Statistical software

GammaGateR

The GammaGateR R Package was developed by Ruby Xiong

MILWRM

The MILWRM Python package (developed and maintained by Harsimran Kaur) is a highly scalable tool for consensus tissue domain detection that can be applied across a large number of whole slide multiplexed immunofluorescence images (Kaur et al. 2024). It can be installed through XX and a tutorial is available XX.

mxnorm

The mxnorm R package (developed by Coleman Harris) includes tools to evaluate image normalization procedures for multiplexed immunofluorescence imaging and is available for installation from CRAN using install.packages('mxnorm') (Harris et al. 2022).

pbj

The pbj R package is a semiparametric bootstrap based joint inference procedure designed to do cluster-style inference for group-level neuroimage analysis. The latest version is currently available on Github and can be installed from R using devtools::install_github('statimagcoll/pbj'). The pbj User’s Guide is a bookdown document describing the methods used in the R package and includes several analysis vignettes.

RESI

The RESI R package is available on CRAN by executing install.packages('RESI') and implements the robust effect size index in R by adding the index with nonparametric bootstrap confidence intervals to almost any coefficient or anova table. The package development was led by Megan Jones and she is also the primary maintainer. The sofware paper was accepted in the Journal of Statistical Software (in press). The preprint is available on ArXiv.

GitHub

Active software projects can be found at the Statistical Imaging Collective Github.