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@@ -504,3 +504,11 @@ GSE274059/GSM8442780/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
 GSE274059/GSM8442780/wsi.tif filter=lfs diff=lfs merge=lfs -text
 GSE274059/GSM8442781/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
 GSE274059/GSM8442781/wsi.tif filter=lfs diff=lfs merge=lfs -text
+GSE275131/GSM8471249/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
+GSE275131/GSM8471249/wsi.tif filter=lfs diff=lfs merge=lfs -text
+GSE275131/GSM8471250/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
+GSE275131/GSM8471250/wsi.tif filter=lfs diff=lfs merge=lfs -text
+GSE275131/GSM8471251/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
+GSE275131/GSM8471251/wsi.tif filter=lfs diff=lfs merge=lfs -text
+GSE275131/GSM8471252/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
+GSE275131/GSM8471252/wsi.tif filter=lfs diff=lfs merge=lfs -text

GSE275131/.sentinel_report.json

@@ -0,0 +1,230 @@
+{
+  "gse_id": "GSE275131",
+  "scan_time": "2026-04-14T18:05:39",
+  "assets": [
+    {
+      "path": "GSE275131_RAW/GSM8471249_WTvehicule_tissue_hires_image.png.gz",
+      "type": "File",
+      "file_size_mb": 4.53,
+      "status": "OK",
+      "category": "Image",
+      "shape": [
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+        2000
+      ],
+      "mode": "RGB",
+      "channels": 3,
+      "is_compressed": true
+    },
+    {
+      "path": "GSE275131_RAW/GSM8471252_3xTgSCDi_aligned_fiducials.jpg.gz",
+      "type": "File",
+      "file_size_mb": 1.27,
+      "status": "OK",
+      "category": "Image",
+      "shape": [
+        1875,
+        2000
+      ],
+      "mode": "RGB",
+      "channels": 3,
+      "is_compressed": true
+    },
+    {
+      "path": "GSE275131_RAW/GSM8471251_WTSCDi_detected_tissue_image.jpg.gz",
+      "type": "File",
+      "file_size_mb": 0.69,
+      "status": "OK",
+      "category": "Image",
+      "shape": [
+        1893,
+        2000
+      ],
+      "mode": "RGB",
+      "channels": 3,
+      "is_compressed": true
+    },
+    {
+      "path": "GSE275131_RAW/GSM8471252_3xTgSCDi_detected_tissue_image.jpg.gz",
+      "type": "File",
+      "file_size_mb": 0.66,
+      "status": "OK",
+      "category": "Image",
+      "shape": [
+        1875,
+        2000
+      ],
+      "mode": "RGB",
+      "channels": 3,
+      "is_compressed": true
+    },
+    {
+      "path": "GSE275131_RAW/GSM8471250_3xTgvehicule_detected_tissue_image.jpg.gz",
+      "type": "File",
+      "file_size_mb": 0.64,
+      "status": "OK",
+      "category": "Image",
+      "shape": [
+        1863,
+        2000
+      ],
+      "mode": "RGB",
+      "channels": 3,
+      "is_compressed": true
+    },
+    {
+      "path": "GSE275131_RAW/GSM8471249_WTvehicule_aligned_fiducials.jpg.gz",
+      "type": "File",
+      "file_size_mb": 1.46,
+      "status": "OK",
+      "category": "Image",
+      "shape": [
+        1992,
+        2000
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+      "mode": "RGB",
+      "channels": 3,
+      "is_compressed": true
+    },
+    {
+      "path": "GSE275131_RAW/GSM8471251_WTSCDi_aligned_fiducials.jpg.gz",
+      "type": "File",
+      "file_size_mb": 1.33,
+      "status": "OK",
+      "category": "Image",
+      "shape": [
+        1893,
+        2000
+      ],
+      "mode": "RGB",
+      "channels": 3,
+      "is_compressed": true
+    },
+    {
+      "path": "GSE275131_RAW/GSM8471249_WTvehicule_tissue_lowres_image.png.gz",
+      "type": "File",
+      "file_size_mb": 0.35,
+      "status": "OK",
+      "category": "Image",
+      "shape": [
+        598,
+        600
+      ],
+      "mode": "RGB",
+      "channels": 3,
+      "is_compressed": true
+    },
+    {
+      "path": "GSE275131_RAW/GSM8471252_3xTgSCDi_tissue_lowres_image.png.gz",
+      "type": "File",
+      "file_size_mb": 0.31,
+      "status": "OK",
+      "category": "Image",
+      "shape": [
+        563,
+        600
+      ],
+      "mode": "RGB",
+      "channels": 3,
+      "is_compressed": true
+    },
+    {
+      "path": "GSE275131_RAW/GSM8471250_3xTgvehicule_tissue_lowres_image.png.gz",
+      "type": "File",
+      "file_size_mb": 0.31,
+      "status": "OK",
+      "category": "Image",
+      "shape": [
+        559,
+        600
+      ],
+      "mode": "RGB",
+      "channels": 3,
+      "is_compressed": true
+    },
+    {
+      "path": "GSE275131_RAW/GSM8471251_WTSCDi_tissue_hires_image.png.gz",
+      "type": "File",
+      "file_size_mb": 4.1,
+      "status": "OK",
+      "category": "Image",
+      "shape": [
+        1893,
+        2000
+      ],
+      "mode": "RGB",
+      "channels": 3,
+      "is_compressed": true
+    },
+    {
+      "path": "GSE275131_RAW/GSM8471251_WTSCDi_tissue_lowres_image.png.gz",
+      "type": "File",
+      "file_size_mb": 0.32,
+      "status": "OK",
+      "category": "Image",
+      "shape": [
+        568,
+        600
+      ],
+      "mode": "RGB",
+      "channels": 3,
+      "is_compressed": true
+    },
+    {
+      "path": "GSE275131_RAW/GSM8471250_3xTgvehicule_tissue_hires_image.png.gz",
+      "type": "File",
+      "file_size_mb": 3.94,
+      "status": "OK",
+      "category": "Image",
+      "shape": [
+        1863,
+        2000
+      ],
+      "mode": "RGB",
+      "channels": 3,
+      "is_compressed": true
+    },
+    {
+      "path": "GSE275131_RAW/GSM8471252_3xTgSCDi_tissue_hires_image.png.gz",
+      "type": "File",
+      "file_size_mb": 4.02,
+      "status": "OK",
+      "category": "Image",
+      "shape": [
+        1875,
+        2000
+      ],
+      "mode": "RGB",
+      "channels": 3,
+      "is_compressed": true
+    },
+    {
+      "path": "GSE275131_RAW/GSM8471249_WTvehicule_detected_tissue_image.jpg.gz",
+      "type": "File",
+      "file_size_mb": 0.72,
+      "status": "OK",
+      "category": "Image",
+      "shape": [
+        1992,
+        2000
+      ],
+      "mode": "RGB",
+      "channels": 3,
+      "is_compressed": true
+    },
+    {
+      "path": "GSE275131_RAW/GSM8471250_3xTgvehicule_aligned_fiducials.jpg.gz",
+      "type": "File",
+      "file_size_mb": 1.26,
+      "status": "OK",
+      "category": "Image",
+      "shape": [
+        1863,
+        2000
+      ],
+      "mode": "RGB",
+      "channels": 3,
+      "is_compressed": true
+    }
+  ]
+}

GSE275131/GSM8471249/.standardization_success

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+Success

GSE275131/GSM8471249/spatial.h5ad

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+size 104536930

GSE275131/GSM8471250/.standardization_success

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+Success

GSE275131/GSM8471250/spatial.h5ad

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+size 99533234

GSE275131/GSM8471251/.standardization_success

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+Success

GSE275131/GSM8471251/spatial.h5ad

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+size 94199458

GSE275131/GSM8471252/.standardization_success

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+Success

GSE275131/GSM8471252/spatial.h5ad

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+version https://git-lfs.github.com/spec/v1
+oid sha256:3af6b84923af5a51ca2bd71165e099536f7a4cbaa57a12a8de7568feae1ca99b
+size 116261714

GSE275131/audit_report.json

@@ -0,0 +1,50 @@
+{
+  "gse_id": "GSE275131",
+  "global_score": 100.0,
+  "threshold_limit": 0.03,
+  "summary": {
+    "total_samples": 4,
+    "passed_samples": 4,
+    "structural_fail_samples": 0,
+    "alignment_fail_samples": 0,
+    "error_samples": 0
+  },
+  "samples": [
+    {
+      "sample_id": "GSM8471252",
+      "status": "PASS",
+      "score": 100,
+      "spillover": 0.0,
+      "spot_count": 4992,
+      "reason": null,
+      "weight": 0.2508794853754146
+    },
+    {
+      "sample_id": "GSM8471250",
+      "status": "PASS",
+      "score": 100,
+      "spillover": 0.0,
+      "spot_count": 4984,
+      "reason": null,
+      "weight": 0.2504774349180822
+    },
+    {
+      "sample_id": "GSM8471251",
+      "status": "PASS",
+      "score": 100,
+      "spillover": 0.0,
+      "spot_count": 4969,
+      "reason": null,
+      "weight": 0.24972359031058397
+    },
+    {
+      "sample_id": "GSM8471249",
+      "status": "PASS",
+      "score": 100,
+      "spillover": 0.0,
+      "spot_count": 4953,
+      "reason": null,
+      "weight": 0.24891948939591918
+    }
+  ]
+}

GSE275131/standardize_GSE275131.py

@@ -0,0 +1,125 @@
+import os
+import sys
+import glob
+import json
+import gzip
+import io
+import pandas as pd
+import scanpy as sc
+import numpy as np
+from PIL import Image
+from concurrent.futures import ThreadPoolExecutor
+
+# Inject Expert Scripts Path
+sys.path.append("/cpfs01/projects-HDD/cfff-afe2df89e32e_HDD/jjh_19301050235/.agents/skills/ara-evolutionary-standardizer/scripts")
+import registry_utils
+
+GSE_ID = "GSE275131"
+INPUT_DIR = "/cpfs01/projects-HDD/cfff-afe2df89e32e_HDD/jjh_19301050235/my_data/preprint_data/Spatial-Clip/data/auto_standardize_react/data/2026_unzip_v4/GSE275131/GSE275131_RAW"
+OUTPUT_DIR = "/cpfs01/projects-HDD/cfff-afe2df89e32e_HDD/jjh_19301050235/my_data/preprint_data/Spatial-Clip/data/auto_standardize_react/data/2026_standardized/GSE275131"
+
+def process_gsm(gsm_id, files):
+    try:
+        sample_name = gsm_id
+        target_path = os.path.join(OUTPUT_DIR, sample_name)
+        os.makedirs(target_path, exist_ok=True)
+
+        # 1. Load Matrix
+        h5_path = files.get('matrix_h5')
+        if not h5_path:
+            return f"{gsm_id}: Missing H5"
+        adata = sc.read_10x_h5(h5_path)
+        adata.var_names_make_unique()
+
+        # 2. Load Coordinates
+        pos_path = files.get('positions')
+        # Handle .csv.gz
+        if pos_path.endswith('.gz'):
+            with gzip.open(pos_path, 'rt') as f:
+                pos_df = pd.read_csv(f, header=None, index_col=0)
+        else:
+            pos_df = pd.read_csv(pos_path, header=None, index_col=0)
+            
+        # Visium tissue_positions.csv format: barcode, in_tissue, array_row, array_col, pxl_row_in_fullres, pxl_col_in_fullres
+        pos_df.columns = ["in_tissue", "array_row", "array_col", "pxl_row_in_fullres", "pxl_col_in_fullres"]
+        
+        # 3. Load Scaling
+        scaling_path = files.get('scalefactors')
+        with (gzip.open(scaling_path, 'rt') if scaling_path.endswith('.gz') else open(scaling_path, 'r')) as f:
+            scalefactors = json.load(f)
+        
+        # 4. Load Image (Supporting .png.gz)
+        img_path = files.get('hires_image')
+        if img_path.endswith('.gz'):
+            with gzip.open(img_path, 'rb') as f:
+                img_data = f.read()
+                img = Image.open(io.BytesIO(img_data))
+        else:
+            img = Image.open(img_path)
+        
+        img.save(os.path.join(target_path, "wsi.tif"))
+        
+        # 5. Align Coordinates to Image Space
+        scale = scalefactors['tissue_hires_scalef']
+        
+        # Align barcodes
+        common_barcodes = adata.obs_names.intersection(pos_df.index)
+        adata = adata[common_barcodes].copy()
+        pos_df = pos_df.loc[common_barcodes]
+        
+        # Calculate scaled coords
+        adata.obs['x'] = pos_df['pxl_col_in_fullres'].astype(float) * scale
+        adata.obs['y'] = pos_df['pxl_row_in_fullres'].astype(float) * scale
+        adata.obs['pxl_col_in_fullres'] = adata.obs['x']
+        adata.obs['pxl_row_in_fullres'] = adata.obs['y']
+        
+        # 6. Metadata (9 Fields) - Mandatory Top-level uns keys
+        adata.uns['organism'] = "mouse"
+        adata.uns['tissue'] = "brain"
+        adata.uns['disease'] = "Alzheimer's disease"
+        adata.uns['sex'] = "Not Reported (Verified by Source)"
+        adata.uns['age'] = "Not Reported (Verified by Source)"
+        adata.uns['technology'] = "10X Visium"
+        adata.uns['stain_type'] = "H&E"
+        adata.uns['publication_doi'] = "10.1101/2024.08.14.607865"
+        adata.uns['repository_id'] = f"GEO:{GSE_ID}"
+        
+        # Save H5AD
+        adata.write_h5ad(os.path.join(target_path, "spatial.h5ad"))
+        
+        # Sentinel success
+        with open(os.path.join(target_path, ".standardization_success"), "w") as f:
+            f.write("Success")
+            
+        return f"{gsm_id}: Success"
+    except Exception as e:
+        import traceback
+        traceback.print_exc()
+        return f"{gsm_id}: Failed - {str(e)}"
+
+def run():
+    # Group files by GSM
+    gsm_map = {}
+    for f in os.listdir(INPUT_DIR):
+        if f.startswith("GSM"):
+            gsm_id = f.split("_")[0]
+            if gsm_id not in gsm_map:
+                gsm_map[gsm_id] = {}
+            
+            if f.endswith(".h5"): gsm_map[gsm_id]['matrix_h5'] = os.path.join(INPUT_DIR, f)
+            if "positions" in f: gsm_map[gsm_id]['positions'] = os.path.join(INPUT_DIR, f)
+            if "scalefactors" in f: gsm_map[gsm_id]['scalefactors'] = os.path.join(INPUT_DIR, f)
+            if "hires_image" in f: gsm_map[gsm_id]['hires_image'] = os.path.join(INPUT_DIR, f)
+
+    with ThreadPoolExecutor(max_workers=128) as executor:
+        results = list(executor.map(lambda g: process_gsm(g, gsm_map[g]), gsm_map))
+    
+    for r in results:
+        print(r)
+    
+    # Update Registry
+    status = "success" if any("Success" in r for r in results) else "failed"
+    registry_utils.update_gse_registry(GSE_ID, status)
+
+if __name__ == "__main__":
+    run()

GSE275131/tree_scan.txt

@@ -0,0 +1,46 @@
+
+[TREE SCAN] /cpfs01/projects-HDD/cfff-afe2df89e32e_HDD/jjh_19301050235/my_data/preprint_data/Spatial-Clip/data/auto_standardize_react/data/2026_unzip_v4/GSE275131
+--------------------------------------------------
+├── GSE275131_RAW
+  ├── .extraction_success
+  ├── GSM8471249_WTvehicule_aligned_fiducials.jpg.gz
+  ├── GSM8471249_WTvehicule_barcodes.tsv.gz [CELL_BARCODES]
+  ├── GSM8471249_WTvehicule_detected_tissue_image.jpg.gz
+  ├── GSM8471249_WTvehicule_features.tsv.gz [GENE_FEATURES]
+  ├── GSM8471249_WTvehicule_matrix.mtx.gz [RAW_MATRIX]
+  ├── GSM8471249_WTvehicule_raw_feature_bc_matrix.h5 [MATRIX_H5]
+  ├── GSM8471249_WTvehicule_scalefactors_json.json.gz
+  ├── GSM8471249_WTvehicule_tissue_hires_image.png.gz
+  ├── GSM8471249_WTvehicule_tissue_lowres_image.png.gz
+  ├── GSM8471249_WTvehicule_tissue_positions.csv.gz
+  ├── GSM8471250_3xTgvehicule_aligned_fiducials.jpg.gz
+  ├── GSM8471250_3xTgvehicule_barcodes.tsv.gz [CELL_BARCODES]
+  ├── GSM8471250_3xTgvehicule_detected_tissue_image.jpg.gz
+  ├── GSM8471250_3xTgvehicule_features.tsv.gz [GENE_FEATURES]
+  ├── GSM8471250_3xTgvehicule_matrix.mtx.gz [RAW_MATRIX]
+  ├── GSM8471250_3xTgvehicule_raw_feature_bc_matrix.h5 [MATRIX_H5]
+  ├── GSM8471250_3xTgvehicule_scalefactors_json.json.gz
+  ├── GSM8471250_3xTgvehicule_tissue_hires_image.png.gz
+  ├── GSM8471250_3xTgvehicule_tissue_lowres_image.png.gz
+  ├── GSM8471250_3xTgvehicule_tissue_positions.csv.gz
+  ├── GSM8471251_WTSCDi_aligned_fiducials.jpg.gz
+  ├── GSM8471251_WTSCDi_barcodes.tsv.gz [CELL_BARCODES]
+  ├── GSM8471251_WTSCDi_detected_tissue_image.jpg.gz
+  ├── GSM8471251_WTSCDi_features.tsv.gz [GENE_FEATURES]
+  ├── GSM8471251_WTSCDi_matrix.mtx.gz [RAW_MATRIX]
+  ├── GSM8471251_WTSCDi_raw_feature_bc_matrix.h5 [MATRIX_H5]
+  ├── GSM8471251_WTSCDi_scalefactors_json.json.gz
+  ├── GSM8471251_WTSCDi_tissue_hires_image.png.gz
+  ├── GSM8471251_WTSCDi_tissue_lowres_image.png.gz
+  ├── GSM8471251_WTSCDi_tissue_positions.csv.gz
+  ├── GSM8471252_3xTgSCDi_aligned_fiducials.jpg.gz
+  ├── GSM8471252_3xTgSCDi_barcodes.tsv.gz [CELL_BARCODES]
+  ├── GSM8471252_3xTgSCDi_detected_tissue_image.jpg.gz
+  ├── GSM8471252_3xTgSCDi_features.tsv.gz [GENE_FEATURES]
+  ├── GSM8471252_3xTgSCDi_matrix.mtx.gz [RAW_MATRIX]
+  ├── GSM8471252_3xTgSCDi_raw_feature_bc_matrix.h5 [MATRIX_H5]
+  ├── GSM8471252_3xTgSCDi_scalefactors_json.json.gz
+  ├── GSM8471252_3xTgSCDi_tissue_hires_image.png.gz
+  ├── GSM8471252_3xTgSCDi_tissue_lowres_image.png.gz
+  ├── GSM8471252_3xTgSCDi_tissue_positions.csv.gz
+├── filelist.txt