diff --git a/.gitattributes b/.gitattributes index bed0738c7eeb449bca98b5d2f33c89a1ee56349a..1a3348799657a27cd9a595002bbe2aeb2adbd940 100644 --- a/.gitattributes +++ b/.gitattributes @@ -58,3 +58,45 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text # Video files - compressed *.mp4 filter=lfs diff=lfs merge=lfs -text *.webm filter=lfs diff=lfs merge=lfs -text +data/pherc0248/ε.txt filter=lfs diff=lfs merge=lfs -text +data/pherc0248/ε_stack.tif filter=lfs diff=lfs merge=lfs -text +data/pherc0248/ε_z.tif filter=lfs diff=lfs merge=lfs -text +data/pherc0248/λ.txt filter=lfs diff=lfs merge=lfs -text +data/pherc0248/λ_stack.tif filter=lfs diff=lfs merge=lfs -text +data/pherc0248/λ_z.tif filter=lfs diff=lfs merge=lfs -text +data/pherc0248/ν.txt filter=lfs diff=lfs merge=lfs -text +data/pherc0248/ν_stack.tif filter=lfs diff=lfs merge=lfs -text +data/pherc0248/ν_z.tif filter=lfs diff=lfs merge=lfs -text +data/pherc0248/π.txt filter=lfs diff=lfs merge=lfs -text +data/pherc0248/π_stack.tif filter=lfs diff=lfs merge=lfs -text +data/pherc0248/π_z.tif filter=lfs diff=lfs merge=lfs -text +data/pherc0248/φ.txt filter=lfs diff=lfs merge=lfs -text +data/pherc0248/φ_stack.tif filter=lfs diff=lfs merge=lfs -text +data/pherc0248/φ_z.tif filter=lfs diff=lfs merge=lfs -text +data/pherc0250/δ.txt filter=lfs diff=lfs merge=lfs -text +data/pherc0250/δ_stack.tif filter=lfs diff=lfs merge=lfs -text +data/pherc0250/δ_z.tif filter=lfs diff=lfs merge=lfs -text +data/pherc0250/κ.txt filter=lfs diff=lfs merge=lfs -text +data/pherc0250/κ_stack.tif filter=lfs diff=lfs merge=lfs -text +data/pherc0250/κ_z.tif filter=lfs diff=lfs merge=lfs -text +data/pherc0250/ο.txt filter=lfs diff=lfs merge=lfs -text +data/pherc0250/ο_stack.tif filter=lfs diff=lfs merge=lfs -text +data/pherc0250/ο_z.tif filter=lfs diff=lfs merge=lfs -text +data/pherc0250/ρ.txt filter=lfs diff=lfs merge=lfs -text +data/pherc0250/ρ_stack.tif filter=lfs diff=lfs merge=lfs -text +data/pherc0250/ρ_z.tif filter=lfs diff=lfs merge=lfs -text +data/pherc0250/ϲ.txt filter=lfs diff=lfs merge=lfs -text +data/pherc0250/ϲ_stack.tif filter=lfs diff=lfs merge=lfs -text +data/pherc0250/ϲ_z.tif filter=lfs diff=lfs merge=lfs -text +data/pherc0500p2/η.txt filter=lfs diff=lfs merge=lfs -text +data/pherc0500p2/η_stack.tif filter=lfs diff=lfs merge=lfs -text +data/pherc0500p2/η_z.tif filter=lfs diff=lfs merge=lfs -text +data/pherc0500p2/ιτ.txt filter=lfs diff=lfs merge=lfs -text +data/pherc0500p2/ιτ_stack.tif filter=lfs diff=lfs merge=lfs -text +data/pherc0500p2/ιτ_z.tif filter=lfs diff=lfs merge=lfs -text +data/pherc0500p2/ν.txt filter=lfs diff=lfs merge=lfs -text +data/pherc0500p2/ν2.txt filter=lfs diff=lfs merge=lfs -text +data/pherc0500p2/ν2_stack.tif filter=lfs diff=lfs merge=lfs -text +data/pherc0500p2/ν2_z.tif filter=lfs diff=lfs merge=lfs -text +data/pherc0500p2/ν_stack.tif filter=lfs diff=lfs merge=lfs -text +data/pherc0500p2/ν_z.tif filter=lfs diff=lfs merge=lfs -text diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000000000000000000000000000000000000..fe64a14c1781f5c9849272697eb07126f0820b77 --- /dev/null +++ b/LICENSE @@ -0,0 +1,26 @@ +Optical profilometry of opened Herculaneum papyri + +Copyright (c) 2026 Vesuvius Challenge. + +Except where otherwise indicated, the data, annotations, fold splits, +configuration files, documentation, and other non-code research files in +this release are licensed under the Creative Commons +Attribution-NonCommercial 4.0 International License (CC BY-NC 4.0). + +You may share and adapt the licensed material for noncommercial purposes, +provided that you give appropriate credit, link to the license, and indicate +whether changes were made. No warranties are given. + +License deed and legal code: +https://creativecommons.org/licenses/by-nc/4.0/ + +Suggested attribution: + + Vesuvius Challenge (2026). Optical profilometry of opened Herculaneum papyri. + https://doi.org/10.1038/s41598-026-58467-1. Licensed under CC BY-NC 4.0. + +nnU-Net is not included in this release and is distributed separately under +the Apache License 2.0. + +Third-party material, if expressly identified, is excluded from this license +and remains subject to its own license or permission terms. diff --git a/README.md b/README.md index e5f99753cd5578d5f86c70bb7da94c52f8fe692b..0881b7a18bcce24548295553f423ceeb56672861 100644 --- a/README.md +++ b/README.md @@ -1,3 +1,40 @@ --- +pretty_name: "Optical profilometry of opened Herculaneum papyri" license: cc-by-nc-4.0 +task_categories: [image-segmentation] +size_categories: [n<1K] +tags: [image, 3d, archaeology] --- + +# Optical profilometry of opened Herculaneum papyri + +Dataset accompanying [“Ink detection from surface topography of the Herculaneum papyri”](https://doi.org/10.1038/s41598-026-58467-1). + +The release contains 14 co-registered profilometry regions encompassing 16 letters from PHerc. 248, PHerc. 250, and PHerc. 500P2. + +- Native lateral sampling: 0.68793625 µm/pixel in X and Y +- Vertical sensitivity: 8 nm + +## Data + +Each sample under `data/` has four files with identical dimensions and a top-left origin: + +- `.txt`: semicolon-delimited X, Y, and calibrated Z values in µm; missing reconstructions are `nan` +- `_z.tif`: per-sample normalized uint16 height map +- `_stack.tif`: co-registered RGB brightfield image +- `_label.png`: grayscale ink annotation; experiment preprocessing treats nonzero values as foreground + +Use the text files when calibrated physical heights are required. Exact height-map preprocessing is specified in `configs/experiment.json`. + +## Metadata and configurations + +- `manifest.csv`: dimensions, physical extents, sampling, acquisition dates, and file paths +- `configs/case_manifest.json`: stable machine-learning case IDs and sample mapping +- `configs/sampling.json`: native, vertical, and factor-derived sampling values +- `configs/experiment.json`: preprocessing, experiments, training settings, and software versions +- `configs/nnunet/`: dataset descriptor and nine resolution-specific nnU-Net plans +- `folds/splits_final.json`: five cross-validation and three leave-one-papyrus-out splits + +## License + +Data, annotations, folds, and configurations are CC BY-NC 4.0. See `LICENSE`. Please cite the associated paper above. diff --git a/configs/case_manifest.json b/configs/case_manifest.json new file mode 100644 index 0000000000000000000000000000000000000000..1103e5b9b60e32723955a00f5f2323e5fc17a7a6 --- /dev/null +++ b/configs/case_manifest.json @@ -0,0 +1,160 @@ +{ + "schema_version": "1.0", + "dataset_version": "1.0.0", + "samples": [ + { + "case_id": "248_090925_E", + "papyrus_id": "PHerc. 248", + "papyrus_dir": "pherc0248", + "sample_id": "ε", + "acquisition_date": "2025-09-09", + "raw_height_txt": "data/pherc0248/ε.txt", + "normalized_height_tif": "data/pherc0248/ε_z.tif", + "brightfield_tif": "data/pherc0248/ε_stack.tif", + "label_png": "data/pherc0248/ε_label.png" + }, + { + "case_id": "248_090925_F", + "papyrus_id": "PHerc. 248", + "papyrus_dir": "pherc0248", + "sample_id": "φ", + "acquisition_date": "2025-09-09", + "raw_height_txt": "data/pherc0248/φ.txt", + "normalized_height_tif": "data/pherc0248/φ_z.tif", + "brightfield_tif": "data/pherc0248/φ_stack.tif", + "label_png": "data/pherc0248/φ_label.png" + }, + { + "case_id": "248_090925_L", + "papyrus_id": "PHerc. 248", + "papyrus_dir": "pherc0248", + "sample_id": "λ", + "acquisition_date": "2025-09-09", + "raw_height_txt": "data/pherc0248/λ.txt", + "normalized_height_tif": "data/pherc0248/λ_z.tif", + "brightfield_tif": "data/pherc0248/λ_stack.tif", + "label_png": "data/pherc0248/λ_label.png" + }, + { + "case_id": "248_090925_N", + "papyrus_id": "PHerc. 248", + "papyrus_dir": "pherc0248", + "sample_id": "ν", + "acquisition_date": "2025-09-09", + "raw_height_txt": "data/pherc0248/ν.txt", + "normalized_height_tif": "data/pherc0248/ν_z.tif", + "brightfield_tif": "data/pherc0248/ν_stack.tif", + "label_png": "data/pherc0248/ν_label.png" + }, + { + "case_id": "248_090925_PI", + "papyrus_id": "PHerc. 248", + "papyrus_dir": "pherc0248", + "sample_id": "π", + "acquisition_date": "2025-09-09", + "raw_height_txt": "data/pherc0248/π.txt", + "normalized_height_tif": "data/pherc0248/π_z.tif", + "brightfield_tif": "data/pherc0248/π_stack.tif", + "label_png": "data/pherc0248/π_label.png" + }, + { + "case_id": "250_090925_C", + "papyrus_id": "PHerc. 250", + "papyrus_dir": "pherc0250", + "sample_id": "ϲ", + "acquisition_date": "2025-09-09", + "raw_height_txt": "data/pherc0250/ϲ.txt", + "normalized_height_tif": "data/pherc0250/ϲ_z.tif", + "brightfield_tif": "data/pherc0250/ϲ_stack.tif", + "label_png": "data/pherc0250/ϲ_label.png" + }, + { + "case_id": "250_090925_D", + "papyrus_id": "PHerc. 250", + "papyrus_dir": "pherc0250", + "sample_id": "δ", + "acquisition_date": "2025-09-09", + "raw_height_txt": "data/pherc0250/δ.txt", + "normalized_height_tif": "data/pherc0250/δ_z.tif", + "brightfield_tif": "data/pherc0250/δ_stack.tif", + "label_png": "data/pherc0250/δ_label.png" + }, + { + "case_id": "250_090925_K", + "papyrus_id": "PHerc. 250", + "papyrus_dir": "pherc0250", + "sample_id": "κ", + "acquisition_date": "2025-09-09", + "raw_height_txt": "data/pherc0250/κ.txt", + "normalized_height_tif": "data/pherc0250/κ_z.tif", + "brightfield_tif": "data/pherc0250/κ_stack.tif", + "label_png": "data/pherc0250/κ_label.png" + }, + { + "case_id": "250_090925_O", + "papyrus_id": "PHerc. 250", + "papyrus_dir": "pherc0250", + "sample_id": "ο", + "acquisition_date": "2025-09-09", + "raw_height_txt": "data/pherc0250/ο.txt", + "normalized_height_tif": "data/pherc0250/ο_z.tif", + "brightfield_tif": "data/pherc0250/ο_stack.tif", + "label_png": "data/pherc0250/ο_label.png" + }, + { + "case_id": "250_090925_P", + "papyrus_id": "PHerc. 250", + "papyrus_dir": "pherc0250", + "sample_id": "ρ", + "acquisition_date": "2025-09-09", + "raw_height_txt": "data/pherc0250/ρ.txt", + "normalized_height_tif": "data/pherc0250/ρ_z.tif", + "brightfield_tif": "data/pherc0250/ρ_stack.tif", + "label_png": "data/pherc0250/ρ_label.png" + }, + { + "case_id": "500P2_230925_H", + "papyrus_id": "PHerc. 500P2", + "papyrus_dir": "pherc0500p2", + "sample_id": "η", + "acquisition_date": "2025-09-23", + "raw_height_txt": "data/pherc0500p2/η.txt", + "normalized_height_tif": "data/pherc0500p2/η_z.tif", + "brightfield_tif": "data/pherc0500p2/η_stack.tif", + "label_png": "data/pherc0500p2/η_label.png" + }, + { + "case_id": "500P2_230925_IT", + "papyrus_id": "PHerc. 500P2", + "papyrus_dir": "pherc0500p2", + "sample_id": "ιτ", + "acquisition_date": "2025-09-23", + "raw_height_txt": "data/pherc0500p2/ιτ.txt", + "normalized_height_tif": "data/pherc0500p2/ιτ_z.tif", + "brightfield_tif": "data/pherc0500p2/ιτ_stack.tif", + "label_png": "data/pherc0500p2/ιτ_label.png" + }, + { + "case_id": "500P2_230925_N", + "papyrus_id": "PHerc. 500P2", + "papyrus_dir": "pherc0500p2", + "sample_id": "ν", + "acquisition_date": "2025-09-23", + "raw_height_txt": "data/pherc0500p2/ν.txt", + "normalized_height_tif": "data/pherc0500p2/ν_z.tif", + "brightfield_tif": "data/pherc0500p2/ν_stack.tif", + "label_png": "data/pherc0500p2/ν_label.png" + }, + { + "case_id": "500P2_230925_N2", + "papyrus_id": "PHerc. 500P2", + "papyrus_dir": "pherc0500p2", + "sample_id": "ν2", + "acquisition_date": "2025-09-23", + "raw_height_txt": "data/pherc0500p2/ν2.txt", + "normalized_height_tif": "data/pherc0500p2/ν2_z.tif", + "brightfield_tif": "data/pherc0500p2/ν2_stack.tif", + "label_png": "data/pherc0500p2/ν2_label.png" + } + ] +} diff --git a/configs/experiment.json b/configs/experiment.json new file mode 100644 index 0000000000000000000000000000000000000000..330d4c8b91b174d7e683f5c0421b0757a7d5cc58 --- /dev/null +++ b/configs/experiment.json @@ -0,0 +1,310 @@ +{ + "schema_version": "1.0", + "dataset_version": "1.0.0", + "references": { + "case_manifest": "case_manifest.json", + "sampling": "sampling.json", + "folds": "../folds/splits_final.json", + "nnunet_dataset": "nnunet/dataset.json", + "nnunet_plans_directory": "nnunet/plans" + }, + "preprocessing": { + "raw_height_import": { + "delimiter": "semicolon", + "decimal_separator": ".", + "coordinate_handling": "full_numeric_export_top_left_matched_to_label_shape", + "empty_rows_and_columns": "remove_fully_empty", + "trailing_nonfinite_rows_and_columns": "remove", + "shape_matching": { + "anchor": "top_left", + "excess_rows_and_columns": "crop_bottom_and_right", + "missing_rows_and_columns": "pad_bottom_and_right_with_nonfinite" + } + }, + "nonfinite_inpainting": { + "method": "OpenCV Telea", + "radius_pixels": 3, + "temporary_image_dtype": "uint8", + "temporary_scaling": { + "method": "percentile_linear_scaling", + "lower_percentile": 0.5, + "upper_percentile": 99.5, + "output_range": [ + 0, + 255 + ], + "map_back_to_original_height_range": true + }, + "restore_original_finite_measurements": true + }, + "normalized_height_output": { + "method": "per_sample_normalization", + "normalized_range": [ + 0, + 1 + ], + "output_dtype": "uint16", + "output_range": [ + 0, + 65535 + ] + }, + "labels": { + "foreground_rule": "nonzero_is_foreground", + "downsampling_interpolation": "nearest_neighbour" + }, + "lateral_downsampling": { + "image_method": "nonoverlapping_block_mean", + "crop_to_factor_multiple": "bottom_and_right" + }, + "isotropic_z_binning": { + "bin_width_um": "native_lateral_sampling_um_per_pixel multiplied by resolution_factor", + "quantization": "floor", + "formula": "floor(height_um / bin_width_um) multiplied by bin_width_um" + } + }, + "experiments": { + "matched_resolution": { + "description": "Independent training and testing at each lateral resolution factor.", + "training_input": "continuous_height_at_training_factor", + "test_input": "continuous_height_at_training_factor", + "train_factors": [ + 1, + 2, + 3, + 4, + 6, + 8, + 10, + 16, + 32 + ], + "test_factors": "same_as_training_factor", + "folds": [ + 0, + 1, + 2, + 3, + 4 + ] + }, + "fixed_native_model": { + "description": "The native-resolution model is evaluated on continuous-height inputs block-averaged at each test factor, bilinearly upsampled to the native grid, and then normalized per sample and converted to uint16.", + "evaluation_mode": "inference_only", + "train_factor": 1, + "model_training_input": "native_height_normalized_per_sample_to_uint16", + "test_source_representation": "inpainted_continuous_height_before_normalization", + "test_factors": [ + 1, + 2, + 3, + 4, + 6, + 8, + 10, + 16, + 32 + ], + "downsampling": { + "method": "nonoverlapping_block_mean", + "factor_multiple_handling": "edge_pad_bottom_and_right" + }, + "upsampling": { + "method": "bilinear_interpolation", + "target": "native_grid", + "final_crop": "bottom_and_right_to_original_shape" + }, + "post_upsampling": { + "normalization": "per_sample_to_0_1", + "output_dtype": "uint16" + }, + "folds": [ + 0, + 1, + 2, + 3, + 4 + ] + }, + "isotropic_z_binning": { + "description": "Height values are quantized at the physical bin width associated with each lateral resolution factor.", + "evaluation_mode": "inference_only", + "models": "matched_resolution_models_at_the_same_factor", + "model_training_input": "continuous_height", + "test_input": "z_binned_height", + "factors": [ + 1, + 2, + 3, + 4, + 6, + 8, + 10, + 16, + 32 + ], + "folds": [ + 0, + 1, + 2, + 3, + 4 + ] + }, + "detrending": { + "description": "A least-squares plane is subtracted from each height map before the native-resolution pipeline.", + "method": "least_squares_plane_subtraction", + "resolution_factor": 1, + "training_input": "detrended_continuous_height", + "test_input": "detrended_continuous_height", + "folds": [ + 0, + 1, + 2, + 3, + 4 + ] + }, + "leave_one_papyrus_out": { + "description": "Each partition holds out all samples from one papyrus.", + "resolution_factor": 1, + "training_input": "continuous_height", + "test_input": "continuous_height", + "folds": [ + 5, + 6, + 7 + ], + "held_out_papyri_by_fold": { + "5": "PHerc. 500P2", + "6": "PHerc. 250", + "7": "PHerc. 248" + } + } + }, + "dataset_mappings": { + "continuous_height": [ + { + "factor": 1, + "dataset_id": 701, + "dataset_name": "Dataset701_Profilometry2D" + }, + { + "factor": 2, + "dataset_id": 702, + "dataset_name": "Dataset702_Profilometry2D" + }, + { + "factor": 3, + "dataset_id": 703, + "dataset_name": "Dataset703_Profilometry2D" + }, + { + "factor": 4, + "dataset_id": 704, + "dataset_name": "Dataset704_Profilometry2D" + }, + { + "factor": 6, + "dataset_id": 706, + "dataset_name": "Dataset706_Profilometry2D" + }, + { + "factor": 8, + "dataset_id": 708, + "dataset_name": "Dataset708_Profilometry2D" + }, + { + "factor": 10, + "dataset_id": 710, + "dataset_name": "Dataset710_Profilometry2D" + }, + { + "factor": 16, + "dataset_id": 716, + "dataset_name": "Dataset716_Profilometry2D" + }, + { + "factor": 32, + "dataset_id": 732, + "dataset_name": "Dataset732_Profilometry2D" + } + ], + "isotropic_z_binned_height": [ + { + "factor": 1, + "dataset_id": 801, + "dataset_name": "Dataset801_Profilometry2D_z0p68793625_ds1" + }, + { + "factor": 2, + "dataset_id": 802, + "dataset_name": "Dataset802_Profilometry2D_z1p3758725_ds2" + }, + { + "factor": 3, + "dataset_id": 803, + "dataset_name": "Dataset803_Profilometry2D_z2p06380875_ds3" + }, + { + "factor": 4, + "dataset_id": 804, + "dataset_name": "Dataset804_Profilometry2D_z2p751745_ds4" + }, + { + "factor": 6, + "dataset_id": 806, + "dataset_name": "Dataset806_Profilometry2D_z4p1276175_ds6" + }, + { + "factor": 8, + "dataset_id": 808, + "dataset_name": "Dataset808_Profilometry2D_z5p50349_ds8" + }, + { + "factor": 10, + "dataset_id": 810, + "dataset_name": "Dataset810_Profilometry2D_z6p8793625_ds10" + }, + { + "factor": 16, + "dataset_id": 816, + "dataset_name": "Dataset816_Profilometry2D_z11p00698_ds16" + }, + { + "factor": 32, + "dataset_id": 832, + "dataset_name": "Dataset832_Profilometry2D_z22p01396_ds32" + } + ] + }, + "training": { + "framework": "nnUNetv2", + "trainer": "nnUNetTrainer", + "configuration": "2d", + "plans_identifier": "nnUNetResEncUNetPlans_24G", + "epochs": 1000, + "training_iterations_per_epoch": 250, + "validation_iterations_per_epoch": 50, + "early_stopping": false, + "checkpoint_for_inference": "checkpoint_best.pth", + "loss": "Dice plus cross-entropy", + "optimizer": { + "name": "SGD", + "nesterov": true, + "initial_learning_rate": 0.01, + "weight_decay": 0.00003, + "schedule": "polynomial_decay" + }, + "foreground_oversampling_fraction": 0.33 + }, + "software": { + "python": "3.12.2", + "numpy": "1.26.4", + "opencv_python": "4.11.0.86", + "pytorch": "2.5.1", + "torchvision": "0.20.1", + "nnunetv2": "2.5.1", + "nnunet_git_commit": "834b80f" + } +} diff --git a/configs/nnunet/dataset.json b/configs/nnunet/dataset.json new file mode 100644 index 0000000000000000000000000000000000000000..797b472c7eb1b7487473aeba0ab8c7cf1947b3b0 --- /dev/null +++ b/configs/nnunet/dataset.json @@ -0,0 +1,12 @@ +{ + "channel_names": { + "0": "T2" + }, + "labels": { + "background": 0, + "foreground": 1 + }, + "numTraining": 14, + "file_ending": ".tif", + 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"500P2_230925_IT", + "500P2_230925_N", + "500P2_230925_N2" + ], + "val": [ + "248_090925_E", + "250_090925_K", + "500P2_230925_H" + ] + }, + { + "train": [ + "248_090925_E", + "248_090925_F", + "248_090925_L", + "248_090925_PI", + "250_090925_C", + "250_090925_K", + "250_090925_O", + "250_090925_P", + "500P2_230925_H", + "500P2_230925_N", + "500P2_230925_N2" + ], + "val": [ + "248_090925_N", + "250_090925_D", + "500P2_230925_IT" + ] + }, + { + "train": [ + "248_090925_E", + "248_090925_F", + "248_090925_L", + "248_090925_N", + "248_090925_PI", + "250_090925_C", + "250_090925_D", + "250_090925_K", + "250_090925_P", + "500P2_230925_H", + "500P2_230925_IT" + ], + "val": [ + "250_090925_O", + "500P2_230925_N", + "500P2_230925_N2" + ] + }, + { + "train": [ + "248_090925_E", + "248_090925_L", + "248_090925_N", + "250_090925_C", + "250_090925_D", + "250_090925_K", + "250_090925_O", + "500P2_230925_H", + "500P2_230925_IT", + "500P2_230925_N", + "500P2_230925_N2" + ], + "val": [ + "248_090925_F", + "248_090925_PI", + "250_090925_P" + ] + }, + { + "train": [ + "248_090925_E", + "248_090925_F", + "248_090925_N", + "248_090925_PI", + "250_090925_D", + "250_090925_K", + "250_090925_O", + "250_090925_P", + "500P2_230925_H", + "500P2_230925_IT", + "500P2_230925_N", + "500P2_230925_N2" + ], + "val": [ + "248_090925_L", + "250_090925_C" + ] + }, + { + "train": [ + "248_090925_E", + "248_090925_F", + "248_090925_N", + "248_090925_PI", + "248_090925_L", + "250_090925_D", + "250_090925_K", + "250_090925_O", + "250_090925_P", + "250_090925_C" + ], + "val": [ + "500P2_230925_H", + "500P2_230925_IT", + "500P2_230925_N", + "500P2_230925_N2" + ] + }, + { + "train": [ + "248_090925_E", + "248_090925_F", + "248_090925_N", + "248_090925_PI", + "248_090925_L", + "500P2_230925_H", + "500P2_230925_IT", + "500P2_230925_N", + "500P2_230925_N2" + ], + "val": [ + "250_090925_D", + "250_090925_K", + "250_090925_O", + "250_090925_P", + "250_090925_C" + ] + }, + { + "train": [ + "250_090925_D", + "250_090925_K", + "250_090925_O", + "250_090925_P", + "250_090925_C", + "500P2_230925_H", + "500P2_230925_IT", + "500P2_230925_N", + "500P2_230925_N2" + ], + "val": [ + "248_090925_E", + "248_090925_F", + "248_090925_N", + "248_090925_PI", + "248_090925_L" + ] + } +] diff --git a/manifest.csv b/manifest.csv new file mode 100644 index 0000000000000000000000000000000000000000..ca9a8e5dfcee36852f63d30137c1a72e10deb52c --- /dev/null +++ b/manifest.csv @@ -0,0 +1,15 @@ +papyrus_dir,papyrus_id,sample_id,acquisition_date,width_px,height_px,pixel_count,x_extent_um,y_extent_um,lateral_sampling_x_um,lateral_sampling_y_um,raw_height_txt,normalized_height_tif,brightfield_tif,label_png +pherc0248,PHerc. 248,ε,2025-09-09,4493,4491,20178063,3090.2097,3088.8337,0.68793625,0.68793625,data/pherc0248/ε.txt,data/pherc0248/ε_z.tif,data/pherc0248/ε_stack.tif,data/pherc0248/ε_label.png +pherc0248,PHerc. 248,φ,2025-09-09,5358,3619,19390602,3685.2744,2488.9534,0.68793625,0.68793625,data/pherc0248/φ.txt,data/pherc0248/φ_z.tif,data/pherc0248/φ_stack.tif,data/pherc0248/φ_label.png +pherc0248,PHerc. 248,λ,2025-09-09,4496,4489,20182544,3092.2734,3087.4578,0.68793625,0.68793625,data/pherc0248/λ.txt,data/pherc0248/λ_z.tif,data/pherc0248/λ_stack.tif,data/pherc0248/λ_label.png +pherc0248,PHerc. 248,ν,2025-09-09,6221,3608,22445368,4278.9634,2481.3860,0.68793625,0.68793625,data/pherc0248/ν.txt,data/pherc0248/ν_z.tif,data/pherc0248/ν_stack.tif,data/pherc0248/ν_label.png +pherc0248,PHerc. 248,π,2025-09-09,4183,3620,15142460,2876.9495,2489.6414,0.68793625,0.68793625,data/pherc0248/π.txt,data/pherc0248/π_z.tif,data/pherc0248/π_stack.tif,data/pherc0248/π_label.png +pherc0250,PHerc. 250,ϲ,2025-09-09,3622,4490,16262780,2491.0171,3088.1458,0.68793625,0.68793625,data/pherc0250/ϲ.txt,data/pherc0250/ϲ_z.tif,data/pherc0250/ϲ_stack.tif,data/pherc0250/ϲ_label.png +pherc0250,PHerc. 250,δ,2025-09-09,6619,4478,29639882,4552.7622,3079.8906,0.68793625,0.68793625,data/pherc0250/δ.txt,data/pherc0250/δ_z.tif,data/pherc0250/δ_stack.tif,data/pherc0250/δ_label.png +pherc0250,PHerc. 250,κ,2025-09-09,5361,5354,28702794,3687.3384,3682.5227,0.68793625,0.68793625,data/pherc0250/κ.txt,data/pherc0250/κ_z.tif,data/pherc0250/κ_stack.tif,data/pherc0250/κ_label.png +pherc0250,PHerc. 250,ο,2025-09-09,4492,5365,24099580,3089.5217,3690.0901,0.68793625,0.68793625,data/pherc0250/ο.txt,data/pherc0250/ο_z.tif,data/pherc0250/ο_stack.tif,data/pherc0250/ο_label.png +pherc0250,PHerc. 250,ρ,2025-09-09,4483,7101,31833783,3083.3303,4884.3472,0.68793625,0.68793625,data/pherc0250/ρ.txt,data/pherc0250/ρ_z.tif,data/pherc0250/ρ_stack.tif,data/pherc0250/ρ_label.png +pherc0500p2,PHerc. 500P2,η,2025-09-23,5369,3617,19419673,3692.8418,2487.5774,0.68793625,0.68793625,data/pherc0500p2/η.txt,data/pherc0500p2/η_z.tif,data/pherc0500p2/η_stack.tif,data/pherc0500p2/η_label.png +pherc0500p2,PHerc. 500P2,ιτ,2025-09-23,7105,5352,38025960,4887.0991,3681.1470,0.68793625,0.68793625,data/pherc0500p2/ιτ.txt,data/pherc0500p2/ιτ_z.tif,data/pherc0500p2/ιτ_stack.tif,data/pherc0500p2/ιτ_label.png +pherc0500p2,PHerc. 500P2,ν,2025-09-23,5365,3622,19432030,3690.0901,2491.0171,0.68793625,0.68793625,data/pherc0500p2/ν.txt,data/pherc0500p2/ν_z.tif,data/pherc0500p2/ν_stack.tif,data/pherc0500p2/ν_label.png +pherc0500p2,PHerc. 500P2,ν2,2025-09-23,4499,3628,16322372,3094.3372,2495.1448,0.68793625,0.68793625,data/pherc0500p2/ν2.txt,data/pherc0500p2/ν2_z.tif,data/pherc0500p2/ν2_stack.tif,data/pherc0500p2/ν2_label.png