`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: str | None = 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: str | None = 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`#