giovp / spatialdata-sandbox Goto Github PK

Available datasets

• merfish
• mibitof
• nanostring
• toy/artificial dataset
• visium

Missign datasets

• maldi (from metaspace, see link in the comments)
• nanostring (GeoMX DSP, see link in the coments)
• vizgen merfish (any of these https://vizgen.com/data-release-program/)
• multimodal multi-fov dataset from the paper Spatially resolved clonal copy number alterations in benign and malignant tissue
• codex/ t-CyCIF (see link in the comments)
• 3D single molecule dataset with time and multiple samples (described in the comments)
• 3D multi-fov high content hiPSCs https://zenodo.org/record/7120354#.YzRXy-xBxzU
• 2 datasets from Molecular Cartography from Resolve Biosciences, described in the comments
• stereoseq data https://www.sciencedirect.com/science/article/pii/S0092867422003993?via%3Dihub
• lightset data (link in the comments and zulip discussion)
• slideseq + tcr-seq zulip discussion
• xenium (implement reader in spatialdata-io and add a dataset from 10x)
• EEL FISH
• BaSISS, breast cancer (see commonts)
• upcoming BICCN Zhuang lab data or Allen Institute MERSCOPE data (suggestion from Brian Long)
• in-situ sequencing dataset and other notebooks with analysis from a course from NBISweden

current metadata in readme does not allow to download the visium dataset. The folder should contain:

• a single python executable that downloads all the relevant data and splits it in building blocks in the data folder
• a single python executable that write the data according to current ngff specs proposal (see readme and available examples).

@ilia-kats could you take a look into this? thank you!