Basic Usage
See the readme file in the root of the repository for instructions on how to get the program running.
The "Input Parameters" panel is where you set all the parameters for the simulation. It consists of multiple sections:
- Fluorophore Illumination Response [1] – The illumination response of the fluorophore used.
- Pulse Scheme [2] – The sequence of laser pulses that are fired during imaging.
- Imaging System Settings [3] – Properties of the imaging system.
- Sample Settings [4] – The properties of the captured sample. You may load a predefined sample structure here; if you don't, the generated FRC curves may not be consistent with the expected images later on.
- Detector Settings [5] – Properties of the detector used in imaging; this may either be a point detector or a camera.
Each section contains a panel for loading and saving configurations at the top [6]. This panel may also contain a menu for loading preset configurations. There is also a configuration panel for all input parameters simultaneously [7].
If you want to see how an individual parameter affects the results, you can click the button next to its input field to set a value range or list [8]. Note that this is not available for all input fields. You may set value ranges/lists for multiple parameters at the same time, but keep in mind that this could dramatically increase the simulation time.
After you have set up the parameters, you may click the "SIMULATE" button in the "Output Controls" panel [9] to run the simulation.
There are two views for simulation results: the "FRC/Resolution Output" panel [1] and the "Virtual Imaging Output" panel [2].
The "FRC/Resolution Output" panel [1] displays the simulated FRC curve. It also displays the resolution at the FRC value threshold of your choice.
The "Virtual Imaging Output" panel [2] allows you to load an image of a sample, and see the simulated expected image that would be captured in the environment described by the input parameters you set. It is hidden by default, and is made visible by clicking its tab on the left edge of the window.
If you set any value ranges or lists in the input parameters prior to starting the simulation, you will be able to drag the sliders [3] to see how each parameter affects the output. You may check the box next to a slider [4] to view a graph of the resolution as a function of the corresponding parameter in the "FRC/Resolution Output" panel. The "Set to optimal values" button [5] will move the sliders to the values that give the best resolution.
The simulation results can be saved to the disk from the "File" menu in the toolbar [6]. Saved simulation results can also be loaded from the "File" menu. When a saved simulation is loaded, the input parameters that generated the results are loaded as well.