msireg
R package for co-registration of Mass Spectrometry images with Microscopy images using SimpleITK
Science Score: 57.0%
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Low similarity (13.1%) to scientific vocabulary
Last synced: 6 months ago
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Repository
R package for co-registration of Mass Spectrometry images with Microscopy images using SimpleITK
Basic Info
- Host: GitHub
- Owner: sslakkimsetty
- License: gpl-3.0
- Language: HTML
- Default Branch: main
- Size: 15.3 MB
Statistics
- Stars: 5
- Watchers: 1
- Forks: 0
- Open Issues: 2
- Releases: 0
Created over 3 years ago
· Last pushed over 1 year ago
Metadata Files
Readme
License
Citation
README.Rmd
---
output:
github_document:
html_preview: false
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# msireg
The goal of _msireg_ is to co-register mass spectrometry images (MSI) with microscopic optical images using `SimpleIK`.
## Installation
You can install the development version of msireg from [GitHub](https://github.com/) with:
```{r, eval=FALSE}
if ( !require(devtools) ) { # if not installed already
install.packages("devtools")
}
devtools::install_github("sslakkimsetty/msireg")
```
## Example usage
```{r, eval=FALSE}
```
# Details
_msicoreg_ 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.
# References
[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/)
Owner
- Name: Sai Srikanth Lakkimsetty
- Login: sslakkimsetty
- Kind: user
- Location: Boston, MA
- Repositories: 2
- Profile: https://github.com/sslakkimsetty
PhD student in Vitek Lab at Northeastern University
Citation (CITATION.cff)
cff-version: 1.2.0 message: "If you use this software, please cite it as below." authors: - family-names: "Lakkimsetty" given-names: "Sai Srikanth" orcid: "https://orcid.org/0000-0001-9552-1121" title: "R package for co-registration of Mass Spectrometry images with Microscopy images using SimpleITK" version: 0.1 date-released: 2022-09-03 url: "https://github.com/sslakkimsetty/msireg"
GitHub Events
Total
- Issues event: 1
- Watch event: 3
Last Year
- Issues event: 1
- Watch event: 3
Dependencies
DESCRIPTION
cran
- BiocParallel * imports
- Cardinal * imports
- EBImage * imports
- Rtsne * imports
- SimpleITK * imports
- graphics * imports
- sp * imports
- knitr * suggests
- testthat >= 3.0.0 suggests