Modules

API

SAiryscanAPI	Main API to build an Airyscan data reconstruction pipeline
SAiryscanPipeline	Build and run a reconstruction pipeline in a single image
SAiryscanLoop	Apply a SAiryscan reconstruction method on all the frames and channels

Registration

SAiryscanRegistration	Interface for Airyscan detectors registration method
SRegisterPosition	Register the detectors stack by translating each image to the detector position is array
SRegisterFourierPhase	Register the detectors stack by translating each image to the detector position is array
SRegisterMSE	Register the detectors stack by translating each image to the detector position is array

Reconstruction

SAiryscanReconstruction	Interface for Airyscan high resolution image reconstruction method
IFED	Airyscan reconstruction using the IFED method
ISFED	Implementation of the ISFED reconstruction method
ISM	Reconstruct a high resolution image by summing the co-registered detectors: ISM method
PseudoConfocal	Reconstruct an image equivalent to a confocal image by summing the inner detectors
SpitfireJoinDeconv	Gray scaled image deconvolution with the Spitfire algorithm
SpitfireJoinDenoise	Gray scaled image deconvolution with the Spitfire algorithm
SSpitfireFlow	Workflow for spitfire denoising
SureMap	Calculate the Sure weights map for IFED and ISFED
IFEDDenoising	Reconstruct a high resolution image with a ISFED method including a denoising step
ISFEDDenoising	Reconstruct a high resolution image with a ISFED method including a denoising step

Enhancing

SAiryscanEnhancing	Interface for Airyscan enhancing filter applied after the reconstruction
SAiryscanGaussian	Apply a gaussian filter
SAiryscanWiener	Apply a gaussian filter
SAiryscanRichardsonLucy	Apply a Richardson-Lucy deconvolution
SpitfireDeconv	Gray scaled image deconvolution with the Spitfire algorithm

Example data

celegans

2D Celegans sample expressing the ERM-1::mNeonGreen fusion protein.

Internal patterns

Internal patterns are light implementations of patterns like observer/observable, singleton to read settings, and interface for image file reading.

SAiryscanReader	Read a CZI Zeiss raw data
Settings	Singleton to access the Settings container
SettingsContainer	Container for the SAiryscan library settings
SObservable	Interface for any data processing class
SObserver	Interface of observer to notify progress
SObserverConsole	Implementation of an observer that print messages and progress to console