Field Detail

• private final java.lang.String backgroundEstimation

  Describes an estimate of the background color based on surrounding pixel's color. The variable stores the name of the method to obtain the background estimation e.g. "Difference of Gaussians"

• private final java.lang.Integer blinking

  Blinking occurs when some fluorophores switch from a bright to a dark state due to photo-induced switching. SRM are capable of detecting such blinking objects. In context of SMT - Single Molecule Tracking This variable describes the number of frames which are allowed between to signals in order to be traced (called a blink) e.g. 2 frames

• private final java.lang.Float conversion

  The conversion factor applied for the analysis e.g 0.43 e-/ADU todo maybe rename it to conversionFactor? what conversion is meant specifically?

• private final java.lang.Float cutOff

  It describes the limiting spatial frequency of the microscope Based on this value the smallest object resolvable by the microscope can be determined It is given in photons, e.g. 1.5 photons

• private final Dimensionality dimensionality

  Describes the dimensionality of an image

  See Also:

  Dimensionality

• private final java.lang.Boolean driftCorrection

  During sample collection, in the process of analysing the sample, it can drift. Without correcting this drift the spatial resolution in the final reconstructed image will be poor Either drift correction is present or not

• private final java.lang.Boolean experimentalPSF

  PSF stands for point spread function and describes the three-dimensional diffraction pattern of light emitted from an infinitely small point source. An experimental PSF is acquired from measurements on a particular imaging setup and is used to calibrate the microscope This setting is optional

• private final java.lang.Float filterSize

  Size of the filter in pixels The convolution kernell is a window (usually rectangular). Its size is described by a positive integer such as y x y A sample value would be 1.3 px

• private final java.lang.Float maxJumpDistance

  Describes the maximal distance that a molecule can "jump" within two frames in order to be traced In context of SMT - Single Molecule Tracking Measured in pixels e.g 1.5 pixels

• private final java.lang.Integer offset

  Offset applied in the analysis This is e.g. 100 ADU The collected signal from the light source can be shifted via an offset amount through pre-amplification

• private final PixelSize pixelSize

  Describes the size of the image pixels. The PixelSize is characterized by 5 elements: (time, channel, x, y, z) in nm

  See Also:

  PixelSize

• private final java.lang.Float roiSize

  ROI stands for region of interest. This region is defined by a number of pixels. All pixels contained within the area of interest describe it. An image that comprises an ROI of 2x5 pixels has a ROI size of 10 pixels

• private final java.lang.Boolean sCMOS

  sCMOS stands for scientific Complementary metal–oxide–semiconductor, its an image sensor which offers rapid frame rates, a wide dynamic range, high quantum efficiency, high resolution and a large field of view simultaneously in one image Describes if a sCMOS is used or not

• private final java.lang.Integer trackLength

  Describes the number of frames in which a molecules could be detected/tracked In context of SMT - Single Molecule Tracking Measured in frames, e.g. a molecules was tracked in 5 frames

Constructor Detail

• SRMAnalysisParameters(Dimensionality dimensionality, java.lang.String backgroundEstimation, java.lang.Float filterSize, java.lang.Float cutOff, java.lang.Float roiSize, PixelSize pixelSize, java.lang.Float conversion, java.lang.Integer offset, java.lang.Boolean experimentalPSF, java.lang.Boolean sCMOS, java.lang.Boolean driftCorrection, java.lang.Float maxJumpDistance, java.lang.Integer blinking, java.lang.Integer trackLength)

  Returns a super resolution microscopy parameter.

  Parameters:

  dimensionality - SRMAnalysisParameters.dimensionality

  backgroundEstimation - SRMAnalysisParameters.backgroundEstimation

  filterSize - SRMAnalysisParameters.filterSize

  cutOff - SRMAnalysisParameters.cutOff

  roiSize - SRMAnalysisParameters.roiSize

  pixelSize - SRMAnalysisParameters.pixelSize

  conversion - SRMAnalysisParameters.conversion

  offset - SRMAnalysisParameters.offset

  experimentalPSF - SRMAnalysisParameters.experimentalPSF

  sCMOS - SRMAnalysisParameters.sCMOS

  driftCorrection - SRMAnalysisParameters.driftCorrection

  maxJumpDistance - SRMAnalysisParameters.maxJumpDistance

  blinking - SRMAnalysisParameters.blinking

  trackLength - SRMAnalysisParameters.trackLength