Docker image

As a way to quickly allow users use Giotto and to simplify the install process, we provide a premade docker image containing both the latest version of the analyzer and the viewer.
docker-giotto-4.7z (750MB)
See Docker details here Docker instructions.

Installing modules separately

The two modules of Giotto, analyzer and viewer, can be installed separately.

The analyzer is an R package named Giotto. It consists of basic functionalities of spatial toolkit including data structures and methods to store data matrices, construct spatial grid and network, and others. Giotto analyzer is maintained separately at our Github page RubD/Giotto To install just the analyzer, run the command within R:
See Installation for details.

The viewer is a set of two Python packages (in pip repository): smfish-image-processing, and giotto-viewer. It requires opencv-python, scikit-image as pre-requisites. Also requires ImageMagick commonly available in Linux, and Ruby, tileup Ruby package. See Installation for details.