Standardized preprocessing and quality control (QC) Python pipelines for kidney spatial transcriptomics and spatial omics datasets.
- 1. Overview
- 2. Python Environment Setup
- 3. Repository Architecture & Usage
- 4. Sample Catalog
- 5. Platform Summary
- 6. Disclaimer & Attribution
- 7. License
SpatialRenal is a curated repository hosting reproducible, per-sample preprocessing and quality control (QC) Python scripts for published kidney spatial transcriptomics datasets.
- 132 Spatial Samples: Covering 16 studies across human and mouse kidney models.
- 6 Spatial Platforms Supported:
- 10x Genomics Visium (39 samples)
- 10x Genomics Visium CytAssist (14 samples)
- 10x Genomics Visium HD (5 samples)
- 10x Genomics Xenium in situ (23 samples)
- NanoString CosMx SMI (3 samples)
- NanoString GeoMx DSP (48 samples)
- Code & Metadata Only: To ensure lightweight versioning and open access, this repository contains only Python processing scripts and provenance documentation — no compiled files, binary datasets, or raw sequencing archives are stored directly in this repository.
- Standardized Sample Units: Each sample directory under
sample/is standalone, embedding the sample's biological metadata and platform-calibrated QC threshold parameters.
The sample preprocessing pipelines rely on standard Python spatial transcriptomics and scientific computing libraries. Python 3.10, 3.11, or 3.12 is recommended.
# 1. Create a dedicated conda environment
conda create -n spatialrenal python=3.12 -y
# 2. Activate the environment
conda activate spatialrenal
# 3. Install core spatial transcriptomics dependencies from conda-forge
conda install -c conda-forge -y \
anndata \
scanpy \
numpy \
pandas \
scipy \
matplotlib \
pillow \
tifffile \
zarr \
h5py# Create and activate virtual environment
python3 -m venv spatialrenal_env
source spatialrenal_env/bin/activate
# Install required packages
pip install --upgrade pip
pip install \
"scanpy>=1.10.0" \
"anndata>=0.10.0" \
"numpy>=1.24.0" \
"pandas>=2.0.0" \
"scipy>=1.10.0" \
"matplotlib>=3.8.0" \
"pillow>=10.0.0" \
"tifffile>=2024.0.0" \
"zarr>=2.16.0" \
"h5py>=3.10.0"Verify that all necessary packages are properly installed:
python -c "import scanpy, anndata, numpy, pandas, scipy, matplotlib, PIL, tifffile, zarr, h5py; print('✓ SpatialRenal environment is ready!')"The repository is organized by platform, where each sample lives in its own directory:
SpatialRenal/
├── LICENSE # MIT License
├── README.md # Main registry & documentation
└── sample/
├── 10x_Visium/ # 10x Genomics Visium samples
│ └── GSMxxxxxxx/
│ ├── README.md # Sample metadata, raw file requirements, and GEO links
│ └── process.py # Preprocessing & QC pipeline
├── 10x_Visium_CytAssist/ # 10x Genomics Visium CytAssist samples
├── 10x_Visium_HD/ # 10x Genomics Visium HD samples
├── 10x_Xenium_in_situ/ # 10x Genomics Xenium in situ samples
├── NanoString_CosMx_SMI/ # NanoString CosMx SMI samples
└── NanoString_GeoMx_DSP/ # NanoString GeoMx DSP samples
- Locate the sample: Find your sample of interest in the Sample Catalog below and navigate into its directory.
- Review raw file requirements: Open the sample's
README.mdto see the expected author-distributed raw files and direct GEO download links. - Acquire raw files: Download the raw files from GEO and place them inside a local
raw/subdirectory within the sample folder. - Execute processing:
cd sample/<Platform>/<GSM> mkdir -p raw data tmp # (Place downloaded raw files into raw/) python process.py --raw-dir raw --data-dir data --tmp-dir tmp
- Outputs produced:
raw/<GSM>_raw_counts.h5: Unfiltered raw count matrix (AnnData-compatible HDF5 with coordinates).data/<GSM>_processed.h5: QC-filtered and metadata-annotated AnnData object.data/<GSM>_processed.qc.json: Standardized QC metrics summary (JSON).data/<GSM>_qc_report.txt: Human-readable QC log.data/<GSM>_umi_counts.png: High-resolution spatial UMI count visualization.
| GSM Accession | Sample ID | Species | Study / Series | Disease Condition / Context | Pipeline Link |
|---|---|---|---|---|---|
| GSM6047778 | V10S15-102_XY03_IU-21-015-2 | Homo sapiens | kidney-PT-regen (GSE298953) | reference (nephrectomy control) (reference kidney; reused from GSE183456) | GSM6047778 |
| GSM6047779 | V10S15-102_XY02_IU-21-019-5 | Homo sapiens | kidney-PT-regen (GSE298953) | reference (nephrectomy control) (reference kidney; reused from GSE183456) | GSM6047779 |
| GSM8110784 | Hyperuricemia mice1 | Mus musculus | hyperuricemia-mouse (GSE258959) | hyperuricemia (Uox-KO) (Uox-KO (hyperuricemia), male, C57BL/6J) | GSM8110784 |
| GSM8110785 | Hyperuricemia mice2 | Mus musculus | hyperuricemia-mouse (GSE258959) | hyperuricemia (Uox-KO) (Uox-KO (hyperuricemia), male, C57BL/6J) | GSM8110785 |
| GSM8110786 | Control mice1 | Mus musculus | hyperuricemia-mouse (GSE258959) | control (control, male, C57BL/6J) | GSM8110786 |
| GSM8110787 | Control mice2 | Mus musculus | hyperuricemia-mouse (GSE258959) | control (control, male, C57BL/6J) | GSM8110787 |
| GSM9026963 | IU-21-019-2 | Homo sapiens | kidney-PT-regen (GSE298953) | reference (nephrectomy control) (reference kidney; nephrectomy) | GSM9026963 |
| GSM9045323 | WT and KO | Mus musculus | kidney-repair-matrix (GSE299736) | AKI repair (AKI repair; pooled WT+KO) | GSM9045323 |
| GSM9108683 | ctrl | Homo sapiens | ANCA-vasculitis (GSE302677) | control (kidney cortex, control) | GSM9108683 |
| GSM9108684 | aav1 (mild AAV) | Homo sapiens | ANCA-vasculitis (GSE302677) | ANCA-AAV (mild) (kidney cortex, mild AAV) | GSM9108684 |
| GSM9108685 | aav2 (severe AAV) | Homo sapiens | ANCA-vasculitis (GSE302677) | ANCA-AAV (severe) (kidney cortex, severe AAV) | GSM9108685 |
| GSM9231917 | V10S15-103_XY01_IU-21-015F | Homo sapiens | DKD-MEF2C (GSE307817) | DKD (diabetic kidney disease; nephrectomy) | GSM9231917 |
| GSM9231918 | V10S15-103_XY03_IU-21-019F | Homo sapiens | DKD-MEF2C (GSE307817) | DKD (diabetic kidney disease; nephrectomy) | GSM9231918 |
| GSM9231919 | V42N07-395_XY04_IU94 | Homo sapiens | DKD-MEF2C (GSE307817) | DKD (diabetic kidney disease; biopsy) | GSM9231919 |
| GSM9231920 | V42D20-364_XY04_IU92 | Homo sapiens | DKD-MEF2C (GSE307817) | DKD (diabetic kidney disease; biopsy) | GSM9231920 |
| GSM9231921 | V42N07-395_XY01_IU98 | Homo sapiens | DKD-MEF2C (GSE307817) | DKD (diabetic kidney disease; biopsy) | GSM9231921 |
| GSM9231922 | V42D20-364_XY01_IU103 | Homo sapiens | DKD-MEF2C (GSE307817) | DKD (diabetic kidney disease; biopsy) | GSM9231922 |
| GSM9231923 | V42N07-339_XY04_F44 | Homo sapiens | DKD-MEF2C (GSE307817) | DKD (diabetic kidney disease; nephrectomy) | GSM9231923 |
| GSM9231924 | V10S15-103_XY02_IU-21-016F | Homo sapiens | DKD-MEF2C (GSE307817) | DKD (diabetic kidney disease; nephrectomy) | GSM9231924 |
| GSM9231925 | V10S15-103_XY04_IU-21-020F | Homo sapiens | DKD-MEF2C (GSE307817) | DKD (diabetic kidney disease; nephrectomy) | GSM9231925 |
| GSM9231926 | V42N07-339_XY01_3781 | Homo sapiens | DKD-MEF2C (GSE307817) | DKD (diabetic kidney disease; nephrectomy) | GSM9231926 |
| GSM9231927 | V42N07-399_XY01_3723 | Homo sapiens | DKD-MEF2C (GSE307817) | DKD (diabetic kidney disease; nephrectomy) | GSM9231927 |
| GSM9231928 | V42N07-399_XY04_3775 | Homo sapiens | DKD-MEF2C (GSE307817) | DKD (diabetic kidney disease; nephrectomy) | GSM9231928 |
| GSM9247127 | UUO 7d ligated SK3747 | Mus musculus | EPO-cell-neighborhood (GSE308511) | EPO/hypoxia model (UUO 7d, ligated, roxadustat) | GSM9247127 |
| GSM9247128 | UUO 7d ligated SK3753 | Mus musculus | EPO-cell-neighborhood (GSE308511) | EPO/hypoxia model (UUO 7d, ligated, roxadustat) | GSM9247128 |
| GSM9247129 | UUO 7d contralat SK3747 | Mus musculus | EPO-cell-neighborhood (GSE308511) | EPO/hypoxia model (UUO 7d, contralateral, roxadustat) | GSM9247129 |
| GSM9247130 | UUO 7d contralat SK3753 | Mus musculus | EPO-cell-neighborhood (GSE308511) | EPO/hypoxia model (UUO 7d, contralateral, roxadustat) | GSM9247130 |
| GSM9247131 | healthy roxadustat SK7543 | Mus musculus | EPO-cell-neighborhood (GSE308511) | EPO/hypoxia model (healthy, roxadustat) | GSM9247131 |
| GSM9247132 | healthy roxadustat SK9682 | Mus musculus | EPO-cell-neighborhood (GSE308511) | EPO/hypoxia model (healthy, roxadustat) | GSM9247132 |
| GSM9247133 | healthy hypoxia SK4156 | Mus musculus | EPO-cell-neighborhood (GSE308511) | EPO/hypoxia model (healthy, hypoxia (0.1% CO)) | GSM9247133 |
| GSM9247134 | healthy hypoxia SO4157 | Mus musculus | EPO-cell-neighborhood (GSE308511) | EPO/hypoxia model (healthy, hypoxia (0.1% CO)) | GSM9247134 |
| GSM9247135 | healthy normoxia SM1758 | Mus musculus | EPO-cell-neighborhood (GSE308511) | EPO/hypoxia model (healthy, tamoxifen ctrl (normoxia)) | GSM9247135 |
| GSM9247136 | healthy normoxia SM1763 | Mus musculus | EPO-cell-neighborhood (GSE308511) | EPO/hypoxia model (healthy, tamoxifen ctrl (normoxia)) | GSM9247136 |
| GSM9247137 | UUO 3d ligated SK1441 | Mus musculus | EPO-cell-neighborhood (GSE308511) | EPO/hypoxia model (UUO 3d, ligated) | GSM9247137 |
| GSM9247138 | UUO 3d ligated SK1440 | Mus musculus | EPO-cell-neighborhood (GSE308511) | EPO/hypoxia model (UUO 3d, ligated) | GSM9247138 |
| GSM9579055 | NZB/WF1 30w rep1 | Mus musculus | lupus-nephritis-mouse (GSE322686) | lupus nephritis (lupus nephritis, NZB/WF1 F1 female, 30 weeks) | GSM9579055 |
| GSM9579056 | NZB/WF1 30w rep2 | Mus musculus | lupus-nephritis-mouse (GSE322686) | lupus nephritis (lupus nephritis, NZB/WF1 F1 female, 30 weeks) | GSM9579056 |
| GSM9579057 | NZB/WF1 30w rep3 | Mus musculus | lupus-nephritis-mouse (GSE322686) | lupus nephritis (lupus nephritis, NZB/WF1 F1 female, 30 weeks) | GSM9579057 |
| GSM9579058 | NZB/WF1 30w rep4 | Mus musculus | lupus-nephritis-mouse (GSE322686) | lupus nephritis (lupus nephritis, NZB/WF1 F1 female, 30 weeks) | GSM9579058 |
| GSM Accession | Sample ID | Species | Study / Series | Disease Condition / Context | Pipeline Link |
|---|---|---|---|---|---|
| GSM8323120 | visium_sham | Mus musculus | mouse-IRI-repair (GSE269884) | sham (control) (bIRI sham) | GSM8323120 |
| GSM8323121 | visium_hour4 | Mus musculus | mouse-IRI-repair (GSE269884) | AKI/IRI (bilateral IRI) (bIRI) | GSM8323121 |
| GSM8323122 | visium_hour12 | Mus musculus | mouse-IRI-repair (GSE269884) | AKI/IRI (bilateral IRI) (bIRI) | GSM8323122 |
| GSM8323123 | visium_day2 | Mus musculus | mouse-IRI-repair (GSE269884) | AKI/IRI (bilateral IRI) (bIRI) | GSM8323123 |
| GSM8323124 | visium_day14 | Mus musculus | mouse-IRI-repair (GSE269884) | AKI/IRI (bilateral IRI) (bIRI) | GSM8323124 |
| GSM8323125 | visium_week6 | Mus musculus | mouse-IRI-repair (GSE269884) | AKI/IRI (bilateral IRI) (bIRI) | GSM8323125 |
| GSM9155022 | control_58055 | Homo sapiens | transplant-rejection-FCGR3A (GSE304669) | transplant control (kidney allograft biopsy; control) | GSM9155022 |
| GSM9155023 | active AMR_58056 | Homo sapiens | transplant-rejection-FCGR3A (GSE304669) | transplant-AMR (kidney allograft biopsy; active AMR) | GSM9155023 |
| GSM9155024 | acute TCMR_58057 | Homo sapiens | transplant-rejection-FCGR3A (GSE304669) | transplant-TCMR (kidney allograft biopsy; acute TCMR) | GSM9155024 |
| GSM9155025 | chronic active AMR_58058 | Homo sapiens | transplant-rejection-FCGR3A (GSE304669) | transplant-CAMR (chronic active) (kidney allograft biopsy; chronic active AMR) | GSM9155025 |
| GSM9895920 | ES (early stable) | Homo sapiens | hypertensive-nephropathy (GSE339455) | hypertensive nephropathy (ES) (hypertensive nephropathy, ES) | GSM9895920 |
| GSM9895921 | EP (early progressor) | Homo sapiens | hypertensive-nephropathy (GSE339455) | hypertensive nephropathy (EP) (hypertensive nephropathy, EP) | GSM9895921 |
| GSM9895922 | LS (late stable) | Homo sapiens | hypertensive-nephropathy (GSE339455) | hypertensive nephropathy (LS) (hypertensive nephropathy, LS) | GSM9895922 |
| GSM9895923 | LP (late progressor) | Homo sapiens | hypertensive-nephropathy (GSE339455) | hypertensive nephropathy (LP) (hypertensive nephropathy, LP) | GSM9895923 |
| GSM Accession | Sample ID | Species | Study / Series | Disease Condition / Context | Pipeline Link |
|---|---|---|---|---|---|
| GSM9467249 | patient1 | Homo sapiens | DKD-HIF-SGLT2i (GSE317226) | DKD (T2D) (type-2 diabetes, pre-SGLT2i) | GSM9467249 |
| GSM9467250 | patient5 | Homo sapiens | DKD-HIF-SGLT2i (GSE317226) | DKD (T2D) (type-2 diabetes, pre-SGLT2i) | GSM9467250 |
| GSM9467251 | patient7 | Homo sapiens | DKD-HIF-SGLT2i (GSE317226) | DKD (T2D) (type-2 diabetes, pre-SGLT2i) | GSM9467251 |
| GSM9467252 | patient9 | Homo sapiens | DKD-HIF-SGLT2i (GSE317226) | DKD (T2D) (type-2 diabetes, pre-SGLT2i) | GSM9467252 |
| GSM9802211 | CAMR-ZLD_Spatial | Homo sapiens | CAMR-scRNA-VisiumHD (GSE334924) | transplant-CAMR (chronic AMR graft biopsy) | GSM9802211 |
| GSM Accession | Sample ID | Species | Study / Series | Disease Condition / Context | Pipeline Link |
|---|---|---|---|---|---|
| GSM8325615 | xenium_shamL | Mus musculus | mouse-IRI-repair (GSE269884) | sham (control) (bIRI sham) | GSM8325615 |
| GSM8325616 | xenium_shamR | Mus musculus | mouse-IRI-repair (GSE269884) | sham (control) (bIRI sham) | GSM8325616 |
| GSM8325617 | xenium_hour4L | Mus musculus | mouse-IRI-repair (GSE269884) | AKI/IRI (bilateral IRI) (bIRI) | GSM8325617 |
| GSM8325618 | xenium_hour4R | Mus musculus | mouse-IRI-repair (GSE269884) | AKI/IRI (bilateral IRI) (bIRI) | GSM8325618 |
| GSM8325619 | xenium_hour12L | Mus musculus | mouse-IRI-repair (GSE269884) | AKI/IRI (bilateral IRI) (bIRI) | GSM8325619 |
| GSM8325620 | xenium_hour12R | Mus musculus | mouse-IRI-repair (GSE269884) | AKI/IRI (bilateral IRI) (bIRI) | GSM8325620 |
| GSM8325621 | xenium_day2L | Mus musculus | mouse-IRI-repair (GSE269884) | AKI/IRI (bilateral IRI) (bIRI) | GSM8325621 |
| GSM8325622 | xenium_day2R | Mus musculus | mouse-IRI-repair (GSE269884) | AKI/IRI (bilateral IRI) (bIRI) | GSM8325622 |
| GSM8325623 | xenium_day14L | Mus musculus | mouse-IRI-repair (GSE269884) | AKI/IRI (bilateral IRI) (bIRI) | GSM8325623 |
| GSM8325624 | xenium_day14R | Mus musculus | mouse-IRI-repair (GSE269884) | AKI/IRI (bilateral IRI) (bIRI) | GSM8325624 |
| GSM8325625 | xenium_week6L | Mus musculus | mouse-IRI-repair (GSE269884) | AKI/IRI (bilateral IRI) (bIRI) | GSM8325625 |
| GSM8325626 | xenium_week6R | Mus musculus | mouse-IRI-repair (GSE269884) | AKI/IRI (bilateral IRI) (bIRI) | GSM8325626 |
| GSM8691119 | B6→B6 syngeneic (Xenium) | Mus musculus | kidney-transplant-rejection (GSE284742) | transplant (syn/allo, mouse) (syngeneic, C57BL/6→C57BL/6) | GSM8691119 |
| GSM8691120 | BALB/c→BALB/c syn (Xenium) | Mus musculus | kidney-transplant-rejection (GSE284742) | transplant (syn/allo, mouse) (syngeneic, BALB/c→BALB/c) | GSM8691120 |
| GSM8691121 | BALB/c→B6 allo (Xenium) | Mus musculus | kidney-transplant-rejection (GSE284742) | transplant (syn/allo, mouse) (allogeneic, BALB/c→C57BL/6) | GSM8691121 |
| GSM8691122 | BALB/c→B6 allo 3 (Xenium) | Mus musculus | kidney-transplant-rejection (GSE284742) | transplant (syn/allo, mouse) (allogeneic, BALB/c→C57BL/6) | GSM8691122 |
| GSM8691123 | B6→BALB/c allo 2 (Xenium) | Mus musculus | kidney-transplant-rejection (GSE284742) | transplant (syn/allo, mouse) (allogeneic, C57BL/6→BALB/c) | GSM8691123 |
| GSM8691124 | B6→BALB/c allo (Xenium) | Mus musculus | kidney-transplant-rejection (GSE284742) | transplant (syn/allo, mouse) (allogeneic, C57BL/6→BALB/c) | GSM8691124 |
| GSM8691125 | B6→BALB/c allo 3 (Xenium) | Mus musculus | kidney-transplant-rejection (GSE284742) | transplant (syn/allo, mouse) (allogeneic, C57BL/6→BALB/c) | GSM8691125 |
| GSM8717006 | 20210907-NMK92M | Mus musculus | kidney-aging-xenium (GSE286051) | normal (aging) (normal kidney, 92 weeks, male) | GSM8717006 |
| GSM8717007 | 20210908-NMK92F | Mus musculus | kidney-aging-xenium (GSE286051) | normal (aging) (normal kidney, 92 weeks, female) | GSM8717007 |
| GSM8717008 | 20240208-NMK12F2 | Mus musculus | kidney-aging-xenium (GSE286051) | normal (aging) (normal kidney, 12 weeks, female) | GSM8717008 |
| GSM8717009 | 20240208-NMK12M2 | Mus musculus | kidney-aging-xenium (GSE286051) | normal (aging) (normal kidney, 12 weeks, male) | GSM8717009 |
| GSM Accession | Sample ID | Species | Study / Series | Disease Condition / Context | Pipeline Link |
|---|---|---|---|---|---|
| GSM8551262 | FK1 | Homo sapiens | human-kidney-dev (GSE278614) | fetal (healthy) (fetal, healthy) | GSM8551262 |
| GSM8551263 | FK4 | Homo sapiens | human-kidney-dev (GSE278614) | fetal (healthy) (fetal, healthy) | GSM8551263 |
| GSM8551264 | HK3524 | Homo sapiens | human-kidney-dev (GSE278614) | fetal (healthy) (fetal, healthy) | GSM8551264 |
| GSM Accession | Sample ID | Species | Study / Series | Disease Condition / Context | Pipeline Link |
|---|---|---|---|---|---|
| GSM9938089 | ROI001 GLM | Homo sapiens | CAMR-GeoMx (GSE342778) | transplant-CAMR (GeoMx) (kidney allograft; patient 1; DSA+CAMR; glomerulus) | GSM9938089 |
| GSM9938090 | ROI002 GLM | Homo sapiens | CAMR-GeoMx (GSE342778) | transplant-CAMR (GeoMx) (kidney allograft; patient 1; DSA+CAMR; glomerulus) | GSM9938090 |
| GSM9938091 | ROI003 GLM | Homo sapiens | CAMR-GeoMx (GSE342778) | transplant-CAMR (GeoMx) (kidney allograft; patient 1; DSA+CAMR; glomerulus) | GSM9938091 |
| GSM9938092 | ROI004 GLM | Homo sapiens | CAMR-GeoMx (GSE342778) | transplant-CAMR (GeoMx) (kidney allograft; patient 1; DSA+CAMR; glomerulus) | GSM9938092 |
| GSM9938093 | ROI005 PTC | Homo sapiens | CAMR-GeoMx (GSE342778) | transplant-CAMR (GeoMx) (kidney allograft; patient 1; DSA+CAMR; peritubular capillary) | GSM9938093 |
| GSM9938094 | ROI006 PTC | Homo sapiens | CAMR-GeoMx (GSE342778) | transplant-CAMR (GeoMx) (kidney allograft; patient 1; DSA+CAMR; peritubular capillary) | GSM9938094 |
| GSM9938095 | ROI007 PTC | Homo sapiens | CAMR-GeoMx (GSE342778) | transplant-CAMR (GeoMx) (kidney allograft; patient 1; DSA+CAMR; peritubular capillary) | GSM9938095 |
| GSM9938096 | ROI008 VSL | Homo sapiens | CAMR-GeoMx (GSE342778) | transplant-CAMR (GeoMx) (kidney allograft; patient 1; DSA+CAMR; vessel) | GSM9938096 |
| GSM9938097 | ROI009 VSL | Homo sapiens | CAMR-GeoMx (GSE342778) | transplant-CAMR (GeoMx) (kidney allograft; patient 1; DSA+CAMR; vessel) | GSM9938097 |
| GSM9938098 | ROI010 VSL | Homo sapiens | CAMR-GeoMx (GSE342778) | transplant-CAMR (GeoMx) (kidney allograft; patient 1; DSA+CAMR; vessel) | GSM9938098 |
| GSM9938099 | ROI011 GLM | Homo sapiens | CAMR-GeoMx (GSE342778) | transplant-CAMR (GeoMx) (kidney allograft; patient 2; DSA-CAMR; glomerulus) | GSM9938099 |
| GSM9938100 | ROI012 GLM | Homo sapiens | CAMR-GeoMx (GSE342778) | transplant-CAMR (GeoMx) (kidney allograft; patient 2; DSA-CAMR; glomerulus) | GSM9938100 |
| GSM9938101 | ROI013 GLM | Homo sapiens | CAMR-GeoMx (GSE342778) | transplant-CAMR (GeoMx) (kidney allograft; patient 2; DSA-CAMR; glomerulus) | GSM9938101 |
| GSM9938102 | ROI014 GLM | Homo sapiens | CAMR-GeoMx (GSE342778) | transplant-CAMR (GeoMx) (kidney allograft; patient 2; DSA-CAMR; glomerulus) | GSM9938102 |
| GSM9938103 | ROI015 PTC | Homo sapiens | CAMR-GeoMx (GSE342778) | transplant-CAMR (GeoMx) (kidney allograft; patient 2; DSA-CAMR; peritubular capillary) | GSM9938103 |
| GSM9938104 | ROI016 PTC | Homo sapiens | CAMR-GeoMx (GSE342778) | transplant-CAMR (GeoMx) (kidney allograft; patient 2; DSA-CAMR; peritubular capillary) | GSM9938104 |
| GSM9938105 | ROI017 PTC | Homo sapiens | CAMR-GeoMx (GSE342778) | transplant-CAMR (GeoMx) (kidney allograft; patient 2; DSA-CAMR; peritubular capillary) | GSM9938105 |
| GSM9938106 | ROI018 VSL | Homo sapiens | CAMR-GeoMx (GSE342778) | transplant-CAMR (GeoMx) (kidney allograft; patient 2; DSA-CAMR; vessel) | GSM9938106 |
| GSM9938107 | ROI019 VSL | Homo sapiens | CAMR-GeoMx (GSE342778) | transplant-CAMR (GeoMx) (kidney allograft; patient 2; DSA-CAMR; vessel) | GSM9938107 |
| GSM9938108 | ROI020 VSL | Homo sapiens | CAMR-GeoMx (GSE342778) | transplant-CAMR (GeoMx) (kidney allograft; patient 2; DSA-CAMR; vessel) | GSM9938108 |
| GSM9938109 | ROI021 GLM | Homo sapiens | CAMR-GeoMx (GSE342778) | transplant-CAMR (GeoMx) (kidney allograft; patient 3; DSA+NER; glomerulus) | GSM9938109 |
| GSM9938110 | ROI022 GLM | Homo sapiens | CAMR-GeoMx (GSE342778) | transplant-CAMR (GeoMx) (kidney allograft; patient 3; DSA+NER; glomerulus) | GSM9938110 |
| GSM9938111 | ROI023 GLM | Homo sapiens | CAMR-GeoMx (GSE342778) | transplant-CAMR (GeoMx) (kidney allograft; patient 3; DSA+NER; glomerulus) | GSM9938111 |
| GSM9938112 | ROI024 GLM | Homo sapiens | CAMR-GeoMx (GSE342778) | transplant-CAMR (GeoMx) (kidney allograft; patient 3; DSA+NER; glomerulus) | GSM9938112 |
| GSM9938113 | ROI025 PTC | Homo sapiens | CAMR-GeoMx (GSE342778) | transplant-CAMR (GeoMx) (kidney allograft; patient 3; DSA+NER; peritubular capillary) | GSM9938113 |
| GSM9938114 | ROI026 PTC | Homo sapiens | CAMR-GeoMx (GSE342778) | transplant-CAMR (GeoMx) (kidney allograft; patient 3; DSA+NER; peritubular capillary) | GSM9938114 |
| GSM9938115 | ROI027 PTC | Homo sapiens | CAMR-GeoMx (GSE342778) | transplant-CAMR (GeoMx) (kidney allograft; patient 3; DSA+NER; peritubular capillary) | GSM9938115 |
| GSM9938116 | ROI028 VSL | Homo sapiens | CAMR-GeoMx (GSE342778) | transplant-CAMR (GeoMx) (kidney allograft; patient 3; DSA+NER; vessel) | GSM9938116 |
| GSM9938117 | ROI029 VSL | Homo sapiens | CAMR-GeoMx (GSE342778) | transplant-CAMR (GeoMx) (kidney allograft; patient 3; DSA+NER; vessel) | GSM9938117 |
| GSM9938118 | ROI030 VSL | Homo sapiens | CAMR-GeoMx (GSE342778) | transplant-CAMR (GeoMx) (kidney allograft; patient 3; DSA+NER; vessel) | GSM9938118 |
| GSM9938119 | ROI031 GLM | Homo sapiens | CAMR-GeoMx (GSE342778) | transplant-CAMR (GeoMx) (kidney allograft; patient 4; DSA-NER; glomerulus) | GSM9938119 |
| GSM9938120 | ROI032 GLM | Homo sapiens | CAMR-GeoMx (GSE342778) | transplant-CAMR (GeoMx) (kidney allograft; patient 4; DSA-NER; glomerulus) | GSM9938120 |
| GSM9938121 | ROI033 GLM | Homo sapiens | CAMR-GeoMx (GSE342778) | transplant-CAMR (GeoMx) (kidney allograft; patient 4; DSA-NER; glomerulus) | GSM9938121 |
| GSM9938122 | ROI034 PTC | Homo sapiens | CAMR-GeoMx (GSE342778) | transplant-CAMR (GeoMx) (kidney allograft; patient 4; DSA-NER; peritubular capillary) | GSM9938122 |
| GSM9938123 | ROI035 PTC | Homo sapiens | CAMR-GeoMx (GSE342778) | transplant-CAMR (GeoMx) (kidney allograft; patient 4; DSA-NER; peritubular capillary) | GSM9938123 |
| GSM9938124 | ROI036 PTC | Homo sapiens | CAMR-GeoMx (GSE342778) | transplant-CAMR (GeoMx) (kidney allograft; patient 4; DSA-NER; peritubular capillary) | GSM9938124 |
| GSM9938125 | ROI037 VSL | Homo sapiens | CAMR-GeoMx (GSE342778) | transplant-CAMR (GeoMx) (kidney allograft; patient 4; DSA-NER; vessel) | GSM9938125 |
| GSM9938126 | ROI038 VSL | Homo sapiens | CAMR-GeoMx (GSE342778) | transplant-CAMR (GeoMx) (kidney allograft; patient 4; DSA-NER; vessel) | GSM9938126 |
| GSM9938127 | ROI039 VSL | Homo sapiens | CAMR-GeoMx (GSE342778) | transplant-CAMR (GeoMx) (kidney allograft; patient 4; DSA-NER; vessel) | GSM9938127 |
| GSM9938128 | ROI040 GLM | Homo sapiens | CAMR-GeoMx (GSE342778) | transplant-CAMR (GeoMx) (kidney allograft; patient 5; normal control (non-transplant); glomerulus) | GSM9938128 |
| GSM9938129 | ROI041 GLM | Homo sapiens | CAMR-GeoMx (GSE342778) | transplant-CAMR (GeoMx) (kidney allograft; patient 5; normal control (non-transplant); glomerulus) | GSM9938129 |
| GSM9938130 | ROI042 GLM | Homo sapiens | CAMR-GeoMx (GSE342778) | transplant-CAMR (GeoMx) (kidney allograft; patient 5; normal control (non-transplant); glomerulus) | GSM9938130 |
| GSM9938131 | ROI043 PTC | Homo sapiens | CAMR-GeoMx (GSE342778) | transplant-CAMR (GeoMx) (kidney allograft; patient 5; normal control (non-transplant); peritubular capillary) | GSM9938131 |
| GSM9938132 | ROI044 PTC | Homo sapiens | CAMR-GeoMx (GSE342778) | transplant-CAMR (GeoMx) (kidney allograft; patient 5; normal control (non-transplant); peritubular capillary) | GSM9938132 |
| GSM9938133 | ROI045 PTC | Homo sapiens | CAMR-GeoMx (GSE342778) | transplant-CAMR (GeoMx) (kidney allograft; patient 5; normal control (non-transplant); peritubular capillary) | GSM9938133 |
| GSM9938134 | ROI046 VSL | Homo sapiens | CAMR-GeoMx (GSE342778) | transplant-CAMR (GeoMx) (kidney allograft; patient 5; normal control (non-transplant); vessel) | GSM9938134 |
| GSM9938135 | ROI047 VSL | Homo sapiens | CAMR-GeoMx (GSE342778) | transplant-CAMR (GeoMx) (kidney allograft; patient 5; normal control (non-transplant); vessel) | GSM9938135 |
| GSM9938136 | ROI048 VSL | Homo sapiens | CAMR-GeoMx (GSE342778) | transplant-CAMR (GeoMx) (kidney allograft; patient 5; normal control (non-transplant); vessel) | GSM9938136 |
| Platform | Samples | Typical Raw Input Format | Output AnnData Structure |
|---|---|---|---|
| 10x Visium | 39 | Space Ranger tarball / MTX + spatial files | obs (spots), obsm['spatial'], X (counts) |
| 10x Visium CytAssist | 14 | Space Ranger tarball / MTX + images | obs (spots), obsm['spatial'], X (counts) |
| 10x Visium HD | 5 | 8µm bin matrices + tissue coordinates / cell segmentation | obs (bins/cells), obsm['spatial'], X (counts) |
| 10x Xenium in situ | 23 | Output bundle / transcripts.zarr / flat mtx + cells.csv / cell boundaries | obs (cells), obsm['spatial'], X (counts) |
| NanoString CosMx SMI | 3 | AtoMx h5ad / raw transcripts & cell matrices | obs (cells), obsm['spatial'], X (counts) |
| NanoString GeoMx DSP | 48 | DCC count files + PKC probe annotation | obs (ROIs/segments), obsm['spatial'], X (counts) |
Important
Educational & Methodological Use Only
- Educational Purpose: The scripts and metadata hosted in this repository are provided solely for bioinformatics educational, methodological, and benchmarking purposes.
- Consult Original Authors: All pipelines are curated from published datasets. Users should always consult the original publications and primary study authors for authoritative metadata, experimental designs, and clinical context.
- Potential Inaccuracies: Curation across diverse studies is subject to human error; scripts and sample descriptions in this repository may contain mislabeling, discrepancies, or inaccuracies compared to primary sources.
- Arbitrary QC Thresholds: Quality control (QC) filtering parameters embedded in the scripts are baseline, arbitrary thresholds. Users must exercise their own scientific judgment to determine suitable criteria and reach their own conclusions.
- No Liability: The repository maintainers assume no responsibility or liability for any errors, omissions, analytical results, or misinterpretations arising from the use of these scripts.
- Proper Attribution: If you use, adapt, or reference this repository for your published studies or presentations, please cite the primary research publications and credit this repository properly.
The scripts and documentation in this repository are distributed under the MIT License.