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This is the code for the Deep Particle Diffusometry-v2 paper: https://www.cambridge.org/core/journals/flow/article/dpdv2-generalised-deep-particle-diffusometry-for-varied-particle-shapes-and-experimental-conditions/94CF46C8556FFE53017F87929727B1F7

The sample datasets can be visualized here: https://engineering.purdue.edu/microfluidics/DPDWebsite.html

The full dataset with Gaussian particle shape can be found here: https://osf.io/j2xwa/ The full dataset with defocused particle shape can be found here: https://osf.io/qych9/

The code to DPD-v2 algorithms can be found here: https://github.itap.purdue.edu/psardana/DPD-v2 The code for DPD-v1 and benchmarking algorithms can be found here: https://github.itap.purdue.edu/psardana/deepParticleDiffusometry

The MicroSIG source code can be found here: https://gitlab.com/defocustracking/microsig-matlab

Connect to Pranshul Sardana via LinkedIn: https://www.linkedin.com/in/pranshulsardana/ Pranshul Sardana's Google Scholar: https://tinyurl.com/psardanaPublications Steve Wereley's Google Scholar: https://tinyurl.com/swereleyPublications

Running to code:

Use "MainThreeDSimulation.m" to run the code

Setting files:

Setting files must be .txt files in ASCII, each row must be a text string with: parameter_name = value. MicroSIG uses 14 parameters:

magnification: Magnification of the simulated lens.
numerical_aperture: Numerical aperture of the simulated lens.
focal_length: This parameter must be chosen empirically from comparison with real images. A typical value is 350.
ri_medium: Refractive index of the immersion medium of the lens, normally 1.
ri_lens: Refractive index of the immersion medium of the lens, normally 1.5
pixel_size: Size of the side of a square pixel (in microns).
pixel_dim_x: Number of pixels in the x-direction of the sensor.
pixel_dim_y: Number of pixels in the y-direction of the sensor.
background_mean: Constant value of the image background.
background_noise: Amplitude of Gaussian noise added to the images.
points_per_pixel: Number of point sources in a particle, normalized for the particle area. Decrease this parameter for large particles. Typical values are between 10 and 20.
n_rays: Number of rays for point source. Decrease this value to speed up the particle computation. Typical values are between 100 and 500.
gain: Additional gain to increase or decrease the image intensity.
cyl_focal_length: Additional parameter for astigmatic imaging. This parameter must be chosen empirically from comparison with real images. A typical value is 4000. When it is set to 0 no astigmatism is present.

For examples/templates see the files settings-1.txt, settings-1a.txt, settings-2.txt in the \examples folder.

License

psardana/defocused-PD-generation

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