Visium
Sample details
Study Name |
|
WebAtlas |
|
Tissue |
Human breast cancer |
Data Source Link |
Steps to reproduce
Follow the steps below to reproduce this sample in the pipeline, and visualise the data yourself in your web browser. It can be followed on any POSIX compatible system (Linux, OS X, etc). This example requires you to have already setup your environment first.
1. Download the sample data
Using wget
Input
mkdir -p input/CytAssist_FFPE_Human_Breast_Cancer
wget https://cf.10xgenomics.com/samples/spatial-exp/2.0.0/CytAssist_FFPE_Human_Breast_Cancer/CytAssist_FFPE_Human_Breast_Cancer_tissue_image.tif -O input/CytAssist_FFPE_Human_Breast_Cancer/tissue_image.tif
wget https://cf.10xgenomics.com/samples/spatial-exp/2.0.0/CytAssist_FFPE_Human_Breast_Cancer/CytAssist_FFPE_Human_Breast_Cancer_analysis.tar.gz -O input/CytAssist_FFPE_Human_Breast_Cancer/analysis.tar.gz
wget https://cf.10xgenomics.com/samples/spatial-exp/2.0.0/CytAssist_FFPE_Human_Breast_Cancer/CytAssist_FFPE_Human_Breast_Cancer_filtered_feature_bc_matrix.h5 -O input/CytAssist_FFPE_Human_Breast_Cancer/filtered_feature_bc_matrix.h5
wget https://cf.10xgenomics.com/samples/spatial-exp/2.0.0/CytAssist_FFPE_Human_Breast_Cancer/CytAssist_FFPE_Human_Breast_Cancer_spatial.tar.gz -O input/CytAssist_FFPE_Human_Breast_Cancer/spatial.tar.gz
Output
--2023-05-17 21:37:57-- https://cf.10xgenomics.com/samples/spatial-exp/2.0.0/CytAssist_FFPE_Human_Breast_Cancer/CytAssist_FFPE_Human_Breast_Cancer_spatial.tar.gz -O ./input/CytAssist_FFPE_Human_Breast_Cancer/spatial.tar.gz
Resolving cf.10xgenomics.com (cf.10xgenomics.com)... 104.18.0.173, 104.18.1.173, 2606:4700::6812:ad, ...
Connecting to cf.10xgenomics.com (cf.10xgenomics.com)|104.18.0.173|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 34479952 (33M) [application/x-tar]
Saving to: ‘input/CytAssist_FFPE_Human_Breast_Cancer/spatial.tar.gz
./input/CytAssist_FFPE_Human_Breas 100%[================================================================>] 32.88M --.-KB/s in 0s
2023-05-17 21:37:58 (7.16 MB/s) - ‘input/CytAssist_FFPE_Human_Breast_Cancer/spatial.tar.gz’ saved [34479952/34479952]
Using curl
Input
mkdir -p input/CytAssist_FFPE_Human_Breast_Cancer
curl -o input/CytAssist_FFPE_Human_Breast_Cancer/tissue_image.tif https://cf.10xgenomics.com/samples/spatial-exp/2.0.0/CytAssist_FFPE_Human_Breast_Cancer/CytAssist_FFPE_Human_Breast_Cancer_tissue_image.tif
curl -o input/CytAssist_FFPE_Human_Breast_Cancer/analysis.tar.gz https://cf.10xgenomics.com/samples/spatial-exp/2.0.0/CytAssist_FFPE_Human_Breast_Cancer/CytAssist_FFPE_Human_Breast_Cancer_analysis.tar.gz
curl -o input/CytAssist_FFPE_Human_Breast_Cancer/filtered_feature_bc_matrix.h5 https://cf.10xgenomics.com/samples/spatial-exp/2.0.0/CytAssist_FFPE_Human_Breast_Cancer/CytAssist_FFPE_Human_Breast_Cancer_filtered_feature_bc_matrix.h5
curl -o input/CytAssist_FFPE_Human_Breast_Cancer/spatial.tar.gz https://cf.10xgenomics.com/samples/spatial-exp/2.0.0/CytAssist_FFPE_Human_Breast_Cancer/CytAssist_FFPE_Human_Breast_Cancer_spatial.tar.gz
Output
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 1207M 100 1207M 0 0 8156k 0 0:02:31 0:02:31 --:--:-- 8416k
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 35.8M 100 35.8M 0 0 7986k 0 0:00:04 0:00:04 --:--:-- 7994k
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 31.7M 100 31.7M 0 0 8071k 0 0:00:04 0:00:04 --:--:-- 8091k
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 32.8M 100 32.8M 0 0 8443k 0 0:00:03 0:00:03 --:--:-- 8451k
2. Extract and process sample data
Input
tar -xzvf input/CytAssist_FFPE_Human_Breast_Cancer/analysis.tar.gz -C input/CytAssist_FFPE_Human_Breast_Cancer
tar -xzvf input/CytAssist_FFPE_Human_Breast_Cancer/spatial.tar.gz -C input/CytAssist_FFPE_Human_Breast_Cancer
Output
analysis/
analysis/umap/
analysis/umap/gene_expression_2_components/
analysis/umap/gene_expression_2_components/projection.csv
...
spatial/scalefactors_json.json
spatial/aligned_fiducials.jpg
spatial/tissue_hires_image.png
3. Run the pipeline
Warning
Users working on newer Silicon-based Macs may encounter problems with the conda environment. Some packages have not yet been compiled for Apple silicon processors therefore, we recommend you install the packages originally compiled for Mac computers with Intel processors. Set an environment variable that specifies the architecture before running the pipeline, like this:
Input
export CONDA_SUBDIR=osx-64
Input
nextflow run main.nf \
-params-file templates/examples/CytAssist_FFPE_Human_Breast_Cancer.yaml \
-entry Full_pipeline \
-profile conda
Output
N E X T F L O W ~ version 22.04.5
Launching `main.nf` [insane_dijkstra] DSL2 - revision: 1b6a73f4d6
[05/d2276b] process > Full_pipeline:Process_files:route_file (spaceranger, CytAssist_FFPE_Human_Breast_Cancer) [100%] 1 of 1 ✔
[0c/3ffdac] process > Full_pipeline:Process_images:Generate_image ([visium, breast-cancer], label, CytAssist_... [100%] 1 of 1 ✔
[f1/efaaae] process > Full_pipeline:Process_images:image_to_zarr (tissue_image.tif) [100%] 2 of 2 ✔
[44/2bcaeb] process > Full_pipeline:Process_images:ome_zarr_metadata (METADATA.ome.xml) [100%] 2 of 2 ✔
[43/04893d] process > Full_pipeline:Output_to_config:Build_config ([visium, breast-cancer]) [100%] 1 of 1 ✔
4. Check execution was successful
The output from the pipeline will indicate if the execution was successful. You can also verify the expected directories are created.
Input
ls -l output/CytAssist_FFPE_Human_Breast_Cancer/0.5.2
Output
total 1103476
-rw-r--r-- 1 dh74 dh74 288446018 May 17 21:42 tmp-visium-breast-cancer.h5ad
drwxrwxr-x 11 dh74 dh74 4096 May 17 21:42 visium-breast-cancer-anndata.zarr
-rw-r--r-- 1 dh74 dh74 4667 May 17 21:43 visium-breast-cancer-config.json
-rw-r--r-- 1 dh74 dh74 841484966 May 17 21:42 visium-breast-cancer-label.tif
drwxrwxr-x 4 dh74 dh74 4096 May 17 21:43 visium-breast-cancer-label.zarr
drwxrwxr-x 4 dh74 dh74 4096 May 17 21:43 visium-breast-cancer-raw.zarr
5. Serve the data output through a local web server
To browse and explore the data, you need to serve the output data through a web server. You can use your preferred web server, but you must ensure the data is served over port 3000, at http://localhost:3000, and that CORS is enabled via the Access-Control-Allow-Origin header.
Input
npx http-server output/CytAssist_FFPE_Human_Breast_Cancer/0.5.2 --port 3000 --cors
Output
Starting up http-server, serving ./
http-server version: 14.1.1
http-server settings:
CORS: true
Cache: 3600 seconds
Connection Timeout: 120 seconds
Directory Listings: visible
AutoIndex: visible
Serve GZIP Files: false
Serve Brotli Files: false
Default File Extension: none
Available on:
http://127.0.0.1:3000
http://192.168.0.23:3000
Hit CTRL-C to stop the server
6. Explore data in your browser
Start your web browser and open: