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# -------
# the Xenium datasets are licensed as CC BY 4.0, as shown here
# https://www.10xgenomics.com/support/software/xenium-onboard-analysis/latest/resources/xenium-example-data
# 10x Genomics Xenium 2.0.0
[[datasets]]
key = "xenium_breast"
group = "xenium"
url = "https://cf.10xgenomics.com/samples/xenium/2.0.0/Xenium_V1_human_Breast_2fov/Xenium_V1_human_Breast_2fov_outs.zip"
archive_name = "Xenium_V1_human_Breast_2fov_outs.zip"
extracted_dir = "Xenium_V1_human_Breast_2fov_outs"
source = "10x Genomics Xenium 2.0.0, CC BY 4.0"
# 10x Genomics Xenium 2.0.0
[[datasets]]
key = "xenium_lung"
group = "xenium"
url = "https://cf.10xgenomics.com/samples/xenium/2.0.0/Xenium_V1_human_Lung_2fov/Xenium_V1_human_Lung_2fov_outs.zip"
archive_name = "Xenium_V1_human_Lung_2fov_outs.zip"
extracted_dir = "Xenium_V1_human_Lung_2fov_outs"
source = "10x Genomics Xenium 2.0.0, CC BY 4.0"
# 10x Genomics Xenium 3.0.0 (5K) Mouse ileum, multimodal cell segmentation
# this file seems to be corrupted; skipping it for now
# https://cf.10xgenomics.com/samples/xenium/3.0.0/Xenium_Prime_MultiCellSeg_Mouse_Ileum_tiny/Xenium_Prime_MultiCellSeg_Mouse_Ileum_tiny.zip
# 10x Genomics Xenium 3.0.0 (5K) Mouse ileum, nuclear expansion
[[datasets]]
key = "xenium_prime_mouse_ileum"
group = "xenium"
url = "https://cf.10xgenomics.com/samples/xenium/3.0.0/Xenium_Prime_Mouse_Ileum_tiny/Xenium_Prime_Mouse_Ileum_tiny_outs.zip"
archive_name = "Xenium_Prime_Mouse_Ileum_tiny_outs.zip"
extracted_dir = "Xenium_Prime_Mouse_Ileum_tiny_outs"
source = "10x Genomics Xenium 3.0.0, CC BY 4.0"
# 10x Genomics Xenium 4.0.0 (v1) Human ovary, nuclear expansion
[[datasets]]
key = "xenium_ovary"
group = "xenium"
url = "https://cf.10xgenomics.com/samples/xenium/4.0.0/Xenium_V1_Human_Ovary_tiny/Xenium_V1_Human_Ovary_tiny_outs.zip"
archive_name = "Xenium_V1_Human_Ovary_tiny_outs.zip"
extracted_dir = "Xenium_V1_Human_Ovary_tiny_outs"
source = "10x Genomics Xenium 4.0.0, CC BY 4.0"
# 10x Genomics Xenium 4.0.0 (v1) Human ovary, multimodal cell segmentation
[[datasets]]
key = "xenium_multicell_ovary"
group = "xenium"
url = "https://cf.10xgenomics.com/samples/xenium/4.0.0/Xenium_V1_MultiCellSeg_Human_Ovary_tiny/Xenium_V1_MultiCellSeg_Human_Ovary_tiny_outs.zip"
archive_name = "Xenium_V1_MultiCellSeg_Human_Ovary_tiny_outs.zip"
extracted_dir = "Xenium_V1_MultiCellSeg_Human_Ovary_tiny_outs"
source = "10x Genomics Xenium 4.0.0, CC BY 4.0"
# 10x Genomics Xenium 4.0.0 (v1+Protein) Human kidney, multimodal cell segmentation
[[datasets]]
key = "xenium_protein_kidney"
group = "xenium"
url = "https://cf.10xgenomics.com/samples/xenium/4.0.0/Xenium_V1_Protein_Human_Kidney_tiny/Xenium_V1_Protein_Human_Kidney_tiny_outs.zip"
archive_name = "Xenium_V1_Protein_Human_Kidney_tiny_outs.zip"
extracted_dir = "Xenium_V1_Protein_Human_Kidney_tiny_outs"
source = "10x Genomics Xenium 4.0.0, CC BY 4.0"
# -------
# the Visium HD dataset is licensed as CC BY 4.0, as shown here
# https://www.10xgenomics.com/support/software/space-ranger/latest/resources/visium-hd-example-data
# 10x Genomics Visium HD 4.0.1 3' Mouse Brain Chunk
[[datasets]]
key = "visium_hd_tiny"
group = "visium_hd"
url = "https://cf.10xgenomics.com/samples/spatial-exp/4.0.1/Visium_HD_Tiny_3prime_Dataset/Visium_HD_Tiny_3prime_Dataset_outs.zip"
archive_name = "Visium_HD_Tiny_3prime_Dataset_outs.zip"
extracted_dir = "Visium_HD_Tiny_3prime_Dataset_outs"
source = "10x Genomics Visium HD 4.0.1, CC BY 4.0"
# -------
# we received written permission to make the following dataset public and integrate it in the CI system of spatialdata-io
# Spatial Genomics seqFISH v2
[[datasets]]
key = "seqfish"
group = "seqfish"
url = "https://s3.embl.de/spatialdata/raw_data/seqfish-2-test-dataset.zip"
archive_name = "seqfish-2-test-dataset.zip"
extracted_dir = "seqfish-2-test-dataset"
source = "Spatial Genomics seqFISH v2, public test data"
test_path = "instrument 2 official"
# -------
# MACSima OMAP datasets are licensed as CC BY 4.0
# OMAP23 for format v1.x.x
[[datasets]]
key = "macsima_omap23"
group = "macsima"
url = "https://zenodo.org/api/records/18196452/files-archive"
archive_name = "OMAP23_small.zip"
extracted_dir = "OMAP23_small"
source = "MACSima OMAP23, CC BY 4.0"
# OMAP10 for format v0.x.x
[[datasets]]
key = "macsima_omap10"
group = "macsima"
url = "https://zenodo.org/api/records/18196366/files-archive"
archive_name = "OMAP10_small.zip"
extracted_dir = "OMAP10_small"
source = "MACSima OMAP10, CC BY 4.0"