Giotto Viewer


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:



Demo of the Giotto Viewer

A demo 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).

A demo of the olfactory bulb (seqFISH+) with ~2000 cells, 10,000 genes can be viewed.

Screenshots

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.

Pre-requisite software
Follow this link (installation) to learn about installation instructions. In short, the list of pre-requisite software includes:
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.