Chapter 1 About masmr

This book provides a quick introduction to masmr: Modular Algorithms for Spotcalling in MERFISH in R.

The masmr package is designed to allow users to build custom image processing pipelines, with a focus on MERFISH decoding.

For queries / comments, kindly direct them to Eugene Kwa ().

1.1 Installation

Currently, this package is hosted on GitHub:

https://github.com/eugenekwaNeuromics/masmr/.

Installation should be achievable with the devtools package:

devtools::install_github('eugenekwaNeuromics/masmr')

Currently depends on the following packages:

  • ggplot2, scales, reshape2, viridis: for plotting.
  • data.table: for quick reading and writing of data files.
  • RBioFormats: for reading a variety of microscopy image formats.
  • imager, EBImage: for image processing functions.
  • tripack: for triangular meshing functions.
  • reticulate: for interfacing with Python (used during cell segmentation).
  • parallel: for getting number of cores on machine.
  • Rcpp, RcppEigen: for functions written in C++.
  • RcppML: for fast non-negative matrix factorization.
  • igraph: for clustering.
  • rlang: for parsing arguments.