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Simulated Fluorescence

In the development branch of autoPACK we have integrated tools to simulate fluorescence from autoPACK results, as well as any object positions from the host. 

The aim of theses tools is, given a set of coordinate representing fluorophore position, to produce 2D images of fluorescence for comparison to observed microscope images.

This is done by applying a point spread functionon the fluorophore positions to convolve them into a 2D projection at the resolution of a microscope with the same point spread function. The current version offers one point spread function, a gaussian filter which represents a simplified point spread function of a STED microscope setup (DOI: 10.1126/science.1226359). It is defined by the resolution that corresponds to the half width at the half maximum (HWHM) of the gaussian. The user inputs the fluorophore positions (a object name, a ingredient name, the current selection in the viewport), the gaussian HWHM (in Angstrom), the final resolution (size in Angstrom of 1pixel), and the grid size and stepsize.
The fluorescence tool can be accessed from either the Viewer tab, the PACKing tab, or the Building tab. Meaning you can view a packing and simulate the fluorescence, run a packing and simulate the fluorescence, open custom file, or create custom object and simulate the fluorescence.

The fluorescence can be found under the Tools menu from the Viewer and Packing windows, or as a button in the Builder Tab.
Theses tools depends on numpy, scipy (ndimage,misc, stats) and PIL.

The following tutorial demonstrates how to use Fluorescence Simulation in Cinema4D.  

TUTORIAL: View a PACKing and simulate fluorescence.

  1. From the main autoPACK gui, go in the View tab
    1. select Test_Spheres2D
    2. click Construct
      1. this will open a new gui window after building the recipe.
    3. Open the Fluorescence Simulation GUI from Tools->generate fluorescence.
    4. Select in the hierarchy the object named "Meshs_ext__i5_n200"
      1. the tool will gather all the child positions and use them as the fluorophore positions
      2. you can manually input a 3d vector offset to apply to all positions
    5. Once selected, click displayXYZ
      1. this will setup, generate and create the 2D plane with the fluorescence images projected on the X,Y, and Z planes.
 
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