Giotto Viewer is a web-based visualization package for spatial transcriptomic data.
It interactively displays spatial gene expression data, and allows users to interact with the data which would be otherwise difficult to do in a static visualization. Specifically, Giotto Viewer allows users to:
- create panels for a comparison of spatial annotations and cell type annotations for individual cells
- switch between displaying different annotations
- intuitively select specific cells of interest
- display staining images and cell morphology information
- finally display transcript localization data
Demo of the Giotto Viewer
of the visual cortex dataset (seqFISH+) with 523 cells, 10,000 genes has been created, and can be viewed.
This dataset contains close to transcriptome-wide measurement of spatial gene expression in all 6 layers of the visual cortex. Cell segmentation, staining images have been saved. Gene expression matrix is published along with the original paper (Eng et al, Nature 2019).
of the olfactory bulb (seqFISH+) with ~2000 cells, 10,000 genes can be viewed.
Olfactory Bulb dataset (2-panel configuration)
Cortex dataset (4-panel configuration)
Getting the Giotto Viewer
Giotto Viewer is maintained in its own repository Bitbucket pages. Bitbucket repositories have been created: giotto-viewer, giotto-viewer.js (the main engine) and giotto-viewer-processing (main engine). See below.
Follow this link (installation
) to learn about installation instructions.
In short, the list of pre-requisite software includes:
- Tile-up Ruby package
- ImageJ library (JAR file)
Tutorial for setting up Giotto Viewer
Once the prerequisite software have been installed, follow this link (TUTORIAL
) to get started with how to set up a dataset for Giotto Viewer. We use the seqFISH+ 10,000 gene dataset as a sample dataset for demonstration.
Tutorial for using Giotto Viewer
Follow this link (TUTORIAL) to learn how to navigate different functions within Giotto Viewer.