

• Index
• Module Index
• Search Page