https://github.com/lcrawlab/ashapesampler_paper_results
Code to reproduce analyses and results provided in the alpha shape sampler paper beyond what is given in the R package.
https://github.com/lcrawlab/ashapesampler_paper_results
Last synced: 7 months ago
JSON representation
Code to reproduce analyses and results provided in the alpha shape sampler paper beyond what is given in the R package.
- Host: GitHub
- URL: https://github.com/lcrawlab/ashapesampler_paper_results
- Owner: lcrawlab
- Created: 2023-11-28T20:45:53.000Z (over 2 years ago)
- Default Branch: main
- Last Pushed: 2024-02-01T17:12:56.000Z (over 2 years ago)
- Last Synced: 2024-02-02T18:56:22.857Z (over 2 years ago)
- Language: HTML
- Homepage:
- Size: 5.46 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# $\alpha$-Shape Sampler Paper Results
Code to reproduce analyses and results provided in the $\alpha$-shape sampler paper beyond what is given in the [R package](https://cran.r-project.org/package=ashapesampler).
## Directory Contents
The list of directories and their corresponding purpose in this repository include:
* `neutrophilML` has all machine learning experiments for replication of analyses with the neutrophil data, including calculating shape characteristics and performing dimensionality reduction in python. In particular, we show how to implement the manifold regularized autoencoder (MRAE).
* `teeth_demo` contains a subsampled dataset of primate mandibular molars and a notebook demonstrating how generate a new tooth.
* `mask_to_complex` contains a notebook for converting a binary mask to a simplicial complex and vice versa in R.
## Relevant Citations
D. Bhaskar, D. Lee, H. Knútsdóttir, C. Tan, M. Zhang, P. Dean, C. Roskelley, and L. Keshet. A methodology for morphological feature extraction and unsupervised cell classification. _bioRxiv_. 623793.
E.T. Winn-Nuñez, H. Witt, D. Bhaskar, R.Y. Huang, I.Y. Wong, J.S. Reichner, and L. Crawford. Generative modeling of biological shapes and images using a probabilistic $\alpha$-shape sampler. _bioRxiv_.