data

Download data

SpatialTranscriptomics Olfactory Bulb

Link to the dataset.

from os import system

data_dir = "spatial_transcriptomics_ob"
system("mkdir -p " + data_dir)
for i in range(1, 13):
    system("wget http://www.spatialtranscriptomicsresearch.org/wp-content/uploads/2016/07/Rep{}_MOB_count_matrix-1.tsv -O {}/Rep{}_MOB_count_matrix-1.tsv".format(i, data_dir, i))

Slide-seq

Slide-seq data requires login to download. File: "Puck_180430_3.tar.gz".

Then, extract it:

mkdir slide-seq
tar xvf Puck_180430_3.tar.gz
mv Puck_180430_3/BeadMapping_6-12_1036/bijectivemapping.mat slide-seq/
rm -rf Puck_180430_3

And convert necessary fields from Matlab format (was using Matlab on O2)

load("./bijectivemapping.mat")
csvwrite('Locations.csv', [UniqueMappedBeads.Locations]')
fid = fopen('Genes.csv', 'w'); fprintf(fid, '%s\n', GeneNames{1:end}); fclose(fid);

osmFISH

wget http://linnarssonlab.org/osmFISH/osmFISH_SScortex_mouse_all_cells.loom

seqFISH+

NIT/3T3 data was published in Zenodo repository. For more details see seqFISH-PLUS GitHub. Data from experiment 1 was downloaded and converted to csv format. Csv file can be obtained from pklab server:

wget http://pklab.med.harvard.edu/viktor/data/spatial/seq_fish_nih3t3.csv

STARmap

Data. Requires downloading from DropBox.

mkdir star_map
# Download data there
unzip visual_160_20171120_BF4_light.zip -d visual_160_20171120_BF4_light
unzip visual_1020_20180505_BY3_1kgenes.zip -d visual_1020_20180505_BY3_1kgenes

Allen smFISH

Data was shared in SpaceTx consortium, but not published yet.

MERFISH

Subset of data from Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region was kindly provided by Jeffrey Moffitt