Download of Demo Datasets

Download of Demo Datasets#

This notebook demonstrates the download of different publicly available Xenium datasets. For the tutorial only the breast cancer notebook is required and downloaded at the beginning of notebook 01. So you might also want to skip this notebook, since the downloads take a lot of time.

InSitupy offers eight functions that each download a different dataset into ‘~/.cache/InSituPy/demo_datasets’. The data is provided by 10x Genomics and is publicly available. Each function returns an InSituData object and has an optional argument overwrite, which can be set to True, whenever a repeated download is desired.

  1. xenium_human_breast_cancer(): In situ gene expression dataset by xenium onboard analysis 1.0.1
    https://www.10xgenomics.com/products/xenium-in-situ/preview-dataset-human-breast

  2. xenium_human_brain_cancer(): In situ gene expression dataset by xenium onboard analysis 2.0.0
    https://www.10xgenomics.com/datasets/ffpe-human-brain-cancer-data-with-human-immuno-oncology-profiling-panel-and-custom-add-on-1-standard

  3. xenium_nondiseased_kidney(): In situ gene expression dataset by xenium onboard analysis 1.5.0
    https://www.10xgenomics.com/resources/datasets/human-kidney-preview-data-xenium-human-multi-tissue-and-cancer-panel-1-standard

  4. xenium_hskin_melanoma(): In situ gene expression dataset by xenium onboard analysis 1.7.0
    https://www.10xgenomics.com/resources/datasets/human-skin-preview-data-xenium-human-skin-gene-expression-panel-add-on-1-standard

  5. xenium_pancreatic_cancer(): In situ gene expression dataset by xenium onboard analysis 1.6.0
    https://www.10xgenomics.com/datasets/pancreatic-cancer-with-xenium-human-multi-tissue-and-cancer-panel-1-standard

  6. xenium_human_lung_cancer(): In situ gene expression dataset by xenium onboard analysis 2.0.0 (Xenium multimodal cell segmentation)
    https://www.10xgenomics.com/datasets/preview-data-ffpe-human-lung-cancer-with-xenium-multimodal-cell-segmentation-1-standard

  7. xenium_human_lymph_node_5k(): In situ gene expression dataset with xenium onboard analysis 3.0.0. (testing of 5000 genes compared to 400 in the previous versions)
    https://www.10xgenomics.com/datasets/preview-data-xenium-prime-gene-expression

  8. xenium_human_lymph_node(): In situ gene expression dataset with xenium onboard analysis 1.5.0
    https://www.10xgenomics.com/datasets/human-lymph-node-preview-data-xenium-human-multi-tissue-and-cancer-panel-1-standard

## The following code ensures that all functions and init files are reloaded before executions.
%load_ext autoreload
%autoreload 2

from insitupy.datasets import (xenium_human_brain_cancer, xenium_human_breast_cancer,
                        xenium_human_kidney_nondiseased, xenium_human_lung_cancer,
                        xenium_human_lymph_node, xenium_human_lymph_node_5k,
                        xenium_human_pancreatic_cancer, xenium_human_skin_melanoma                        )

from insitupy.datasets import list_downloaded_datasets

hbreast = xenium_human_breast_cancer()
hbreast
hbreast.load_all()
hbreast.show()

This dataset exists already. Download is skipped. To force download set `overwrite=True`.
Image exists. Checking md5sum...
The md5sum matches. Download is skipped. To force download set `overwrite=True`.
Image exists. Checking md5sum...
The md5sum matches. Download is skipped. To force download set `overwrite=True`.
Corresponding image data can be found in C:\Users\ge37voy\.cache\InSituPy\demo_datasets\hbreastcancer\unregistered_images
For this dataset following images are available:
slide_id__hbreastcancer__HE__histo.ome.tiff
slide_id__hbreastcancer__CD20_HER2_DAPI__IF.ome.tiff
Loading cells...
Loading images...
Loading transcripts...

list_downloaded_datasets()

Following demo datasets were found:

- hbreastcancer
- hpancreas
- xenium_test_dataset

Below is another example for the human lung cancer dataset#

# hlung = xenium_human_lung_cancer()
# hlung
# hlung.load_all()
# hlung.show()