`spateo.sample_data`#

Module Contents#

Functions#

`download_data`(→ str)	Parse url to get the file name and then download the data to designated folders.
`get_adata`(→ anndata.AnnData)	Download example data to local folder.
`drosophila`([filename, dir_name, backup])	Multiple drosophila spatial transcriptome data.
`mousebrain`(filename[, dir_name, backup])	Mouse brain spatial transcriptome data.
`axolotl`(filename[, dir_name, backup])	axolotl spatial transcriptome data.
`slideseq`([filename, dir_name, backup])	Saptial transcriptomic sample from the mouse hippocampus; data generated using Slide-seqV2. See: Stickels,
`seqfish`([filename, dir_name, backup])	Spatial transcriptomic sample taken at one timepoint in the process of mouse organogenesis; data generated using
`merfish`([filename, dir_name, backup])	Spatial transcriptomic sample taken from the mouse hypothalamus; data generated using MERFISH. See: Moffitt,
`seqscope`([filename, dir_name, backup])	Spatial transcriptomic sample taken from the mouse liver; data generated using Seq-Scope. See: Cho, C. S.,
`starmap`([filename, dir_name, backup])	Spatial transcriptomic sample taken from the mouse brain; data generated using STARmap. See: Wang, X., Allen,

spateo.sample_data.download_data(url: str, file_path: Optional[str] = None, dir_name: str = './data') → str[source]#

Parse url to get the file name and then download the data to designated folders.

Parameters

url: url that deposits the data.
file_path: file path that will store the data locally.
dir_name: name of the directory.

Returns

the file path that points to the downloaded data.

spateo.sample_data.get_adata(url: str, filename: Optional[str] = None, dir_name: str = './data') → anndata.AnnData[source]#

Download example data to local folder.

Parameters

url: url that deposits the data.
filename: file name that will store the data locally.
dir_name: name of the directory.

Returns

AnnData: an Annodata object.

Return type

adata

spateo.sample_data.drosophila(filename: str = 'E7-9h_cellbin_tdr_v2.h5ad', dir_name: str = './data', backup: bool = False)[source]#

Multiple drosophila spatial transcriptome data.

Parameters

filename

file name of the data. Available filename are:

E7-9h_cellbin_tdr_v1.h5ad
E7-9h_cellbin_tdr_v2.h5ad
E7-9h_cellbin_tdr_v2_midgut.h5ad
E7-9h_cellbin_tdr_v3_midgut.h5ad
E7-9h_cellbin_h5ad.zip
E7-9h_bin20_h5ad.zip
E9-10h_cellbin_tdr_v1.h5ad
E9-10h_cellbin_tdr_v2.h5ad
E9-10h_cellbin_tdr_v2_midgut.h5ad
E9-10h_cellbin_tdr_v2_CNS.h5ad

dir_name

dir path that will store the data locally.

backup

Whether to use an alternate link to download data. This is very useful for Chinese scientists.

Returns

Returns adata object.

spateo.sample_data.mousebrain(filename, dir_name: str = './data', backup: bool = False)[source]#

Mouse brain spatial transcriptome data.

Parameters

filename: file name of the data. Available filename are: * mousebrain_bin30.h5ad * mousebrain_bin50_raw.h5ad * mousebrain_bin60.h5ad * mousebrain_bin60_clustered.h5ad * mousebrain_cellbin_clustered.h5ad
dir_name: dir path that will store the data locally.
backup: Whether to use an alternate link to download data. This is very useful for Chinese scientists.

Returns

Returns adata object.

spateo.sample_data.axolotl(filename, dir_name: str = './data', backup: bool = False)[source]#

axolotl spatial transcriptome data.

Parameters

filename: file name of the data. Available filename are: * axolotl_2DPI.h5ad * axolotl_2DPI_right.h5ad
dir_name: dir path that will store the data locally.
backup: Whether to use an alternate link to download data. This is very useful for Chinese scientists.

Returns

Returns adata object.

spateo.sample_data.slideseq(filename='slideseq_mouse_hippocampus.h5ad', dir_name: str = './data', backup: bool = False)[source]#

Saptial transcriptomic sample from the mouse hippocampus; data generated using Slide-seqV2. See: Stickels, R. R., Murray, E., Kumar, P., Li, J., Marshall, J. L., Di Bella, D. J., … & Chen, F. (2021). Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2. Nature biotechnology, 39(3), 313-319.

Parameters

filename: file name of the data. Available filename are: * slideseq_mouse_hippocampus.h5ad
dir_name: dir path that will store the data locally.
backup: Whether to use an alternate link to download data. This is very useful for Chinese scientists.

Returns

Returns adata object containing Slide-seq data.

spateo.sample_data.seqfish(filename='seqfish_mouse_embryo.h5ad', dir_name: str = './data', backup: bool = False)[source]#

Spatial transcriptomic sample taken at one timepoint in the process of mouse organogenesis; data generated using seqFISH. See: Lohoff, T., Ghazanfar, S., Missarova, A., Koulena, N., Pierson, N., Griffiths, J. A., … & Marioni, J. C. (2022). Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis. Nature biotechnology, 40(1), 74-85.

Parameters

filename: file name of the data. Available filename are: * seqfish_mouse_embryo.h5ad
dir_name: dir path that will store the data locally.
backup: Whether to use an alternate link to download data. This is very useful for Chinese scientists.

Returns

Returns adata object containing seqFISH data.

spateo.sample_data.merfish(filename='merfish_mouse_hypothalamus.h5ad', dir_name: str = './data', backup: bool = False)[source]#

Spatial transcriptomic sample taken from the mouse hypothalamus; data generated using MERFISH. See: Moffitt, J. R., Bambah-Mukku, D., Eichhorn, S. W., Vaughn, E., Shekhar, K., Perez, J. D., … & Zhuang, X. (2018). Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region. Science, 362(6416), eaau5324.

Parameters

filename: file name of the data. Available filename are: * merfish_mouse_hypothalamus.h5ad
dir_name: dir path that will store the data locally.
backup: Whether to use an alternate link to download data. This is very useful for Chinese scientists.

Returns

Returns adata object containing MERFISH data.

spateo.sample_data.seqscope(filename='seqscope_mouse_liver.h5ad', dir_name: str = './data', backup: bool = False)[source]#

Spatial transcriptomic sample taken from the mouse liver; data generated using Seq-Scope. See: Cho, C. S., Xi, J., Si, Y., Park, S. R., Hsu, J. E., Kim, M., … & Lee, J. H. (2021). Microscopic examination of spatial transcriptome using Seq-Scope. Cell, 184(13), 3559-3572, and: Xi, J., Lee, J. H., Kang, H. M., & Jun, G. (2022). STtools: a comprehensive software pipeline for ultra-high-resolution spatial transcriptomics data. Bioinformatics Advances, 2(1), vbac061.

Parameters

filename: file name of the data. Available filename are: * seqscope_mouse_liver.h5ad
dir_name: dir path that will store the data locally.
backup: Whether to use an alternate link to download data. This is very useful for Chinese scientists.

Returns

Returns adata object containing Seq-Scope data.

spateo.sample_data.starmap(filename='starmap_mouse_brain.h5ad', dir_name: str = './data', backup: bool = False)[source]#

Spatial transcriptomic sample taken from the mouse brain; data generated using STARmap. See: Wang, X., Allen, W. E., Wright, M. A., Sylwestrak, E. L., Samusik, N., Vesuna, S., … & Deisseroth, K. (2018). Three-dimensional intact-tissue sequencing of single-cell transcriptional states. Science, 361(6400), eaat5691.

Parameters

filename: file name of the data. Available filename are: * starmap_mouse_brain.h5ad
dir_name: dir path that will store the data locally.
backup: Whether to use an alternate link to download data. This is very useful for Chinese scientists.

Returns

Returns adata object containing STARmap data.

spateo.sample_data#

Module Contents#

Functions#

`spateo.sample_data`#