Skip to content

Commit 5cb183b

Browse files
author
SarahOuologuem
committed
update to spatialData
1 parent 463ba6f commit 5cb183b

File tree

1 file changed

+53
-14
lines changed

1 file changed

+53
-14
lines changed

‎docs/usage/setup_for_spatial_workflows.md

Lines changed: 53 additions & 14 deletions
Original file line numberDiff line numberDiff line change
@@ -1,28 +1,67 @@
11
Sample submission file for the ingestion of spatial data
22
===========================
33

4-
The spatial transcriptomics ingestion workflow requires a sample submission file that specifies the location of the input files. The sample submission file is a tab-separated file with one row per sample. Panpipes currently supports the ingestion of `Visium` and `Vizgen` data.
4+
The spatial transcriptomics ingestion workflow requires a sample submission file that specifies the location of the input files. The sample submission file is a tab-separated file with one row per sample. Panpipes currently supports the ingestion of `Visium`, `Vizgen`, and `Xenium` data. The data of different technologies needs to be ingested separately with different sample submission files.
55

6-
The 6 columns of the sample submission file are:
6+
7+
The minimum required (non-optional) columns for each submission file are
78

89
**sample id**: Unique sample ID.
910

10-
**spatial_path**: The root directory containing the data files. Please note, that the folder structure of the root directory needs to be structured as expected by the [squidpy.read.visium](https://squidpy.readthedocs.io/en/stable/api/squidpy.read.visium.html) (for `Visium` data) or [squidpy.read.vizgen](https://squidpy.readthedocs.io/en/stable/api/squidpy.read.vizgen.html) (for `Vizgen` data) functions.
11+
**spatial_path**: The root directory containing the data files. Please note, that the folder structure of the root directory needs to be structured as expected by the [spatialdata_io.visium](https://spatialdata.scverse.org/projects/io/en/latest/generated/spatialdata_io.visium.html) (for `Visium` data), [spatialdata_io.merscope](https://spatialdata.scverse.org/projects/io/en/latest/generated/spatialdata_io.merscope.html) (for `Vizgen` data), or [spatialdata_io.xenium](https://spatialdata.scverse.org/projects/io/en/latest/generated/spatialdata_io.xenium.html) (for `Xenium` data) functions.
12+
13+
**spatial_filetype**: Either "vizgen", "visium", or "xenium".
14+
15+
16+
## Visium
17+
18+
The 7 columns of the Visium sample submission file are:
19+
20+
sample_id | spatial_path | spatial_filetype | visium_feature_bc_matrix | visium_fullres_image_file | visium_tissue_positions_file | visium_scalefactors_file
21+
----------|----------|------------|-----------|----------|-------------|-------------
22+
23+
The following 4 columns are **optional**:
24+
25+
**visium_feature_bc_matrix**: Name of the counts file. Corresponds to the `counts_file` parameter of [spatialdata_io.visium](https://spatialdata.scverse.org/projects/io/en/latest/generated/spatialdata_io.visium.html)
26+
27+
**visium_fullres_image_file**: Path to the full-resolution image. Corresponds to the `fullres_image_file` parameter of [spatialdata_io.visium](https://spatialdata.scverse.org/projects/io/en/latest/generated/spatialdata_io.visium.html)
28+
29+
**visium_tissue_positions_file**: Path to the tissue positions file. Corresponds to the `tissue_positions_file` parameter of [spatialdata_io.visium](https://spatialdata.scverse.org/projects/io/en/latest/generated/spatialdata_io.visium.html)
30+
31+
**visium_scalefactors_file**: Path to the scalefactors file. Corresponds to the `scalefactors_file` parameter of [spatialdata_io.visium](https://spatialdata.scverse.org/projects/io/en/latest/generated/spatialdata_io.visium.html)
32+
33+
#### [Example submission file](https://github.com/DendrouLab/panpipes-tutorials/blob/sarah_spatialData/docs/ingesting_visium_data/sample_file_qc_visium.txt)
34+
35+
36+
## Vizgen
37+
38+
The 6 columns of the Vizgen sample submission file are:
39+
40+
sample_id | spatial_path | spatial_filetype | vpt_cell_by_gene | vpt_cell_metadata | vpt_cell_boundaries
41+
----------|----------|------------|----------|-------------|-------------
42+
43+
The following 3 columns are **optional**:
44+
45+
**vpt_cell_by_gene**: The file name of the output of the vizgen-postprocessing-tool. See [spatialdata_io.merscope](https://spatialdata.scverse.org/projects/io/en/latest/generated/spatialdata_io.merscope.html)
46+
47+
**vpt_cell_metadata**: The file name of the output of the vizgen-postprocessing-tool. See [spatialdata_io.merscope](https://spatialdata.scverse.org/projects/io/en/latest/generated/spatialdata_io.merscope.html)
48+
49+
**vpt_cell_boundaries**: The file name of the output of the vizgen-postprocessing-tool. See [spatialdata_io.merscope](https://spatialdata.scverse.org/projects/io/en/latest/generated/spatialdata_io.merscope.html)
50+
51+
52+
#### Example submission files [MERFISH](https://github.com/DendrouLab/panpipes-tutorials/blob/sarah_spatialData/docs/ingesting_merfish_data/sample_file_qc_merfish.txt) [MERSCOPE](https://github.com/DendrouLab/panpipes-tutorials/blob/sarah_spatialData/docs/ingesting_merscope_data/sample_file_qc_merscope.txt)
53+
54+
## Xenium
55+
56+
The 3 columns of the Xenium sample submission file are:
57+
58+
sample_id | spatial_path | spatial_filetype |
59+
----------|----------|------------
1160

12-
**spatial_filetype**: Either "vizgen" or "visium".
61+
#### [Example submission file](https://github.com/DendrouLab/panpipes-tutorials/blob/sarah_spatialData/docs/ingesting_xenium_data/sample_file_qc_xenium.txt)
1362

14-
**spatial_counts**: The count matrix file. Usually `filtered_feature_bc_matrix.h5` or `raw_feature_bc_matrix.h5` for a `Visium` dataset. For `Vizgen` inputs, this file typically ends with `_cell_by_gene.csv.`
1563

16-
**spatial_metadata**: The metadata csv-file for `Vizgen` data. Leave empty for `Visium` data.
1764

18-
**spatial_transformation**: The transformation csv-file for `Vizgen` data. This column is **optional** for `Vizgen` data. Leave empty for `Visium` data.
1965

20-
**Note, that the columns, `sample_id`, `spatial_path`, `spatial_filetype`, and `spatial_counts` are required for both, `Visium` and `Vizgen` data. The `spatial_metadata`(required) and `spatial_transformation`(optional) columns are `Vizgen`-specific and should be left empty for `Visium` data.**
2166

22-
### <u>Example submission file</u>
2367

24-
| sample_id | spatial_path | spatial_filetype | spatial_counts | spatial_metadata | spatial_transformation |
25-
| --------- |--------------|------------------|-----------------------------------------|------------------------------------------|--------------------|
26-
| V1_Human_Heart |./data_visium/V1_Human_Heart |visium |V1_Human_Heart_filtered_feature_bc_matrix.h5 |
27-
| V1_Human_Lymph_Node |./data_visium/V1_Human_Lymph_Node| visium | V1_Human_Lymph_Node_filtered_feature_bc_matrix.h5 |
28-
Mouse_Brain | ./data_vizgen | vizgen | cell_by_gene_S1R1.csv | cell_metadata_S1R1.csv | images_micron_to_mosaic_pixel_transform.csv

0 commit comments

Comments
 (0)