FluorophoreReceiver¶

public class FluorophoreReceiver¶

Populates a field of view with fluorophores. The FluorophoreGenerator contains a number of methods for creating actual fluorophore instances and in different arrangements, such as placing them on a grid, randomly distributing them in the FOV, and placing them according to input from a text file.

Author:	Marcel Stefko, Kyle M. Douglass

Methods¶

generateFluorophoresFromCSV¶

public static ArrayList<Fluorophore> generateFluorophoresFromCSV(File file, Camera camera, Illumination illumination, PSFBuilder psfBuilder, FluorophoreDynamics fluorDynamics, boolean rescale)¶

Parse a CSV file and generate fluorophores from it.

Parameters:	file – The CSV file. If this is null, then a dialog is opened. camera – The camera for determining the size of the field of view. illumination – The illumination profile on the sample. psfBuilder – Builder for calculating microscope PSFs. fluorDynamics – The fluorophore dynamics properties. rescale – if true, positions are rescaled to fit into frame, otherwise positions outside of frame are cropped
Throws:	IOException – FileNotFoundException –
Returns:	list of fluorophores.

generateFluorophoresGrid2D¶

public static ArrayList<Fluorophore> generateFluorophoresGrid2D(int spacing, Camera camera, Illumination illumination, PSFBuilder psfBuilder, FluorophoreDynamics fluorDynamics)¶

Generate a rectangular grid of fluorophores.

Parameters:	spacing – The distance along the grid between nearest neighbors. camera – The camera for determining the size of the field of view. illumination – The illumination profile on the sample. psfBuilder – Builder for calculating microscope PSFs. fluorDynamics – The fluorophore dynamics properties.
Returns:	The list of fluorophores.

generateFluorophoresGrid3D¶

public static ArrayList<Fluorophore> generateFluorophoresGrid3D(int spacing, double zLow, double zHigh, Camera camera, Illumination illumination, PSFBuilder psfBuilder, FluorophoreDynamics fluorDynamics)¶

Create fluorophores on a 2D grid and step-wise in the axial direction.

Parameters:

spacing – The distance along the grid between nearest neighbors.
zLow – The lower bound on the range in z in units of pixels.
zHigh – The upper bound on the range in z in units of pixels.
camera – The camera for determining the size of the field of view.
illumination – The illumination profile on the sample.
psfBuilder – Builder for calculating microscope PSFs.
fluorDynamics – The fluorophore dynamics properties.

Returns:

The list of fluorophores.

generateFluorophoresRandom2D¶

public static ArrayList<Fluorophore> generateFluorophoresRandom2D(int numFluors, Camera camera, Illumination illumination, PSFBuilder psfBuilder, FluorophoreDynamics fluorDynamics)¶

Randomly populate the field of view with fluorophores.

Parameters:	numFluors – The number of fluorophores to add to the field of view. camera – The camera for determining the size of the field of view. illumination – The illumination profile on the sample. psfBuilder – Builder for calculating microscope PSFs. fluorDynamics – The fluorophore dynamics properties.
Returns:	The list of fluorophores.

generateFluorophoresRandom3D¶

public static ArrayList<Fluorophore> generateFluorophoresRandom3D(int numFluors, double zLow, double zHigh, Camera camera, Illumination illumination, PSFBuilder psfBuilder, FluorophoreDynamics fluorDynamics)¶

Randomly populate the field of view with fluorophores in three dimensions.