The goal of msireg is to co-register mass spectrometry images (MSI)
with microscopic optical images using SimpleIK.
You can install the development version of msireg from GitHub with:
if ( !require(devtools) ) { # if not installed already
install.packages("devtools")
}
devtools::install_github("sslakkimsetty/msireg")msireg co-registers MS images with optical images (H&E stained, AF)
using the family of registration methods from the SimpleITK package.
The package offers processing and summarization of MS imaging data and
optical images. This package uses spatial shrunken centroids method from
the Cardinal package to filter out unimportant features.
[1] Bemis, K. D., Harry, A., Eberlin, L. S., Ferreira, C., van de Ven, S. M., Mallick, P., Stolowitz, M., and Vitek, O.”, “Cardinal: an R package for statistical analysis of mass spectrometry-based imaging experiments.
[2] L.J.P. van der Maaten and G.E. Hinton. Visualizing High-Dimensional Data Using t-SNE. Journal of Machine Learning Research 9(Nov):2579-2605, 2008.
[3] Gregoire Pau, Florian Fuchs, Oleg Sklyar, Michael Boutros, and Wolfgang Huber (2010):“,”EBImage - an R package for image processing with applications to cellular phenotypes.”, “Bioinformatics
[4] Beare, R., Lowekamp, B., & Yaniv, Z. (2018). Image Segmentation, Registration and Characterization in R with SimpleITK. Journal of Statistical Software, 86(8), 1–35. https://doi.org/10.18637/jss.v086.i08
[5] Reference for data (in data/)