VoltRon is a spatial omic analysis toolbox for multi-omics integration using spatial image registration. VoltRon is also capable of analyzing multiple types of spatially-aware data modalities.
Spatially Aware Analysis allows detecting spatial patterns across cells, spots, molecules and other entities.
Support for Big Data for VoltRon objects enables storing large feature data matrices and large microscopic images of tissues on disk without overloading memory, thus allowing analysis on large datasets with ease. VoltRon stores large images as pyramid structures to speed up visualization and data retrieval.
Interoperability across R/Python frameworks allows users to convert VoltRon objects to a large number of objects used by other spatial omic platforms such as Seurat, Squidpy (AnnData), SpatialExperiment (BioConductor) and Giotto.
To ask questions please use VoltRon discussion forum on google groups.
Install from the GitHub repository using devtools (with R version 4.3.0 or higher):
if (!require("devtools", quietly = TRUE))
install.packages("devtools")
devtools::install_github("BIMSBbioinfo/VoltRon")
Depending on the number of required dependencies, installation may be completed under a minute or may take a few minutes.
On Windows and MacOS, OpenCV will be downloaded automatically upon installation. However, Rtools may be required to be downloaded too, hence this may take some time!
On Ubuntu we provide a set of instructions that may help users to build OpenCV with necessary headers [here](https://github.com/BIMSBbioinfo/VoltRon/blob/main/inst/extdata/install_ubuntu.md.
On Fedora you may need opencv-devel
:
yum install opencv-devel
VoltRon incorporates RBioformats
package to import
images from ome.tiff
files, which requires Java
JDK to be available in your system:
See https://cran.r-project.org/web/packages/rJava for more information.
You can also run VoltRon from a container already available in Docker Hub. The docker image is based on the Rocker Project and can be run from the terminal like below:
docker run --rm -ti -e PASSWORD=<yourpassword> -p 8787:8787 amanukyan1385/rstudio-voltron:main
Then, start the RStudio session from the browser at
http://localhost:8787/
and enter rstudio
as
username and <yourpassword>
as password.
See here for more instructions on how to run the container using Docker Desktop.
Manukyan, A., Bahry, E., Wyler, E., Becher, E., Pascual-Reguant, A., Plumbom, I., … & Akalin, A. (2023). VoltRon: A Spatial Omics Analysis Platform for Multi-Resolution and Multi-omics Integration using Image Registration. bioRxiv, 2023-12. d
To ask questions please use VoltRon discussion forum on Google groups.