{ "$schema": "https://vesuvius-challenge-open-data.s3.us-east-1.amazonaws.com/metadata.schema.json", "samples": { "PHerc0332": { "sample": { "id": "PHerc0332", "properties": { "type": "scroll", "volume_transforms": [ { "from_volume_id": "20231027191953", "transforms": [ { "to_volume_id": "20231117143551", "matrix": [ [ 0.4151412067359984, 0.00048378007463328903, -0.00018589243000010215, -68.00272003705008 ], [ -4.8392696705699846e-05, 0.4147879124302306, 5.521936651202975e-05, -254.7753120163574 ], [ 0.0004776395202003243, 0.00033798145979504216, 0.41324998657862283, 58.80085957090315 ] ], "derivation_path": "20231027191953-20231117143551" }, { "to_volume_id": "20231201141544", "matrix": [ [ 0.9999308109657453, -0.0001676620500204413, 0.00013129198269003605, 0.9174690368161557 ], [ 0.00014651126713670845, 1.0003065625100374, -0.00013597433171619054, -0.4375259575383937 ], [ 0.0001755787791800993, 0.000216361230460076, 0.9999379091310834, -9.124087998562956 ] ], "derivation_path": 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"matrix": [ [ -0.3721994124400844, -0.6367370029681384, -0.000644898270619894, 12397.195258341677 ], [ -0.632476560703003, 0.3749153972334453, 0.027737192649237668, 6662.728487653876 ], [ -0.023776046258735816, 0.01500173508319852, -0.7378162519688566, 24928.735880780176 ] ], "derivation_path": "20251211183505-20231117143551.20231117143551-20231027191953\u207b\u00b9.20231027191953-20231201141544" } ] } ], "legacy_data_url": "https://dl.ash2txt.org/full-scrolls/Scroll3/PHerc332.volpkg/" }, "data": [ { "type": "photo", "origins": [ { "path": "samples/PHerc0332/photos/PHerc0332_photo.jpg", "access_roots": [ { "type": "https", "url": "https://data.aws.ash2txt.org", "usage": "public-read" } ], "copy_info": null }, { "path": "PHerc0332/photos/PHerc0332_photo.jpg", "access_roots": [ { "type": "s3", "url": "s3://vesuvius-challenge-open-data", "usage": "public-read" } ], "copy_info": { "source_path": "s3://vesuvius-challenge/PHerc0332/photos/PHerc0332_photo.jpg", "date": "2026-02-23T14:34:30.570330Z", "workflow_execution": "s3copy-pherc0332-f0424443" } } ], "properties": null, "parameters": null, "creation_info": null } ], "description": "PHerc. 332 is a rolled Herculaneum papyrus from the [Biblioteca Nazionale di Napoli](https://www.bnnonline.it/it/121/officina-dei-papiri-ercolanesi), carbonized during the eruption of Mount Vesuvius in 79 AD. It was scanned at the [Diamond Light Source](https://www.diamond.ac.uk) in Oxfordshire, UK.\n\nIt is a smaller scroll known as a *midollo* (marrow), a remnant from physical unwrapping of the larger original. Its small size enabled scanning at extremely high resolution (3.24um)." }, "scans": { "20231027191953": { "id": "20231027191953", "sample_id": "PHerc0332", "long_id": "20231027191953-3.240um-53keV", "creation": { "date": "2023-10-27T19:19:53Z", "process": "xray tomography", "metadata": { "location": "DLS (Diamond Light Source)", "energy_keV": 53.0, "pixel_size_um": 3.24, "scan_name": "PHerc332, 53 keV, 3.24 um, merged" }, "derived_from": null }, "properties": { "energy_keV": 53.0, "detector_distance_mm": null, "pixel_size_um": 3.24 } }, "20251205210228": { "id": "20251205210228", "sample_id": "PHerc0332", "long_id": "20251205210228-2.399um-0.2m-78keV", "creation": { "date": "2025-12-05T22:02:28.467121+01:00", "process": "xray tomography", "metadata": { "location": "ESRF Grenoble", "beamline": "bm18", "energy_keV": 78.0, "detector_distance_mm": 220.0, "pixel_size_um": 2.399, "metadata": { "tomo": { "acquisition": { "scanRadix": "SCROLLS_HEL_2.399um_78keV_0.22m_PHerc_0332_HA", "scanType": "helical", "nb_scans": 1, "date": "2025-12-05T22:02:28.467121+01:00", "beamline": "bm18", "machineMode": "16 bunch", "machineCurrentStart": 83.756978, "machineCurrentStop": 89.55, "sampleDetectorDistance": 220.0, "sourceSampleDistance": 178000.0, "xray_magnification": 1.001236, "energy": 78.0, "scanRange": 360.0, "rotationMode": "continuous", "half_acquisition": true, "tomo_N": 24000, "ref_N": 401, "dark_N": 400, "z_start": -259.5, "z_end": -182.8088, "z_step": 5.113, "detector": { "sensor": "Pco", "sensorPixelSize": 0.0046, "roi_size": "[4416, 2368]", "sensorBinning": 1, "opticsName": "Fixed_X2", "opticsType": "FixedmagOptic", "optical_magnification": 2.0, "samplePixelSize": 0.002399, "scintillator": "GAGG_50um_refl" }, "acq_mode": "SINGLE", "expo_time": 0.013, "subframe": 0.013, "latency_time": 0.0013, "accumulation": 1, "scan_time": 353.219264, "comment": "wba11 = sapphire 2.5mm, wba12 = Ag 0.20mm", "attenuators": { "wba11": { "thickness": 2.5, "type": "sapphire" }, "wba12": { "thickness": 0.2, "type": "Ag" }, "wba13": { "thickness": 0.0, "type": "empty" }, "wba14": { "thickness": 0.0, "type": "empty" }, "wba15": { "thickness": 0.0, "type": "free pass" }, "wba21": { "thickness": 0.0, "type": "empty" }, "wba22": { "thickness": 0.0, "type": "empty" }, "wba23": { "thickness": 0.0, "type": "empty" }, "wba24": { "thickness": 0.0, "type": "empty" }, "wba25": { "thickness": 0.0, "type": "empty" }, "wba31": { "thickness": 0.0, "type": "free pass" }, "wba32": { "thickness": 0.0, "type": "free pass" } }, "motors": { "att11": 79.5, "att12": 139.5, "att13": 1.0, "att14": 1.0, "att15": 198.0, "att21": 198.0, "att22": 198.0, "att23": 198.0, "att24": 198.0, "att25": 198.0, "att31": 198.0, "att32": 198.0, "att33": "error", "dzfocus": -0.0, "dzmag": 10.0, "dzrotc": 0.28, "dzz": 207.03, "foc1twin": 4.68, "foc2twin": 5.15, "focus10x": 0.0, "focus2": 0.38, "focus3": -0.97, "focus5": -2.21, "focus7": -3.33, "focusrefl": -3.07, "focusx05": 0.0, "focusx2": 0.0, "focusx4": 0.0, "fsd": 4.78, "fshg": 11.28, "fsho": 64.97, "fshut_axis": 0.0, "fsl": -59.33, "fsr": 70.61, "fsu": 1.03, "fsvg": 5.81, "fsvo": -1.44, "fur1": -1.49, "girderx": 170.0, "kore": "error", "lfddiaph": 0.0, "lfdfocus": 14.03, "lfdrotc": 0.0, "lfdz": -0.0, "lthx1": -0.9, "lthx2": 0.0, "lthy1": 0.0, "lthy2": 0.0, "lz1": 0.0, "lz2": 0.0, "ostwin": -56.0, "psh1": 9.16, "psh2": 1.68, "pshg": 1.68, "psho": 10.0, "psv1": 0.22, "psv2": -1.0, "psvg": 1.1, "psvo": -0.25, "psx": 0.0, "psy": 0.0, "qsh1": -42.5, "qsh2": 85.0, "qshg": 85.0, "qsho": 0.0, "qsv1": 2.25, "qsv2": -4.5, "qsvg": 4.5, "qsvo": 0.0, "rotc10x": -0.0, "rotc2": "error", "rotc3": 0.56, "rotc5": -45.59, "rotc7": 0.03, "rotc9": -1.87, "rotcrefl": 1.4, "rotctwin": -0.04, "rotcx05": 0.01, "rotcx2": -1.7, "rotcx4": 0.0, "srot": -0.0, "ssh1": -42.29, "ssh2": 84.59, "sshg": 84.59, "ssho": -0.0, "ssv1": 2.4, "ssv2": -4.8, "ssvg": 5.0, "ssvo": 0.0, "sx": 0.0, "sy": 0.0, "sz": -259.5, "tsh1": -41.49, "tsh2": 82.97, "tshg": 82.97, 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Paris 1 Fr 39" }, "data": [ { "type": "photo", "origins": [ { "path": "samples/PHercParis1Fr39/photos/PHercParis1Fr39_photo.jpg", "access_roots": [ { "type": "https", "url": "https://data.aws.ash2txt.org", "usage": "public-read" } ], "copy_info": null }, { "path": "PHercParis1Fr39/photos/PHercParis1Fr39_photo.jpg", "access_roots": [ { "type": "s3", "url": "s3://vesuvius-challenge-open-data", "usage": "public-read" } ], "copy_info": { "source_path": "s3://vesuvius-challenge/PHercParis1Fr39/photos/PHercParis1Fr39_photo.jpg", "date": "2026-02-23T14:34:30.794389Z", "workflow_execution": "s3copy-phercparis1fr39-89d5789d" } } ], "properties": null, "parameters": null, "creation_info": null } ], "description": "PHerc. Paris 1 Fr 39 is a fragment of a Herculaneum papyrus, carbonized during the eruption of Mount Vesuvius in 79 AD. 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"s3copy-pherc0826-040d3565" } } ], "properties": null, "parameters": null, "creation_info": null }, { "type": "photo-mask", "origins": [ { "path": "PHerc0826/photos/PHerc0826_mask.png", "access_roots": [ { "type": "s3", "url": "s3://vesuvius-challenge-open-data", "usage": "public-read" } ], "copy_info": { "source_path": "s3://philodemos/photogrammetry/post-esrf-photos/0826/Masks/DSC05583_mask.png", "date": "2026-02-18T16:04:04.438743Z", "workflow_execution": "s3copy-pherc0826-108a0067" } } ], "properties": null, "parameters": null, "creation_info": null } ] }, "scans": { "20250720174915": { "id": "20250720174915", "sample_id": "PHerc0826", "long_id": "20250720174915-9.362um-1.2m-113keV", "creation": { "date": "2025-07-20T19:49:15.828001+02:00", "process": "xray tomography", "metadata": { "location": "ESRF Grenoble", "beamline": "bm18", "energy_keV": 113.0, "detector_distance_mm": 1200.0, "pixel_size_um": 9.362, "metadata": { "tomo": { "acquisition": { "scanRadix": 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"PHerc1667Cr1Fr3": { "sample": { "id": "PHerc1667Cr1Fr3", "properties": { "type": "fragment", "volume_transforms": null, "legacy_data_url": "https://dl.ash2txt.org/fragments/Frag5/PHerc1667Cr1Fr3.volpkg/", "description": "PHerc. 1667 Cr 1 Fr 3" }, "data": [ { "type": "photo", "origins": [ { "path": "samples/PHerc1667Cr1Fr3/photos/PHerc1667Cr1Fr3_photo.jpg", "access_roots": [ { "type": "https", "url": "https://data.aws.ash2txt.org", "usage": "public-read" } ], "copy_info": null }, { "path": "PHerc1667Cr1Fr3/photos/PHerc1667Cr1Fr3_photo.jpg", "access_roots": [ { "type": "s3", "url": "s3://vesuvius-challenge-open-data", "usage": "public-read" } ], "copy_info": { "source_path": "s3://vesuvius-challenge/PHerc1667Cr1Fr3/photos/PHerc1667Cr1Fr3_photo.jpg", "date": "2026-02-23T14:36:22.815880Z", "workflow_execution": "s3copy-pherc1667cr1fr3-3b6e9112" } } ], "properties": null, "parameters": null, "creation_info": null } ], "description": "PHerc. 1667 Cr 1 Fr 3 is a fragment from the same scroll 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It was partially opened in 1987 via the Oslo method. It was scanned at the [Diamond Light Source](https://www.diamond.ac.uk) in Oxfordshire, UK.\n\nListed on [Chartes.it](https://www.chartes.it/index.php?r=document/view&id=1691).\n\nSee also: [EduceLab-Scrolls paper](https://arxiv.org/abs/2304.02084), [EduceLab 2023 Info Sheet](https://drive.google.com/file/d/1I6JNrR6A9pMdANbn6uAuXbcDNwjk8qZ2/view?usp=sharing)." }, "scans": {}, "volumes": {}, "segments": {} }, "PHerc1451": { "sample": { "id": "PHerc1451", "properties": { "type": "scroll", "volume_transforms": null }, "data": [ { "type": "photo", "origins": [ { "path": "PHerc1451/photos/PHerc1451_photo.jpg", "access_roots": [ { "type": "s3", "url": "s3://vesuvius-challenge-open-data", "usage": "public-read" } ], "copy_info": { "source_path": "s3://philodemos/photogrammetry/scrolls/1451/FullScene/DSC05197.jpg", "date": "2026-02-18T16:04:37.162230Z", "workflow_execution": "s3copy-pherc1451-25e39ca4" } } ], "properties": null, "parameters": null, "creation_info": null }, { "type": "photo-mask", "origins": [ { "path": "PHerc1451/photos/PHerc1451_mask.png", "access_roots": [ { "type": "s3", "url": "s3://vesuvius-challenge-open-data", "usage": "public-read" } ], "copy_info": { "source_path": "s3://philodemos/photogrammetry/scrolls/1451/Masked/DSC05197_masked_mask.png", "date": "2026-02-18T16:04:37.385996Z", "workflow_execution": "s3copy-pherc1451-e8ffa3b5" } } ], "properties": null, "parameters": null, "creation_info": null } ] }, "scans": { "20250509145349": { "id": "20250509145349", "sample_id": "PHerc1451", "long_id": "20250509145349-8.640um-1.2m-116keV", "creation": { "date": "2025-05-09T16:53:49.555428+02:00", "process": "xray tomography", "metadata": { "location": "ESRF Grenoble", "beamline": "bm18", "energy_keV": 116.0, "detector_distance_mm": 1200.02, "pixel_size_um": 8.64, "metadata": { "tomo": { "acquisition": { "scanRadix": "SCROLLS_TA_HEL_4.320um_1.0m_116keV_binmean_2_PHerc1451_HA", "scanType": "helical", "nb_scans": 1, "date": 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Unlike its three siblings this entry was deliberately NOT moved: the ink scan measured (+11.4, +12.1) but that gains only 0.0037 coverage, under the 0.005 bar, so moving it would be chasing the model rather than correcting the labels. Its surface offset is a genuine zero measured against the canonical render. Dice 0.832, recall 0.890 as published.", "reviewed": "2026-09-21" } } } ] } } }, "PHercParis1Fr34": { "sample": { "id": "PHercParis1Fr34", "properties": { "type": "fragment", "volume_transforms": null, "legacy_data_url": "https://dl.ash2txt.org/fragments/Frag3/PHercParis1Fr34.volpkg/", "description": "PHerc. Paris 1 Fr 34" }, "data": [ { "type": "photo", "origins": [ { "path": "samples/PHercParis1Fr34/photos/PHercParis1Fr34_photo.jpg", "access_roots": [ { "type": "https", "url": "https://data.aws.ash2txt.org", "usage": "public-read" } ], "copy_info": null }, { "path": "PHercParis1Fr34/photos/PHercParis1Fr34_photo.jpg", "access_roots": [ { "type": "s3", "url": "s3://vesuvius-challenge-open-data", "usage": "public-read" } ], "copy_info": { "source_path": "s3://vesuvius-challenge/PHercParis1Fr34/photos/PHercParis1Fr34_photo.jpg", "date": "2026-02-23T14:36:23.057593Z", "workflow_execution": "s3copy-phercparis1fr34-fa5bf3ec" } } ], "properties": null, "parameters": null, "creation_info": null } ], "description": "PHerc. Paris 1 Fr 34 is a fragment of a Herculaneum papyrus, carbonized during the eruption of Mount Vesuvius in 79 AD. It was scanned at the [Diamond Light Source](https://www.diamond.ac.uk) in Oxfordshire, UK.\n\nSee also: [EduceLab-Scrolls paper](https://arxiv.org/abs/2304.02084), [EduceLab 2023 Info Sheet](https://drive.google.com/file/d/1I6JNrR6A9pMdANbn6uAuXbcDNwjk8qZ2/view?usp=sharing)." }, "scans": {}, "volumes": {}, "segments": {} }, "PHerc0191": { "sample": { "id": "PHerc0191", "properties": { "type": "scroll", "volume_transforms": null }, "data": [ { "type": "photo", "origins": [ { "path": "PHerc0191/photos/PHerc0191_photo.jpg", "access_roots": [ { "type": "s3", "url": "s3://vesuvius-challenge-open-data", "usage": "public-read" } ], "copy_info": { "source_path": "s3://philodemos/photogrammetry/grenoble-photos/0191/JPGEnhanced/DSC02391.jpg", "date": "2026-02-18T16:05:05.985517Z", "workflow_execution": "s3copy-pherc0191-59c244a1" } } ], "properties": null, "parameters": null, "creation_info": null }, { "type": "photo-mask", "origins": [ { "path": "PHerc0191/photos/PHerc0191_mask.png", "access_roots": [ { "type": "s3", "url": "s3://vesuvius-challenge-open-data", "usage": "public-read" } ], "copy_info": { "source_path": "s3://philodemos/photogrammetry/grenoble-photos/0191/Masks/DSC02391_mask.png", "date": "2026-02-18T16:05:06.211282Z", "workflow_execution": "s3copy-pherc0191-0ef0d728" } } ], "properties": null, "parameters": null, "creation_info": null } ] }, "scans": { "20250720024445": { "id": "20250720024445", "sample_id": "PHerc0191", "long_id": "20250720024445-9.362um-1.2m-113keV", "creation": { "date": "2025-07-20T04:44:45.216425+02:00", "process": "xray tomography", "metadata": { "location": "ESRF Grenoble", "beamline": "bm18", "energy_keV": 113.0, "detector_distance_mm": 1200.0, "pixel_size_um": 9.362, "metadata": { "tomo": { "acquisition": { "scanRadix": "SCROLLS_HEL_4.681um_113keV_1.2m_binmean_2_PHerc_191_HA", "scanType": "helical", "nb_scans": 1, "date": "2025-07-20T04:44:45.216425+02:00", "beamline": "bm18", "machineMode": "16 bunch", 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"detector_distance_mm": 1200.0, "pixel_size_um": 9.362 } } }, "volumes": { "20250821151635": { "id": "20250821151635", "sample_id": "PHerc0191", "scan_id": "20250720024445", "long_id": "20250821151635-9.362um-1.2m-113keV-masked.zarr", "suffix": "masked.zarr", "creation": { "date": "2025-08-21T15:16:35Z", "process": "mask_layers_zarr_export", "metadata": { "window_mode": "f32", "source_f32_min": -0.03, "source_f32_max": 0.145, "target_window_f32_min": -0.03, "target_window_f32_max": 0.145, "window_u16_min": 0, "window_u16_max": 65535, "workflow_name": "mask-layers-sam2long-dkdsl", "workflow_creation": "2025-08-21T15:16:35Z" }, "derived_from": { "type": "scan", "id": "20250720024445" } }, "properties": { "energy_keV": 113.0, "detector_distance_mm": 1200.0, "pixel_size_um": 9.362, "data_format": "uint8", "transforms": null, "shape": [ 18977, 8387, 8387 ], "z_direction_is_top_to_bottom": false, "left_handed_coordinates": false, "text_side": null, "superseded_by": null, "license": { "name": "CC BY-NC 4.0", "url": "https://creativecommons.org/licenses/by-nc/4.0/" } }, "data": [ { "type": "ome-zarr", "origins": [ { "path": "PHerc0191/volumes/20250821151635-9.362um-1.2m-113keV-masked.zarr/", "access_roots": [ { "type": "s3", "url": "s3://vesuvius-challenge-open-data", "usage": "public-read" } ], "copy_info": null } ], "properties": null, "parameters": null, "creation_info": null }, { "type": "surface-prediction-zarr", "origins": [ { "path": "PHerc0191/representations/predictions/surfaces/20250821151635-surface-20260413222639-surface-m7-L0-th0.2.zarr/", "access_roots": [ { "type": "s3", "url": "s3://vesuvius-challenge-open-data", "usage": "public-read" } ], "copy_info": { "source_path": "s3://scrollprize-reconstruction/surfaces/m7/PHerc0191/20250821151635/20250821151635-9.362um-1.2m-113keV-masked.zarr.ome.zarr/", "date": "2026-05-13T17:21:20.487709Z", "workflow_execution": "s3sync-pherc0191-03c9fb52" } } ], "properties": null, "parameters": { "model_id": "20260413222639", "level": 0, "threshold_value": 0.2, "tta": "none" }, "creation_info": { "workflow_name": "surface-inference-9um-pherc0191-20250821151635", "workflow_namespace": "wf-inference", "workflow_uid": "802fb867-72db-4766-895a-fe0df39cb3d0", "workflow_creation_timestamp": "2026-04-24T11:06:42Z", "inference_cache_key": "surface-inference-9um-pherc0191-20250821151635", "blend_key": "surface-inference-9um-pherc0191-20250821151635", "generated_at": "2026-05-06T08:31:12Z", "model_type": "auto", "batch_size": 4, "ome_num_levels": 6, "ome_downsampling_algorithm": "nearest", "zarr_compressor": "lz4", "zarr_compression_level": 7 } }, { "type": "normal-grids", "origins": [ { "path": "PHerc0191/representations/predictions/surfaces/20250821151635-surface-20260413222639-surface-m7-L0-th0.2.normal-grids/", "access_roots": [ { "type": "s3", "url": "s3://vesuvius-challenge-open-data", "usage": "public-read" } ], "copy_info": { "source_path": 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"lasagna_version": 2, "source_to_base": 1.0, "grad_mag_encode_scale": 1000.0, "grad_mag_factor": 1.0 } } ] } }, "segments": {} }, "PHerc1299": { "sample": { "id": "PHerc1299", "properties": { "type": "scroll", "volume_transforms": null }, "data": [ { "type": "photo", "origins": [ { "path": "PHerc1299/photos/PHerc1299_photo.jpg", "access_roots": [ { "type": "s3", "url": "s3://vesuvius-challenge-open-data", "usage": "public-read" } ], "copy_info": { "source_path": "s3://philodemos/photogrammetry/post-esrf-photos/1299/JPGEnhanced/DSC02555.jpg", "date": "2026-07-22T16:16:23.189498Z", "workflow_execution": "s3copy-pherc1299-1f84178e" } } ], "properties": null, "parameters": null, "creation_info": null }, { "type": "photo-mask", "origins": [ { "path": "PHerc1299/photos/PHerc1299_mask.png", "access_roots": [ { "type": "s3", "url": "s3://vesuvius-challenge-open-data", "usage": "public-read" } ], "copy_info": { "source_path": 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"unsharp_sigma": 1.2, "unsharp_method": "gaussian", "padding_type": "edge" } }, "reconstruction": { "method": "GHBP", "prefix": "SCROLLS_HEL_2.403um_77keV_0.22m_PHerc_0139_B_TA2_0001", "rotation_axis_position": "13029.75" }, "postprocessing": { "32BitsConversion": { "dataset_used_min": -0.05972493812441826, "dataset_used_max": 0.3501993417739868 } }, "32bitsData": { "histogram": { "min": -0.3111127018928528, "max": 4.090550422668457, "min_0p002_percentile": -0.019549164921045303, "max_0p998_percentile": 0.13547097146511078, "min_0p00001_percentile": -0.05972493812441826, "max_0p99999_percentile": 0.3501993417739868 } } } } } }, "derived_from": null }, "properties": { "energy_keV": 77.0, "detector_distance_mm": 220.0, "pixel_size_um": 2.403 } }, "20250722040659": { "id": "20250722040659", "sample_id": "PHerc0139", "long_id": "20250722040659-2.403um-0.2m-77keV", "creation": { "date": "2025-07-22T06:06:59.725141+02:00", "process": "xray tomography", "metadata": { "location": "ESRF Grenoble", "beamline": "bm18", "energy_keV": 77.0, "detector_distance_mm": 220.0, "pixel_size_um": 2.403, "comment": "Metadata corrected from ESRF ICAT database. Original TIFF metadata.json incorrectly duplicated metadata from previous scan (B_TA2). Corrected values: acquisition date (2025-07-22 vs 2025-07-21), machineCurrentStart (88.37 vs 80.632008), machineCurrentStop (79.44 vs 76.8), sz position (-346.6452 vs -291.86), yrot (26.0004 vs 5.2), yrot_dial (estimated ~85.04 from mryrot 39.2366 vs 60.04). 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"/data/visitor/in1215/bm18/20250717/RAW_DATA/SCROLLS_HEL_2.403um_77keV_0.22m_PHerc_0139_ROI2_TA2/SCROLLS_HEL_2.403um_77keV_0.22m_PHerc_0139_ROI2_TA2_0001/SCROLLS_HEL_2.403um_77keV_0.22m_PHerc_0139_ROI2_TA2_0001.h5", "BlissLastScan": "/data/visitor/in1215/bm18/20250717/RAW_DATA/SCROLLS_HEL_2.403um_77keV_0.22m_PHerc_0139_ROI2_TA2/SCROLLS_HEL_2.403um_77keV_0.22m_PHerc_0139_ROI2_TA2_0001/SCROLLS_HEL_2.403um_77keV_0.22m_PHerc_0139_ROI2_TA2_0001.h5", "FlatField": "Standard", "DoubleFlatsScheme": false, "DetectorDistortionCorrection": true }, "preprocessing": { "DetectorDistortionCorrection": { "MapXzPathPar": "/gpfs/jazzy/data/bm18/inhouse/PAUL/OPTICS/2xOtus/250720_bi10_slits-aligned/mapfromslit_2368_4416.h5" }, "phase": { "method": "Paganin", "delta_beta": 1000.0, "unsharp_coeff": 4.0, "unsharp_sigma": 1.2, "unsharp_method": "gaussian", "padding_type": "edge" } }, "reconstruction": { "method": "GHBP", "prefix": "SCROLLS_HEL_2.403um_77keV_0.22m_PHerc_0139_ROI2_TA2_0001", "rotation_axis_position": "13029.75" } } } } }, "derived_from": null }, "properties": { "energy_keV": 77.0, "detector_distance_mm": 220.0, "pixel_size_um": 2.403 } }, "20251205005141": { "id": "20251205005141", "sample_id": "PHerc0139", "long_id": "20251205005141-2.399um-0.2m-78keV", "creation": { "date": "2025-12-05T01:51:41.661917+01:00", "process": "xray tomography", "metadata": { "location": "ESRF Grenoble", "beamline": "bm18", "energy_keV": 78.0, "detector_distance_mm": 220.0, "pixel_size_um": 2.399, "metadata": { "tomo": { "acquisition": { "scanRadix": "SCROLLS_HEL_2.399um_78keV_0.22m_PHerc_0139_HA", "scanType": "helical", "nb_scans": 1, "date": "2025-12-05T01:51:41.661917+01:00", "beamline": "bm18", "machineMode": "16 bunch", "machineCurrentStart": 76.241887, "machineCurrentStop": 75.08, "sampleDetectorDistance": 220.0, "sourceSampleDistance": 178000.0, "xray_magnification": 1.001236, "energy": 78.0, "scanRange": 360.0, "rotationMode": "continuous", "half_acquisition": true, "tomo_N": 40000, "ref_N": 401, "dark_N": 400, "z_start": -363.5, "z_end": -184.5538, "z_step": 5.113, "detector": { "sensor": "Pco", "sensorPixelSize": 0.0046, "roi_size": "[4416, 2368]", "sensorBinning": 1, "opticsName": "Fixed_X2", "opticsType": "FixedmagOptic", "optical_magnification": 2.0, "samplePixelSize": 0.002399, "scintillator": "GAGG_50um_refl" }, "acq_mode": "SINGLE", "expo_time": 0.013, "subframe": 0.013, "latency_time": 0.0013, "accumulation": 1, "scan_time": 588.526247, "comment": "wba11 = sapphire 2.5mm, wba12 = Ag 0.20mm", "attenuators": { "wba11": { "thickness": 2.5, "type": "sapphire" }, "wba12": { "thickness": 0.2, "type": "Ag" }, "wba13": { "thickness": 0.0, "type": "empty" }, "wba14": { "thickness": 0.0, "type": "empty" }, "wba15": { "thickness": 0.0, "type": "free pass" }, "wba21": { "thickness": 0.0, "type": "empty" }, "wba22": { "thickness": 0.0, "type": "empty" }, "wba23": { "thickness": 0.0, "type": "empty" }, "wba24": { "thickness": 0.0, "type": "empty" }, "wba25": { "thickness": 0.0, "type": "empty" }, "wba31": { "thickness": 0.0, "type": "free pass" }, "wba32": { "thickness": 0.0, "type": "free pass" } }, "motors": { "att11": 79.5, "att12": 139.5, "att13": 1.0, "att14": 1.0, "att15": 198.0, "att21": 198.0, "att22": 198.0, "att23": 198.0, "att24": 198.0, "att25": 198.0, "att31": 198.0, "att32": 198.0, "att33": "error", "dzfocus": -0.0, "dzmag": 10.0, "dzrotc": 0.28, "dzz": 207.03, "foc1twin": 4.68, "foc2twin": 5.15, "focus10x": 0.0, "focus2": 0.38, "focus3": -0.97, "focus5": -2.21, "focus7": -3.33, "focusrefl": -3.07, "focusx05": 0.0, "focusx2": 0.0, "focusx4": 0.0, "fsd": 4.78, "fshg": 11.28, "fsho": 64.97, "fshut_axis": 0.0, "fsl": -59.33, "fsr": 70.61, "fsu": 1.03, "fsvg": 5.81, "fsvo": -1.44, "fur1": -1.49, "girderx": 170.0, "kore": "error", "lfddiaph": 0.0, "lfdfocus": 14.03, "lfdrotc": 0.0, "lfdz": -0.0, "lthx1": -0.9, "lthx2": 0.0, "lthy1": 0.0, "lthy2": 0.0, "lz1": 0.0, "lz2": 0.0, "ostwin": -56.0, "psh1": 9.16, "psh2": 1.68, "pshg": 1.68, "psho": 10.0, "psv1": 0.22, "psv2": -1.0, "psvg": 1.1, "psvo": -0.25, "psx": 0.0, "psy": 0.0, "qsh1": -42.5, "qsh2": 85.0, "qshg": 85.0, "qsho": 0.0, "qsv1": 2.25, "qsv2": -4.5, "qsvg": 4.5, "qsvo": 0.0, "rotc10x": -0.0, "rotc2": "error", "rotc3": 0.56, "rotc5": -45.59, "rotc7": 0.03, "rotc9": -1.87, "rotcrefl": 1.4, "rotctwin": -0.04, "rotcx05": 0.01, "rotcx2": -1.7, "rotcx4": 0.0, "srot": 0.0, "ssh1": -42.29, "ssh2": 84.59, "sshg": 84.59, "ssho": -0.0, "ssv1": 2.4, "ssv2": -4.8, "ssvg": 5.0, "ssvo": 0.0, "sx": 0.0, "sy": 0.0, "sz": -363.5, "tsh1": -41.49, "tsh2": 82.97, "tshg": 82.97, "tsho": 0.0, "tsv1": 2.3, "tsv2": -4.6, "tsvg": 5.0, "tsvo": 0.0, "yc12": 67.25, "yc3": 350.0, "yc4": 66.96, "yc5": 350.0, "yc6": 350.0, "yc7": 350.5, "yc8": 147.7, "yc9": -39.42, "ycBT": 318.3, "yrot": 3.78, "zc1": -0.04, "zc2": -0.29, "zc3": 0.0, "zc4": 299.7, "zc5": 300.1, "zc6": 1.52, "zc7": -0.17, "zc8": 300.0, "zc9": 271.84, "zcBT": -135.1, "zfocus": "error", "zmag": "error", "zrotc": "error", "zyscint": "error", "zz": "error" }, "motors_dial": { "yrot_dial": 66.3 } }, "processing": { "general": { "WorkFlowScheme": "nabu", "BlissFirstScan": "/data/visitor/in1215/bm18/20251130/RAW_DATA/SCROLLS_HEL_2.399um_78keV_0.22m_PHerc_0139_TA3/SCROLLS_HEL_2.399um_78keV_0.22m_PHerc_0139_TA3_0001/SCROLLS_HEL_2.399um_78keV_0.22m_PHerc_0139_TA3_0001.h5", "BlissLastScan": "/data/visitor/in1215/bm18/20251130/RAW_DATA/SCROLLS_HEL_2.399um_78keV_0.22m_PHerc_0139_TA3/SCROLLS_HEL_2.399um_78keV_0.22m_PHerc_0139_TA3_0001/SCROLLS_HEL_2.399um_78keV_0.22m_PHerc_0139_TA3_0001.h5", "FlatField": "Standard", "DoubleFlatsScheme": false, "DetectorDistortionCorrection": true }, "preprocessing": { "DetectorDistortionCorrection": { "MapXzPathPar": "/gpfs/jazzy/data/bm18/inhouse/PAUL/OPTICS/2xOtus/251206_bi10_dist-map/mapfromslit_2368_4416.h5" }, "phase": { "method": "Paganin", "delta_beta": 1000.0, "unsharp_coeff": 4.0, "unsharp_sigma": 1.2, "unsharp_method": "gaussian", "padding_type": "edge" } }, "reconstruction": { "method": "GHBP", "prefix": "SCROLLS_HEL_2.399um_78keV_0.22m_PHerc_0139_TA3_0001", "rotation_axis_position": "13255.0" }, "postprocessing": { "32BitsConversion": { "dataset_used_min": -0.06549230962991714, "dataset_used_max": 0.37540295720100403 } }, "32bitsData": { "histogram": { "min": -1.4057211875915527, "max": 9.460485458374023, "min_0p002_percentile": -0.013694465160369873, "max_0p998_percentile": 0.13976439833641052, "min_0p00001_percentile": -0.06549230962991714, "max_0p99999_percentile": 0.37540295720100403 } } } } } }, "derived_from": null }, "properties": { "energy_keV": 78.0, "detector_distance_mm": 220.0, "pixel_size_um": 2.399 } }, "20250720065842": { "id": "20250720065842", "sample_id": "PHerc0139", "long_id": "20250720065842-9.362um-1.2m-113keV", "creation": { "date": "2025-07-20T08:58:42.332564+02:00", "process": "xray tomography", "metadata": { "location": "ESRF Grenoble", "beamline": "bm18", "energy_keV": 113.0, "detector_distance_mm": 1200.0, "pixel_size_um": 9.362, "metadata": { "tomo": { "acquisition": { "scanRadix": "SCROLLS_HEL_4.681um_113keV_1.2m_binmean_2_PHerc_0139_HA", "scanType": "helical", "nb_scans": 1, "date": "2025-07-20T08:58:42.332564+02:00", "beamline": "bm18", "machineMode": "16 bunch", "machineCurrentStart": 88.448482, "machineCurrentStop": 76.33, "sampleDetectorDistance": 1200.0, "sourceSampleDistance": 178000.0, "xray_magnification": 1.006742, "energy": 113.0, "scanRange": 360.0, "rotationMode": "continuous", "half_acquisition": true, "tomo_N": 10000, "ref_N": 401, "dark_N": 400, "z_start": -373.3, "z_end": -187.2584, "z_step": 9.302, "detector": { "sensor": "Pco", "sensorPixelSize": 6500.0, "roi_size": "[2208, 1104]", "sensorBinning": 2, "opticsName": "Fixed_X1", "opticsType": "FixedmagOptic", "optical_magnification": 1.0, "samplePixelSize": 0.009362, "scintillator": "GAGG_100um_reflective" }, "acq_mode": "SINGLE", "expo_time": 0.012, "subframe": 0.012, "latency_time": 0.0012, "accumulation": 1, "scan_time": 136.423572, "comment": "wba11 = Mo 1.30mm, wba14 = Ag 0.10mm", "attenuators": { "wba11": { "thickness": 1.3, "type": "Mo" }, "wba12": { "thickness": 5.0, "type": "sapphire" }, "wba13": { "thickness": 0.0, "type": "empty" }, "wba14": { "thickness": 0.0, "type": "empty" }, "wba15": { "thickness": 0.0, "type": "free pass" }, "wba21": { "thickness": 0.0, "type": "empty" }, "wba22": { "thickness": 0.0, "type": "empty" }, "wba23": { "thickness": 0.0, "type": "empty" }, "wba24": { "thickness": 0.0, "type": "empty" }, "wba25": { "thickness": 0.0, "type": "empty" }, "wba31": { "thickness": 0.0, "type": "free pass" }, "wba32": { "thickness": 0.0, "type": "free pass" }, "wba33": { "thickness": 25.0, "type": "SiO2_block" } }, "motors": { "att11": 119.2, "att12": 1.0, "att13": 1.0, "att14": 79.5, "att15": 198.0, "att21": 198.0, "att22": 198.0, "att23": 198.0, "att24": 198.0, "att25": 198.0, "att31": 198.0, "att32": 198.0, "att33": 198.0, "dzfocus": -42.91, "dzmag": 4.19, "dzrotc": -0.01, "dzz": 108.76, "foc1twin": 4.68, "foc2twin": 6.49, "focus10x": -1.34, "focus2": -0.88, "focus3": 0.03, "focus4": -42.91, "focus5": -2.21, "focus6": "error", "focus7": -2.67, "focusrefl": -3.07, "focusx2": 0.0, "focusx4": -0.04, "fsd": 4.11, "fshg": 20.78, "fsho": -64.14, "fshut_axis": 0.0, "fsl": 74.53, "fsr": -53.75, "fsu": 6.12, "fsvg": 10.25, "fsvo": 1.01, "fur1": -1.49, "girderx": -400.05, "kore": "error", "lfddiaph": 0.0, "lfdfocus": -34.58, "lfdrotc": -0.0, "lfdz": 400.0, "lthx1": -0.9, "lthx2": 0.0, "lthy1": 0.0, "lthy2": 0.0, "lz1": 0.0, "lz2": 0.0, "ostwin": -56.0, "psh1": -11.73, "psh2": 3.3, "pshg": 3.3, "psho": -10.0, "psv1": 0.96, "psv2": -1.7, "psvg": 1.8, "psvo": 0.12, "psx": 0.3, "psy": 0.1, "qsh1": -42.5, "qsh2": 85.0, "qshg": 85.0, "qsho": 0.0, "qsv1": 2.25, "qsv2": -4.5, "qsvg": 4.5, "qsvo": 0.0, "rotc10x": -0.11, "rotc2": "error", "rotc3": 0.31, "rotc4": -4.37, "rotc5": -45.59, "rotc6": "error", "rotc7": 0.0, "rotc9": -1.87, "rotcrefl": 1.4, "rotctwin": -0.45, "rotcx2": 1.67, "rotcx4": -1.31, "srot": 0.0, "ssh1": -42.29, "ssh2": 84.59, "sshg": 84.59, "ssho": -0.0, "ssv1": 2.4, "ssv2": -4.8, "ssvg": 5.0, "ssvo": 0.0, "sx": 0.3, "sy": 0.1, "sz": -373.3, "tsh1": -41.49, "tsh2": 82.97, "tshg": 82.97, "tsho": 0.0, "tsv1": 2.3, "tsv2": -4.6, "tsvg": 5.0, "tsvo": 0.0, "yc12": 840.0, "yc3": -68.53, "yc4": 360.0, "yc5": 350.0, "yc6": 47.69, "yc7": 323.8, "yc8": 13.0, "yc9": -39.42, "ycBT": 315.96, "yrot": 6.89, "zc1": -0.5, "zc2": 1.51, "zc3": 0.75, "zc4": 2.16, "zc5": 25.0, "zc6": 296.73, "zc7": 224.01, "zc8": 300.1, "zc9": 272.29, "zcBT": -164.6, "zfocus": "error", "zmag": "error", "zrotc": "error", "zyscint": "error", "zz": "error" }, "motors_dial": { "yrot_dial": 191.55 } } } }, "comment": "Reconstruction parameters deliberately not kept here: this acquisition has three reconstructions (delta_beta 1000, 50 and 0.0001), so a single processing block on the scan would describe only one of them. Each reconstruction carries its own under creation.metadata.processing on its tiff_16bits volume and on the masked.zarr exported from it. The block removed here was the delta_beta 1000 one, byte-identical to the one now on volumes 20250720065842 and 20250728140407." }, "derived_from": null }, "properties": { "energy_keV": 113.0, "detector_distance_mm": 1200.0, "pixel_size_um": 9.362 } }, "20251202104544": { "id": "20251202104544", "sample_id": "PHerc0139", "long_id": "20251202104544-1.129um-0.2m-59keV", "creation": { "date": "2025-12-02T11:45:44.147159+01:00", "process": "xray tomography", "metadata": { "location": "ESRF Grenoble", "beamline": "bm18", "energy_keV": 59.0, "detector_distance_mm": 220.0, "pixel_size_um": 1.129, "metadata": { "zarr_export": { "target_window_f32_min": -0.03, "target_window_f32_max": 0.145, "window_u16_min": 0, "window_u16_max": 23140, "z_crop_start": 16, "z_crop_end": 19296, "workflow_name": "export-1-129um-pherc-0139-roi2-fused-931851", "workflow_creation": "2026-04-13T11:30:53Z" }, "masking": { "method": "SAM2", "sam2_checkpoint": "/recon/models/masking/sam2-checkpoints/sam2.1_hiera_tiny.pt", "sam2_model_cfg": "configs/sam2.1/sam2.1_hiera_t", "finetuned_weights": "/recon/models/masking/sam2-checkpoints/scrollmask_august_t_4000.torch", "dilation_structure": "5", "dilation_iterations": "1", "mask_scale": 32 }, "mosaic": { "description": "Fused mosaic volume stitched from 19 helical half-acquisition tiles (T0 center + T1 ring of 6 + T2 ring of 12). All tiles share identical acquisition parameters (energy, pixel size, z-range, detector, processing). Only the horizontal stage positions (motors.sx, motors.sy) and the per-tile timestamp/comment differ.", "tile_count": 19, "tile_positions": { "T0-01": { "sx_mm": 0.0, "sy_mm": 0.0, "date": "2025-12-02T11:45:44.147159+01:00" }, "T1-01": { "sx_mm": 7.84, "sy_mm": 0.0, "date": "2025-12-02T12:19:51.298309+01:00" }, "T1-02": { "sx_mm": 3.92, "sy_mm": 6.79, "date": "2025-12-02T12:53:59.003378+01:00" }, "T1-03": { "sx_mm": -3.92, "sy_mm": 6.79, "date": "2025-12-02T13:28:05.964862+01:00" }, "T1-04": { "sx_mm": -7.84, "sy_mm": 0.0, "date": "2025-12-02T14:02:14.743097+01:00" }, "T1-05": { "sx_mm": -3.92, "sy_mm": -6.79, "date": "2025-12-02T14:36:20.966578+01:00" }, "T1-06": { "sx_mm": 3.92, "sy_mm": -6.79, "date": "2025-12-02T15:10:26.967803+01:00" }, "T2-01": { "sx_mm": 15.68, "sy_mm": 0.0, "date": "2025-12-02T15:44:35.050001+01:00" }, "T2-02": { "sx_mm": 11.76, "sy_mm": 6.79, "date": "2025-12-02T16:18:41.174781+01:00" }, "T2-03": { "sx_mm": 7.84, "sy_mm": 13.58, "date": "2025-12-02T16:52:48.266168+01:00" }, "T2-04": { "sx_mm": 0.0, "sy_mm": 13.58, "date": "2025-12-02T17:26:54.992105+01:00" }, "T2-05": { "sx_mm": -7.84, "sy_mm": 13.58, "date": "2025-12-02T18:01:01.655569+01:00" }, "T2-06": { "sx_mm": -11.76, "sy_mm": 6.79, "date": "2025-12-02T18:35:08.109495+01:00" }, "T2-07": { "sx_mm": -15.68, "sy_mm": 0.0, "date": "2025-12-02T19:09:24.948184+01:00" }, "T2-08": { "sx_mm": -11.76, "sy_mm": -6.79, "date": "2025-12-02T19:43:39.553171+01:00" }, "T2-09": { "sx_mm": -7.84, "sy_mm": -13.58, "date": "2025-12-02T20:17:54.745316+01:00" }, "T2-10": { "sx_mm": 0.0, "sy_mm": -13.58, "date": "2025-12-02T20:52:09.497686+01:00" }, "T2-11": { "sx_mm": 7.84, "sy_mm": -13.58, "date": "2025-12-02T21:26:23.260547+01:00" }, "T2-12": { "sx_mm": 11.76, "sy_mm": -6.79, "date": "2025-12-02T22:00:38.641405+01:00" } }, "varying_fields": [ "tomo/acquisition/date", "tomo/acquisition/machineCurrentStart", "tomo/acquisition/machineCurrentStop", "tomo/acquisition/motors/psx", "tomo/acquisition/motors/psy", "tomo/acquisition/motors/srot", "tomo/acquisition/motors/sx", "tomo/acquisition/motors/sy", "tomo/acquisition/scanRadix", "tomo/acquisition/scan_time", "tomo/processing/32bitsData/histogram/max_0p998_percentile", "tomo/processing/32bitsData/histogram/max_0p99999_percentile", "tomo/processing/32bitsData/histogram/min_0p00001_percentile", "tomo/processing/32bitsData/histogram/min_0p002_percentile", "tomo/processing/postprocessing/32BitsConversion/dataset_used_max", "tomo/processing/postprocessing/32BitsConversion/dataset_used_min", "tomo/processing/reconstruction/prefix", "tomo/processing/reconstruction/rotation_axis_position" ], "source_scans_prefix": "s3://scrollprize-scans/2025/esrf/20251130/PROCESSED_DATA/READY/mosaic_PHerc_0139_ROI2/" }, "tomo": { "acquisition": { "accumulation": 1, "acq_mode": "ACCUMULATION", "attenuators": { "wba11": { "thickness": 2.5, "type": "sapphire" }, "wba12": { "thickness": 1.0, "type": "sapphire" }, "wba13": { "thickness": 0.0, "type": "empty" }, "wba14": { "thickness": 0.0, "type": "empty" }, "wba15": { "thickness": 0.0, "type": "free pass" }, "wba21": { "thickness": 0.0, "type": "empty" }, "wba22": { "thickness": 0.0, "type": "empty" }, "wba23": { "thickness": 0.0, "type": "empty" }, "wba24": { "thickness": 0.0, "type": "empty" }, "wba25": { "thickness": 0.0, "type": "empty" }, "wba31": { "thickness": 0.0, "type": "free pass" }, "wba32": { "thickness": 0.0, "type": "free pass" } }, "beamline": "bm18", "comment": "wba11 = sapphire 2.5mm, wba12 = sapphire 1.0mm", "dark_N": 200, "detector": { "optical_magnification": 4.0, "opticsName": "Fixed_X4", "opticsType": "FixedmagOptic", "roi_size": "[4416, 2368]", "samplePixelSize": 0.001129, "scintillator": "LuAG_25um_refl", "sensor": "Pco", "sensorBinning": 1, "sensorPixelSize": 0.0046 }, "energy": 59.0, "expo_time": 0.013, "half_acquisition": true, "latency_time": 0.0013, "machineMode": "16 bunch", "motors": { "att11": 79.5, "att12": 39.5, "att13": 1.0, 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"/data/visitor/in1215/bm18/restored_from_s3/SCROLLS_HEL_4.681um_113keV_1.2m_binmean_2_PHerc_0139_TA_0001/SCROLLS_HEL_4.681um_113keV_1.2m_binmean_2_PHerc_0139_TA_0001.h5", "FlatField": "Standard", "DoubleFlatsScheme": false, "DetectorDistortionCorrection": false }, "preprocessing": { "phase": { "method": "Paganin", "delta_beta": 50.0, "unsharp_coeff": 4.0, "unsharp_sigma": 1.2, "unsharp_method": "gaussian", "padding_type": "edge" } }, "reconstruction": { "method": "GHBP", "prefix": "SCROLLS_HEL_4.681um_113keV_1.2m_binmean_2_PHerc_0139_TA_0001_000", "rotation_axis_position": "3310.125" }, "postprocessing": { "32BitsConversion": { "dataset_used_min": -0.16, "dataset_used_max": 0.75 } }, "32bitsData": { "histogram": { "min": -14.772077560424805, "max": 17.080129623413086, "min_0p002_percentile": -0.46742403507232666, "max_0p998_percentile": 0.524914026260376, "min_0p00001_percentile": -1.0235681533813477, "max_0p99999_percentile": 1.4534828662872314 } } }, "comment": "Export of the pag50 reconstruction. Voxel-aligned with 20250728140407 - identity transform, established by 3D cross-correlation of full-resolution blocks; it agrees with its pag0 sibling 20251107132835 to r=0.98 at zero shift. The export's metadata.json reported target_window_f32 -0.03/0.145, the paganin1000 default that its workflow records regardless of the window actually applied; window_u16 0..65535 means the full range of this reconstruction's own 32-bit conversion was written, so the f32 window recorded here is derived from that conversion instead. Masking is unreliable at both z ends, in the same places as 20251107132835: an unmasked blob over z 1144-1310, and the full reconstruction disc including the sample holder from z 20448 to the end." }, "derived_from": { "type": "volume", "id": "20251105184555" } }, "properties": { "energy_keV": 113.0, "detector_distance_mm": 1200.0, "pixel_size_um": 9.362, "data_format": "uint8", "transforms": [ { "to_volume_id": "20250728140407", "transformation_matrix": [ [ 1.0, 0.0, 0.0, 0.0 ], [ 0.0, 1.0, 0.0, 0.0 ], [ 0.0, 0.0, 1.0, 0.0 ] ], "from_landmarks": null, "to_landmarks": null } ], "shape": [ 20961, 6621, 6621 ], "z_direction_is_top_to_bottom": true, "left_handed_coordinates": false, "text_side": null, "superseded_by": null, "license": { "name": "CC BY-NC 4.0", "url": "https://creativecommons.org/licenses/by-nc/4.0/" }, "render_segments": false }, "data": [ { "type": "ome-zarr", "origins": [ { "path": "PHerc0139/volumes/20251107135911-9.362um-1.2m-113keV-pag50-masked.zarr/", "access_roots": [ { "type": "s3", "url": "s3://vesuvius-challenge-open-data", "usage": "public-read" } ], "copy_info": { "source_path": "s3://scrollprize-volumes/esrf/20250717/paganin-experiments/paganin50-v2/SCROLLS_HEL_4.681um_113keV_1.2m_binmean_2_PHerc_0139_TA_0001_masked.zarr/", "date": "2026-09-29T14:43:25.128320Z", "workflow_execution": "s3sync-pherc0139-98b1e1fc" } } ], "properties": null, "parameters": null, "creation_info": null } ] }, "20251107132835": { "id": "20251107132835", "sample_id": "PHerc0139", "scan_id": "20250720065842", "long_id": "20251107132835-9.362um-1.2m-113keV-pag0-masked.zarr", "suffix": "masked.zarr", "creation": { "date": "2025-11-07T13:28:35Z", "process": "mask_layers_zarr_export", "metadata": { "window_mode": "u16", "source_f32_min": -0.09, "source_f32_max": 0.4, "target_window_f32_min": -0.09, "target_window_f32_max": 0.4, "window_u16_min": 0, "window_u16_max": 65535, "workflow_name": "mask-layers-sam2long-tp7pt", "workflow_creation": "2025-11-07T13:28:35Z", "processing": { "general": { "WorkFlowScheme": "nabu", "BlissFirstScan": "/data/visitor/in1215/bm18/restored_from_s3/SCROLLS_HEL_4.681um_113keV_1.2m_binmean_2_PHerc_0139_TA_0001/SCROLLS_HEL_4.681um_113keV_1.2m_binmean_2_PHerc_0139_TA_0001.h5", "BlissLastScan": "/data/visitor/in1215/bm18/restored_from_s3/SCROLLS_HEL_4.681um_113keV_1.2m_binmean_2_PHerc_0139_TA_0001/SCROLLS_HEL_4.681um_113keV_1.2m_binmean_2_PHerc_0139_TA_0001.h5", "FlatField": "Standard", "DoubleFlatsScheme": false, "DetectorDistortionCorrection": false }, "preprocessing": { "phase": { "method": "Paganin", "delta_beta": 0.0001, "unsharp_coeff": 0.0, "unsharp_sigma": 0.0, "unsharp_method": "gaussian", "padding_type": "edge" } }, "reconstruction": { "method": "GHBP", "prefix": "SCROLLS_HEL_4.681um_113keV_1.2m_binmean_2_PHerc_0139_TA_0001", "rotation_axis_position": "3310.125" }, "postprocessing": { "32BitsConversion": { "dataset_used_min": -0.09, "dataset_used_max": 0.4 } }, "32bitsData": { "histogram": { "min": -7.920702934265137, "max": 9.530128479003906, "min_0p002_percentile": -0.23978209495544434, "max_0p998_percentile": 0.3018922805786133, "min_0p00001_percentile": -0.5400238037109375, "max_0p99999_percentile": 0.8061695098876953 } } }, "comment": "Export of the pag0 reconstruction. Voxel-aligned with 20250728140407 - identity transform, established by 3D cross-correlation of full-resolution blocks at three locations including one ~2300 px off the rotation axis, where the disabled detector distortion correction would have shown. The export's metadata.json reported target_window_f32 -0.03/0.145, the paganin1000 default that its workflow records regardless of the window actually applied; window_u16 0..65535 means the full range of this reconstruction's own 32-bit conversion was written, so the f32 window recorded here is derived from that conversion instead. Masking is unreliable at both z ends: an unmasked blob over z 1144-1310, and the full reconstruction disc including the sample holder from z 20448 to the end of the array." }, "derived_from": { "type": "volume", "id": "20251105184744" } }, "properties": { "energy_keV": 113.0, "detector_distance_mm": 1200.0, "pixel_size_um": 9.362, "data_format": "uint8", "transforms": [ { "to_volume_id": "20250728140407", "transformation_matrix": [ [ 1.0, 0.0, 0.0, 0.0 ], [ 0.0, 1.0, 0.0, 0.0 ], [ 0.0, 0.0, 1.0, 0.0 ] ], "from_landmarks": null, "to_landmarks": null } ], "shape": [ 20961, 6621, 6621 ], "z_direction_is_top_to_bottom": true, "left_handed_coordinates": false, "text_side": null, "superseded_by": null, "license": { "name": "CC BY-NC 4.0", "url": "https://creativecommons.org/licenses/by-nc/4.0/" }, "render_segments": false }, "data": [ { "type": "ome-zarr", "origins": [ { "path": "PHerc0139/volumes/20251107132835-9.362um-1.2m-113keV-pag0-masked.zarr/", "access_roots": [ { "type": "s3", "url": 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"PHerc0490B/representations/predictions/surfaces/20250521151215-surface-20260413222639-surface-m7-L0-th0.2.normal-grids/", "access_roots": [ { "type": "s3", "url": "s3://vesuvius-challenge-open-data", "usage": "public-read" } ], "copy_info": { "source_path": "s3://scrollprize-reconstruction/surfaces/m7/PHerc0490B/20250521151215/20250521151215-8.640um-1.2m-116keV-masked.zarr.ome.zarr/normal_grids/", "date": "2026-07-07T09:45:22.064334Z", "workflow_execution": "s3sync-pherc0490b-3b3707b9" } } ], "properties": null, "parameters": { "model_id": "20260413222639", "level": 0, "threshold_value": 0.2 }, "creation_info": { "grid_step": 64, "input_level": 0, "prune_min_length_px": 20.0, "sparse_volume": 1, "spiral_step": 20.0 } } ] } }, "segments": {} }, "PHercParis2Fr47": { "sample": { "id": "PHercParis2Fr47", "properties": { "type": "fragment", "volume_transforms": null, "legacy_data_url": "https://dl.ash2txt.org/fragments/Frag1/PHercParis2Fr47.volpkg/", "description": "PHerc. Paris 2 Fr 47" }, "data": [ { "type": "photo", "origins": [ { "path": "samples/PHercParis2Fr47/photos/PHercParis2Fr47_photo.jpg", "access_roots": [ { "type": "https", "url": "https://data.aws.ash2txt.org", "usage": "public-read" } ], "copy_info": null }, { "path": "PHercParis2Fr47/photos/PHercParis2Fr47_photo.jpg", "access_roots": [ { "type": "s3", "url": "s3://vesuvius-challenge-open-data", "usage": "public-read" } ], "copy_info": { "source_path": "s3://vesuvius-challenge/PHercParis2Fr47/photos/PHercParis2Fr47_photo.jpg", "date": "2026-02-23T14:36:23.290969Z", "workflow_execution": "s3copy-phercparis2fr47-a940fd1f" } } ], "properties": null, "parameters": null, "creation_info": null } ], "description": "PHerc. Paris 2 Fr 47 is a fragment of a Herculaneum papyrus, carbonized during the eruption of Mount Vesuvius in 79 AD. 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-0.1415777060228669, 7703.857635663877 ] ], "derivation_path": "20260323082859-20251217075048.20251217075048-20231117161658" }, { "to_volume_id": "20251217075048", "matrix": [ [ 0.4721544678851165, -0.005989111464099385, 0.0016708195225342399, 2919.873929688601 ], [ 0.000484315421225838, 0.47497577904661076, -0.0027421945495009485, 2418.1187496004713 ], [ -0.0011650130739805234, 0.009565094365789098, 0.4662024977628025, 12502.427483641877 ] ], "derivation_path": "20260323082859-20251217075048" } ] } ], "legacy_data_url": "https://dl.ash2txt.org/full-scrolls/Scroll4/PHerc1667.volpkg/" }, "data": [ { "type": "photo", "origins": [ { "path": "samples/PHerc1667/photos/PHerc1667_photo.jpg", "access_roots": [ { "type": "https", "url": "https://data.aws.ash2txt.org", "usage": "public-read" } ], "copy_info": null }, { "path": "PHerc1667/photos/PHerc1667_photo.jpg", "access_roots": [ { "type": "s3", "url": "s3://vesuvius-challenge-open-data", "usage": "public-read" } ], "copy_info": { "source_path": "s3://vesuvius-challenge/PHerc1667/photos/PHerc1667_photo.jpg", "date": "2026-02-23T14:36:23.520198Z", "workflow_execution": "s3copy-pherc1667-34d67db3" } } ], "properties": null, "parameters": null, "creation_info": null } ], "description": "PHerc. 1667 is a rolled Herculaneum papyrus from the [Biblioteca Nazionale di Napoli](https://www.bnnonline.it/it/121/officina-dei-papiri-ercolanesi), carbonized during the eruption of Mount Vesuvius in 79 AD. It was scanned at the [Diamond Light Source](https://www.diamond.ac.uk) in Oxfordshire, UK.\n\nIt is similar in size to PHerc. 332 (Scroll 3)." }, "scans": { "20231107190228": { "id": "20231107190228", "sample_id": "PHerc1667", "long_id": "20231107190228-3.240um-88keV", "creation": { "date": "2023-11-07T19:02:28Z", "process": "xray tomography", "metadata": { "location": "DLS (Diamond Light Source)", "energy_keV": 88.0, "pixel_size_um": 3.24, "scan_name": "PHerc1667, 88 keV, 3.24 um, merged volume" }, "derived_from": null }, "properties": { "energy_keV": 88.0, "detector_distance_mm": null, "pixel_size_um": 3.24 } }, "20251204164204": { "id": "20251204164204", "sample_id": "PHerc1667", "long_id": "20251204164204-2.399um-0.2m-78keV", "creation": { "date": "2025-12-04T17:42:04.506198+01:00", "process": "xray tomography", "metadata": { "location": "ESRF Grenoble", "beamline": "bm18", "energy_keV": 78.0, "detector_distance_mm": 220.0, "pixel_size_um": 2.399, "metadata": { "tomo": { "acquisition": { "scanRadix": "SCROLLS_HEL_2.399um_78keV_0.22m_PHerc_1667_HA", "scanType": "helical", "nb_scans": 1, "date": "2025-12-04T17:42:04.506198+01:00", "beamline": "bm18", "machineMode": "16 bunch", "machineCurrentStart": 74.516165, "machineCurrentStop": 77.58, "sampleDetectorDistance": 220.0, "sourceSampleDistance": 178000.0, "xray_magnification": 1.001236, "energy": 78.0, "scanRange": 360.0, "rotationMode": "continuous", "half_acquisition": true, "tomo_N": 23000, "ref_N": 401, "dark_N": 400, "z_start": -269.5, "z_end": -182.5832, "z_step": 5.113, "detector": { "sensor": "Pco", "sensorPixelSize": 0.0046, "roi_size": "[4416, 2368]", "sensorBinning": 1, "opticsName": "Fixed_X2", "opticsType": "FixedmagOptic", "optical_magnification": 2.0, "samplePixelSize": 0.002399, "scintillator": "GAGG_50um_refl" }, "acq_mode": "SINGLE", "expo_time": 0.013, "subframe": 0.013, "latency_time": 0.0013, "accumulation": 1, "scan_time": 338.498171, "comment": "wba11 = sapphire 2.5mm, wba12 = Ag 0.20mm", "attenuators": { "wba11": { "thickness": 2.5, "type": "sapphire" }, "wba12": { "thickness": 0.2, "type": "Ag" }, "wba13": { "thickness": 0.0, "type": "empty" }, "wba14": { "thickness": 0.0, "type": "empty" }, "wba15": { "thickness": 0.0, "type": "free pass" }, "wba21": { "thickness": 0.0, "type": "empty" }, "wba22": { "thickness": 0.0, "type": "empty" }, "wba23": { "thickness": 0.0, "type": "empty" }, "wba24": { "thickness": 0.0, "type": "empty" }, "wba25": { "thickness": 0.0, "type": "empty" }, "wba31": { "thickness": 0.0, "type": "free pass" }, "wba32": { "thickness": 0.0, "type": "free pass" } }, "motors": { "att11": 79.5, "att12": 139.5, "att13": 1.0, "att14": 1.0, "att15": 198.0, "att21": 198.0, "att22": 198.0, "att23": 198.0, "att24": 198.0, "att25": 198.0, "att31": 198.0, "att32": 198.0, "att33": "error", "dzfocus": -0.0, "dzmag": 10.0, "dzrotc": 0.28, "dzz": 207.03, "foc1twin": 4.68, "foc2twin": 5.15, "focus10x": 0.0, "focus2": 0.38, "focus3": -0.97, "focus5": -2.21, "focus7": -3.33, "focusrefl": -3.07, "focusx05": 0.0, "focusx2": 0.0, "focusx4": 0.0, "fsd": 4.78, "fshg": 11.28, "fsho": 64.97, "fshut_axis": 0.0, "fsl": -59.33, "fsr": 70.61, "fsu": 1.03, "fsvg": 5.81, "fsvo": -1.44, "fur1": -1.49, "girderx": 170.0, "kore": "error", "lfddiaph": 0.0, "lfdfocus": 14.03, "lfdrotc": 0.0, "lfdz": -0.0, "lthx1": -0.9, "lthx2": 0.0, "lthy1": 0.0, "lthy2": 0.0, "lz1": 0.0, "lz2": 0.0, "ostwin": -56.0, "psh1": 9.16, "psh2": 1.68, "pshg": 1.68, "psho": 10.0, "psv1": 0.22, "psv2": -1.0, "psvg": 1.1, "psvo": -0.25, "psx": 0.0, "psy": 0.0, "qsh1": -42.5, "qsh2": 85.0, "qshg": 85.0, "qsho": 0.0, "qsv1": 2.25, "qsv2": -4.5, "qsvg": 4.5, "qsvo": 0.0, "rotc10x": -0.0, "rotc2": "error", "rotc3": 0.56, "rotc5": -45.59, "rotc7": 0.03, "rotc9": -1.87, "rotcrefl": 1.4, "rotctwin": -0.04, "rotcx05": 0.01, "rotcx2": -1.7, "rotcx4": 0.0, "srot": 0.0, "ssh1": -42.29, "ssh2": 84.59, "sshg": 84.59, "ssho": -0.0, "ssv1": 2.4, "ssv2": -4.8, "ssvg": 5.0, "ssvo": 0.0, "sx": 0.0, "sy": 0.0, "sz": -269.5, "tsh1": -41.49, "tsh2": 82.97, "tshg": 82.97, "tsho": 0.0, "tsv1": 2.3, "tsv2": -4.6, "tsvg": 5.0, "tsvo": 0.0, "yc12": 67.25, "yc3": 350.0, "yc4": 66.96, "yc5": 350.0, "yc6": 350.0, "yc7": 350.5, "yc8": 147.7, "yc9": -39.42, "ycBT": 318.3, "yrot": 4.36, "zc1": -0.04, "zc2": -0.29, "zc3": 0.0, "zc4": 299.7, "zc5": 300.1, "zc6": 1.52, "zc7": -0.17, "zc8": 300.0, "zc9": 271.84, "zcBT": -135.1, "zfocus": "error", "zmag": "error", "zrotc": "error", "zyscint": "error", "zz": "error" }, "motors_dial": { "yrot_dial": 65.72 } }, "processing": { "preprocessing": { "phase": { "method": "Paganin", "delta_beta": 1000.0, "unsharp_coeff": 4.0, "unsharp_sigma": 1.2, "unsharp_method": "gaussian", "padding_type": "edge" } }, "reconstruction": { "method": "GHBP", "prefix": "SCROLLS_HEL_2.399um_78keV_0.22m_PHerc_1667_TA_0001", "rotation_axis_position": "7663.75" }, "32bitsData": { "histogram": { "min": -0.32644790410995483, "max": 3.4791736602783203, "min_0p002_percentile": 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"https", "url": "https://data.aws.ash2txt.org", "usage": "public-read" } ], "copy_info": null }, { "path": "PHercParis4/photos/PHercParis4_photo.jpg", "access_roots": [ { "type": "s3", "url": "s3://vesuvius-challenge-open-data", "usage": "public-read" } ], "copy_info": { "source_path": "s3://vesuvius-challenge/PHercParis4/photos/PHercParis4_photo.jpg", "date": "2026-02-23T14:36:23.749455Z", "workflow_execution": "s3copy-phercparis4-92e55787" } } ], "properties": null, "parameters": null, "creation_info": null } ], "description": "PHerc. Paris 4 is a rolled Herculaneum papyrus from the [Institut de France](https://www.institutdefrance.fr/en/home/), carbonized during the eruption of Mount Vesuvius in 79 AD. It was scanned at the [Diamond Light Source](https://www.diamond.ac.uk) in Oxfordshire, UK.\n\nThis is the scroll for which we have by far the most segments, where the [first letters](https://scrollprize.org/firstletters) were discovered and the [2023 Grand Prize](https://scrollprize.org/grandprize) was claimed." }, "scans": { "20260315072529": { "id": "20260315072529", "sample_id": "PHercParis4", "long_id": "20260315072529-2.400um-0.2m-137keV", "creation": { "date": "2026-03-15T08:25:29.330739+01:00", "process": "xray tomography", "metadata": { "location": "ESRF Grenoble", "beamline": "bm18", "energy_keV": 137.0, "detector_distance_mm": 220.0, "pixel_size_um": 2.4, "metadata": { "tomo": { "acquisition": { "scanRadix": "2.4um_137keV_PHerc-Paris4_ROI1", "scanType": "helical", "nb_scans": 5, "start_date": "2026-03-15T06:26:01.084619+01:00", "end_date": "2026-03-15T08:25:29.330739+01:00", "beamline": "bm18", "machineMode": "16 bunch", "machineCurrentStart": 57.350201, "machineCurrentStop": 83.21, "sampleDetectorDistance": 220.0, "sourceSampleDistance": 178000.0, "xray_magnification": 1.001236, "energy": 137.0, "scanRange": 360.0, "rotationMode": "continuous", "half_acquisition": false, "tomo_N": 13000, "ref_N": 401, "dark_N": 400, "z_start": -258.5, "z_end": -238.04, "z_step": 5.115, "detector": { "sensor": "Pco", "sensorPixelSize": 0.0046, "roi_size": "[4416, 2368]", "sensorBinning": 1, "opticsName": "Fixed_X2", "opticsType": "FixedmagOptic", "optical_magnification": 2.0, "samplePixelSize": 0.0024, "scintillator": "GAGG_50um_refl" }, "acq_mode": "SINGLE", "expo_time": 0.12, "subframe": 0.12, "latency_time": null, "accumulation": 1, "scan_time": 6885.88893, "scan_time_total": 7168.24612, "comment": "wba11 = Mo 1.30mm, wba12 = Ag 0.20mm, wba13 = Au 0.10mm, wba14 = Ag 0.20mm", "attenuators": { "wba11": { "thickness": 5.0, "type": "sapphire" }, "wba12": { "thickness": 0.0, "type": "empty" }, "wba13": { "thickness": 0.0, "type": "empty" }, "wba14": { "thickness": 0.1, "type": "Au" }, "wba15": { "thickness": 0.0, "type": "free pass" }, "wba21": { "thickness": 0.0, "type": "empty" }, "wba22": { "thickness": 15.0, "type": "sapphire" }, "wba23": { "thickness": 0.0, "type": "empty" }, "wba24": { "thickness": 0.0, "type": "empty" }, "wba25": { "thickness": 0.0, "type": "empty" }, "wba31": { "thickness": 0.0, "type": "free pass" }, "wba32": { "thickness": 0.0, "type": "free pass" } }, "motors": { "att11": 99.5, "att12": 139.5, "att13": 159.5, "att14": 99.5, "att15": 198.0, "att21": 198.1, "att22": 198.0, "att23": 198.0, "att24": 198.1, "att25": 198.0, "att31": 199.5, "att32": 198.1, "att33": "error", "dzfocus": -0.0, "dzmag": 5.77, "dzrotc": 0.23, "dzz": 160.56, "foc1twin": 4.68, "foc2twin": 5.15, "focus10x": 0.0, "focus2": -1.91, "focus3": 0.0, "focus5": -2.21, "focus7": -2.84, "focusrefl": -3.07, "focusx05": -0.06, "focusx2": 0.0, "focusx4": 0.0, "fsd": 0.7, "fshg": 10.9, "fsho": 64.39, "fshut_axis": 0.0, "fsl": -58.94, "fsr": 69.84, "fsu": 5.17, "fsvg": 5.87, "fsvo": 2.24, "fur1": -1.49, "girderx": 139.38, "hzsrot": "error", "kore": "error", "lfddiaph": 0.0, "lfdfocus": 13.64, "lfdrotc": 0.01, "lfdz": -0.0, "lthx1": -0.9, "lthx2": 0.0, "lthy1": 0.0, "lthy2": 0.0, "lz1": -0.0, "lz2": 0.0, "ostwin": -56.0, "psh1": 9.11, "psh2": 1.79, "pshg": 1.79, "psho": 10.0, "psv1": 0.88, "psv2": -1.05, "psvg": 1.15, "psvo": 0.36, "psx": 6.88, "psy": 6.88, "qsh1": -42.5, "qsh2": 85.0, "qshg": 85.0, "qsho": 0.0, "qsv1": 2.82, "qsv2": -4.5, "qsvg": 4.5, "qsvo": 0.0, "rotc10x": -0.0, "rotc2": "error", "rotc3": -0.61, "rotc5": -45.59, "rotc7": 0.03, "rotc9": -1.87, "rotcrefl": 1.4, "rotctwin": -0.04, "rotcx05": 0.0, "rotcx2": 0.0, "rotcx4": 0.0, "srot": 0.0, "ssh1": -42.29, "ssh2": 84.59, "sshg": 84.59, "ssho": -0.0, "ssv1": 2.15, "ssv2": -4.3, "ssvg": 4.5, "ssvo": 0.0, "sx": 6.88, "sy": 6.88, "sz": -258.5, "tsh1": -41.49, "tsh2": 82.97, "tshg": 82.97, "tsho": 0.0, "tsv1": 2.05, "tsv2": -4.1, "tsvg": 4.5, "tsvo": 0.0, "yc12": 67.17, "yc3": 366.82, "yc4": 442.14, "yc5": 362.0, "yc6": 371.0, "yc7": 350.0, "yc8": -1.05, "yc9": -39.42, "ycBT": 358.09, "yrot": 4.8, "zc1": 5.52, "zc2": 4.17, "zc3": 4.55, "zc4": 300.5, "zc5": 300.1, "zc6": 13.82, "zc7": 4.23, "zc8": 299.8, "zc9": 271.84, "zcBT": 119.06, "zfocus": "error", "zmag": "error", "zrotc": "error", "zyscint": "error", "zz": "error" }, "motors_dial": { "yrot_dial": 65.34 } }, "processing": { "general": { "WorkFlowScheme": "nabu", "BlissFirstScan": "/data/visitor/in1215/bm18/20260311/RAW_DATA/2.4um_137keV_PHerc-Paris4_ROI1/2.4um_137keV_PHerc-Paris4_ROI1_0001/2.4um_137keV_PHerc-Paris4_ROI1_0001.h5", "BlissLastScan": "/data/visitor/in1215/bm18/20260311/RAW_DATA/2.4um_137keV_PHerc-Paris4_ROI1/2.4um_137keV_PHerc-Paris4_ROI1_0001/2.4um_137keV_PHerc-Paris4_ROI1_0001.h5", "FlatField": "Standard", "DoubleFlatsScheme": true, "DetectorDistortionCorrection": true, "LutPathScheme": true, "AutoCorrectZTranslations": false }, "preprocessing": { "double_flat_field": { 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