Examples¶

Dataset Information¶

See Spatial Datasets to find raw and pre-processed input data and Giotto scripts (work in progress).

The typical run time range for the different datasets on a personal computer is around 10~45 minutes. All of the examples are gradually updated to the latest Giotto version! Click on the images below to try out some of the example datasets.

Dataset Availability¶

Where to find seqFISH+ and other ready-to-use datasets?

Checkout https://github.com/RubD/spatial-datasets to find already preprocessed datasets.

Where to find other spatial datasets?

Checkout https://www.spatialomics.org/SpatialDB/ to download expression matrix and location information.

How to automatically download tutorial datasets?¶

merFISH Example

# choose your directory
my_working_dir = getwd()

# standardly download data to working directory
getSpatialDataset(dataset = 'merfish_preoptic', directory = my_working_dir)

# use wget to download data to working directory (much faster)
getSpatialDataset(dataset = 'merfish_preoptic', directory = my_working_dir, method = 'wget')

# avoid certification issues with wget
getSpatialDataset(dataset = 'merfish_preoptic', directory = my_working_dir, method = 'wget', extra = '--no-check-certificate')

# see download.file for more options
?download.file