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alihashmiii/README.md

𐌀li ℍashmi, ℙh.𝔻.

I have a PhD in biophysics. I am primarily interested in the mathematical/computational and experimental approaches for exploring the physical basis of biological development. I am broadly interested in scientific programming, symbolic computing, image processing/computer vision and machine learning!

Following are the examples of some codes/scripts I have developed:

❂ 3D Vertex Model: A Mathematica code for simulating biological tissues in 3D ❂ 2D Vertex Model: Simulate biological tissues in 2D ❂ Force Inference: Infer forces from an epithelial tissue ❂ Nematic Defect: compute nematic defects from phase contrast images of tissues ❂ UNET segmentation: The first UNET implementation in Mathematica/Wolfram Language ❂ Elliptic Fourier Descriptor: Elliptic Fourier Descriptors for describing shapes ❂ CurvatureMeasure: Determine curvature of objects ❂ SMtrack and Lineage-Mapper: Track single molecules and cells respectively

Pinned

  1. Elliptical-Fourier-Descriptors Elliptical-Fourier-Descriptors Public

    elliptical fourier descriptors with and without lobe contributions

    Mathematica 13 4

  2. 3D-Vertex-Model 3D-Vertex-Model Public

    vertex model implementation to simulate biological tissue in 3D

    Mathematica 10 2

  3. Force-Inference Force-Inference Public

    implementation of the Bayesian Force Inference technique based on the work of Ishihara and Sugimura

    Mathematica 4 2

  4. UNet-Segmentation-Wolfram UNet-Segmentation-Wolfram Public

    neural network for obtaining binarized mask for objects in grayscale images

    Mathematica 14 6

  5. 2D-vertex-model 2D-vertex-model Public

    vertex model for simulating two-dimensional epithelial tissues

    Mathematica 6 2

  6. Nematic-Defect Nematic-Defect Public

    compute nematic defects from images

    Mathematica