diff --git a/ingestion_tools/dataset_configs/10000.yaml b/ingestion_tools/dataset_configs/10000.yaml index 967e5bf76..e8d70a0f4 100644 --- a/ingestion_tools/dataset_configs/10000.yaml +++ b/ingestion_tools/dataset_configs/10000.yaml @@ -99,11 +99,13 @@ annotations: corresponding_author_status: true annotation_software: pyTOM + Keras version: "1.0" + is_curator_recommended: true sources: - columns: xyz file_format: csv glob_string: particle_lists/{run_name}_fas.csv shape: Point + is_visualization_default: false - metadata: annotation_object: id: GO:0022626 @@ -116,11 +118,13 @@ annotations: authors: *annotation_authors annotation_software: pyTOM + Keras version: "1.0" + is_curator_recommended: true sources: - shape: Point columns: xyz file_format: csv glob_string: particle_lists/{run_name}_cyto_ribosomes.csv + is_visualization_default: true # Label 1 - cytoplasm - metadata: annotation_object: @@ -140,11 +144,13 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: SemanticSegmentationMask file_format: mrc glob_string: &segmask1_glob 'labels/180426_{mapped_segmask_name}.labels.mrc' mask_label: 1 + is_visualization_default: false # Label 2 - Mitochondria - metadata: annotation_object: @@ -164,11 +170,13 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: SemanticSegmentationMask file_format: mrc glob_string: *segmask1_glob mask_label: 2 + is_visualization_default: true # Label 3 - Vesicle - metadata: annotation_object: @@ -188,11 +196,13 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: SemanticSegmentationMask file_format: mrc glob_string: *segmask1_glob mask_label: 3 + is_visualization_default: false # Label 4 - Microtubule - metadata: annotation_object: @@ -212,11 +222,13 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: SemanticSegmentationMask file_format: mrc glob_string: *segmask1_glob mask_label: 4 + is_visualization_default: true # Label 5 - ER - metadata: annotation_object: @@ -236,11 +248,13 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: SemanticSegmentationMask file_format: mrc glob_string: *segmask1_glob mask_label: 5 + is_visualization_default: true # Label 6 - Nuclear envelope - metadata: annotation_object: @@ -260,11 +274,13 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: SemanticSegmentationMask file_format: mrc glob_string: *segmask1_glob mask_label: 6 + is_visualization_default: true # Label 7 - Nucleus - metadata: annotation_object: @@ -284,11 +300,13 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: SemanticSegmentationMask file_format: mrc glob_string: *segmask1_glob mask_label: 7 + is_visualization_default: false # Label 8 - Vacuole - metadata: annotation_object: @@ -308,11 +326,13 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: SemanticSegmentationMask file_format: mrc glob_string: *segmask1_glob mask_label: 8 + is_visualization_default: false # Label 9 - Lipid droplet - metadata: annotation_object: @@ -332,11 +352,13 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: SemanticSegmentationMask file_format: mrc glob_string: *segmask1_glob mask_label: 9 + is_visualization_default: false # Label 10 - Golgi apparatus - metadata: annotation_object: @@ -356,11 +378,13 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: SemanticSegmentationMask file_format: mrc glob_string: *segmask1_glob mask_label: 10 + is_visualization_default: true # Label 11 - Vesicular body - metadata: annotation_object: @@ -380,11 +404,13 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: SemanticSegmentationMask file_format: mrc glob_string: *segmask1_glob mask_label: 11 + is_visualization_default: false # Label 13 - Non-specified compartment - metadata: annotation_object: @@ -404,11 +430,13 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: false sources: - shape: SemanticSegmentationMask file_format: mrc glob_string: *segmask1_glob mask_label: 13 + is_visualization_default: false # Membranes - metadata: annotation_object: @@ -428,11 +456,13 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: SemanticSegmentationMask file_format: mrc glob_string: 'labels/{run_name}_membranes.mrc' mask_label: 1 + is_visualization_default: false runs: {} tiltseries: scales: [] diff --git a/ingestion_tools/dataset_configs/10001.yaml b/ingestion_tools/dataset_configs/10001.yaml index f450a5d89..f54a7a3fe 100644 --- a/ingestion_tools/dataset_configs/10001.yaml +++ b/ingestion_tools/dataset_configs/10001.yaml @@ -127,11 +127,13 @@ annotations: corresponding_author_status: true annotation_software: pyTOM + Keras version: "1.0" + is_curator_recommended: true sources: - columns: xyz file_format: csv glob_string: particle_lists/{run_name}_fas.csv shape: Point + is_visualization_default: false - metadata: annotation_object: id: GO:0022626 @@ -144,11 +146,13 @@ annotations: authors: *annotation_authors annotation_software: pyTOM + Keras version: "1.0" + is_curator_recommended: true sources: - shape: Point columns: xyz file_format: csv glob_string: particle_lists/{run_name}_cyto_ribosomes.csv + is_visualization_default: true # Label 1 - cytoplasm - metadata: annotation_object: @@ -168,11 +172,13 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: SemanticSegmentationMask file_format: mrc glob_string: &segmask1_glob 'labels/{run_name}_organelles.mrc' mask_label: 1 + is_visualization_default: false # Label 2 - Mitochondria - metadata: annotation_object: @@ -192,11 +198,13 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: SemanticSegmentationMask file_format: mrc glob_string: *segmask1_glob mask_label: 2 + is_visualization_default: true # Label 3 - Vesicle - metadata: annotation_object: @@ -216,11 +224,13 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: SemanticSegmentationMask file_format: mrc glob_string: *segmask1_glob mask_label: 3 + is_visualization_default: false # Label 4 - Microtubule - metadata: annotation_object: @@ -240,11 +250,13 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: SemanticSegmentationMask file_format: mrc glob_string: *segmask1_glob mask_label: 4 + is_visualization_default: true # Label 5 - ER - metadata: annotation_object: @@ -264,11 +276,13 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: SemanticSegmentationMask file_format: mrc glob_string: *segmask1_glob mask_label: 5 + is_visualization_default: true # Label 6 - Nuclear envelope - metadata: annotation_object: @@ -288,11 +302,13 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: SemanticSegmentationMask file_format: mrc glob_string: *segmask1_glob mask_label: 6 + is_visualization_default: true # Label 7 - Nucleus - metadata: annotation_object: @@ -312,11 +328,13 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: SemanticSegmentationMask file_format: mrc glob_string: *segmask1_glob mask_label: 7 + is_visualization_default: false # Label 8 - Vacuole - metadata: annotation_object: @@ -336,11 +354,13 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: SemanticSegmentationMask file_format: mrc glob_string: *segmask1_glob mask_label: 8 + is_visualization_default: false # Label 9 - Lipid droplet - metadata: annotation_object: @@ -360,11 +380,13 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: SemanticSegmentationMask file_format: mrc glob_string: *segmask1_glob mask_label: 9 + is_visualization_default: false # Label 10 - Golgi apparatus - metadata: annotation_object: @@ -384,11 +406,13 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: SemanticSegmentationMask file_format: mrc glob_string: *segmask1_glob mask_label: 10 + is_visualization_default: true # Label 11 - Vesicular body - metadata: annotation_object: @@ -408,11 +432,13 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: SemanticSegmentationMask file_format: mrc glob_string: *segmask1_glob mask_label: 11 + is_visualization_default: false # Label 13 - Non-specified compartment - metadata: annotation_object: @@ -432,11 +458,13 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: false sources: - shape: SemanticSegmentationMask file_format: mrc glob_string: *segmask1_glob mask_label: 13 + is_visualization_default: false # Membranes - metadata: annotation_object: @@ -456,12 +484,13 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: SemanticSegmentationMask file_format: mrc glob_string: 'labels/{run_name}_membranes.mrc' mask_label: 1 - + is_visualization_default: false tomograms: voxel_spacing: 13.48 fiducial_alignment_status: NON_FIDUCIAL diff --git a/ingestion_tools/dataset_configs/10002.yaml b/ingestion_tools/dataset_configs/10002.yaml index 65fb3624c..ca06ad2b1 100644 --- a/ingestion_tools/dataset_configs/10002.yaml +++ b/ingestion_tools/dataset_configs/10002.yaml @@ -151,10 +151,12 @@ annotations: precision: ~ recall: ~ ground_truth_used: Ground truth from related paper + is_curator_recommended: true sources: - file_format: mrc shape: SegmentationMask glob_string: labels/{run_name}_actin_ground_truth.mrc + is_visualization_default: true - metadata: dates: *repo-dates annotation_method: 2D CNN + 3D CNN hyperparameter tuning @@ -173,10 +175,12 @@ annotations: name: actin filament description: Actin DeePiCt training prediction state: ~ + is_curator_recommended: false sources: - file_format: mrc shape: SegmentationMask glob_string: prediction/{run_name}_*.mrc + is_visualization_default: false # - columns: zyx # file_format: xml # glob_string: actin_ground_truth_coordinates/{run_name}_*.xml diff --git a/ingestion_tools/dataset_configs/10003.yaml b/ingestion_tools/dataset_configs/10003.yaml index 312e76b6d..70f10b54a 100644 --- a/ingestion_tools/dataset_configs/10003.yaml +++ b/ingestion_tools/dataset_configs/10003.yaml @@ -78,6 +78,7 @@ annotations: recall: 90 ground_truth_used: author estimation version: '1.0' + is_curator_recommended: true sources: - shape: OrientedPoint file_format: relion3_star @@ -85,6 +86,7 @@ annotations: order: zyx glob_string: run_ct17_it034_data.star filter_value: '{mapped_tomo_name}.tomostar' + is_visualization_default: true runs: {} tiltseries: scales: [] diff --git a/ingestion_tools/dataset_configs/10004.yaml b/ingestion_tools/dataset_configs/10004.yaml index 0a678b180..29fcf258d 100644 --- a/ingestion_tools/dataset_configs/10004.yaml +++ b/ingestion_tools/dataset_configs/10004.yaml @@ -109,11 +109,13 @@ annotations: recall: 60 ground_truth_used: Author estimation annotation_software: STOPGAP + RELION + is_curator_recommended: true sources: - columns: xyz file_format: csv_with_header glob_string: '{run_name}/annoRibosome_bin4.txt' shape: Point + is_visualization_default: true runs: {} tiltseries: scales: [] diff --git a/ingestion_tools/dataset_configs/10005.yaml b/ingestion_tools/dataset_configs/10005.yaml index 785b3b08b..d234ef587 100644 --- a/ingestion_tools/dataset_configs/10005.yaml +++ b/ingestion_tools/dataset_configs/10005.yaml @@ -74,12 +74,14 @@ annotations: corresponding_author_status: true annotation_software: ~ version: '1.0' + is_curator_recommended: true sources: - columns: xyz file_format: csv glob_string: coorinates_dmt48/s{run_name}_dmt48_coordinates_bin2.txt shape: Point delimiter: ' ' + is_visualization_default: true - metadata: annotation_object: id: GO:0097545 @@ -97,12 +99,14 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - columns: xyz file_format: csv glob_string: coordinates_dmt96/s{run_name}_dmt96_coordinates_bin2.txt shape: Point delimiter: ' ' + is_visualization_default: true runs: {} tiltseries: scales: [] diff --git a/ingestion_tools/dataset_configs/10006.yaml b/ingestion_tools/dataset_configs/10006.yaml index 085e6ad75..d2f401bb4 100644 --- a/ingestion_tools/dataset_configs/10006.yaml +++ b/ingestion_tools/dataset_configs/10006.yaml @@ -121,6 +121,7 @@ annotations: # precision: REQUIRED IF ground_truth_used is specified # recall: REQUIRED IF ground_truth_used is specified ground_truth_used: author estimation + is_curator_recommended: true sources: - file_format: relion4_star glob_string: motl_star/czii-remapped-points.star @@ -128,6 +129,7 @@ annotations: shape: OrientedPoint binning: 2 filter_value: '{run_name}' + is_visualization_default: true runs: {} tiltseries: scales: [] diff --git a/ingestion_tools/dataset_configs/10007.yaml b/ingestion_tools/dataset_configs/10007.yaml index 1e2c2a815..e85148ade 100644 --- a/ingestion_tools/dataset_configs/10007.yaml +++ b/ingestion_tools/dataset_configs/10007.yaml @@ -81,6 +81,7 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: OrientedPoint file_format: tomoman_relion_star @@ -88,6 +89,7 @@ annotations: order: zyx glob_string: '{run_name}/metadata/particles/*.star' filter_value: ~ + is_visualization_default: true runs: {} tiltseries: scales: [] diff --git a/ingestion_tools/dataset_configs/10008.yaml b/ingestion_tools/dataset_configs/10008.yaml index f8598e518..7eb3ec6e7 100644 --- a/ingestion_tools/dataset_configs/10008.yaml +++ b/ingestion_tools/dataset_configs/10008.yaml @@ -105,6 +105,7 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: OrientedPoint file_format: stopgap_star @@ -112,6 +113,7 @@ annotations: order: zyx glob_string: 'subtomo/hdcr/hdcr_tm_bin2_motl_12.star' filter_value: "{run_name}" + is_visualization_default: true - metadata: annotation_object: id: GO:0022626 @@ -130,6 +132,7 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: OrientedPoint file_format: stopgap_star @@ -137,6 +140,7 @@ annotations: order: zyx glob_string: 'subtomo/ribo/ribo_tm_bin1_motl_12.star' filter_value: "{run_name}" + is_visualization_default: true runs: {} tiltseries: scales: [] diff --git a/ingestion_tools/dataset_configs/10009.yaml b/ingestion_tools/dataset_configs/10009.yaml index a8db3d9b1..819a50e9a 100644 --- a/ingestion_tools/dataset_configs/10009.yaml +++ b/ingestion_tools/dataset_configs/10009.yaml @@ -170,6 +170,7 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: OrientedPoint file_format: stopgap_star @@ -177,6 +178,7 @@ annotations: order: zyx glob_string: "motivelists/allmotl_S_newbin2_3.star" filter_value: "{run_name}" + is_visualization_default: true - metadata: annotation_object: id: GO:0097537 @@ -195,6 +197,7 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: OrientedPoint file_format: stopgap_star @@ -202,6 +205,7 @@ annotations: order: zyx glob_string: 'motivelists/allmotl_Y_newbin2_3.star' filter_value: "{run_name}" + is_visualization_default: true - metadata: annotation_object: id: GO:0035869 @@ -220,6 +224,7 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: OrientedPoint file_format: stopgap_star @@ -227,6 +232,7 @@ annotations: order: zyx glob_string: 'motivelists/allmotl_H_cleanbin2.star' filter_value: "{run_name}" + is_visualization_default: true - metadata: annotation_object: id: GO:0035869 @@ -245,6 +251,7 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: OrientedPoint file_format: stopgap_star @@ -252,6 +259,7 @@ annotations: order: zyx glob_string: 'motivelists/MTD_MIP_bin2_recentered_shiftedorg_9.star' filter_value: "{run_name}" + is_visualization_default: true - metadata: annotation_object: id: GO:0030992 @@ -270,6 +278,7 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: OrientedPoint file_format: stopgap_star @@ -277,6 +286,7 @@ annotations: order: zyx glob_string: 'motivelists/allmotl_B2_newbin2_3.star' filter_value: "{run_name}" + is_visualization_default: true - metadata: annotation_object: id: GO:0030991 @@ -295,6 +305,7 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: OrientedPoint file_format: stopgap_star @@ -302,6 +313,7 @@ annotations: order: zyx glob_string: 'motivelists/allmotl_A2_newbin2_3.star' filter_value: "{run_name}" + is_visualization_default: true - metadata: annotation_object: id: GO:0005858 @@ -320,6 +332,7 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - shape: OrientedPoint file_format: stopgap_star @@ -327,6 +340,7 @@ annotations: order: zyx glob_string: 'motivelists/allmotl_D_newbin2_3.star' filter_value: "{run_name}" + is_visualization_default: true overrides_by_run: # The tiltseries / tomograms dicts will be hit with a originaldict.update(dict from this section) - run_regex: "TS_11$" tiltseries: diff --git a/ingestion_tools/dataset_configs/10010.yaml b/ingestion_tools/dataset_configs/10010.yaml index 5596d2139..fa6a59fbc 100644 --- a/ingestion_tools/dataset_configs/10010.yaml +++ b/ingestion_tools/dataset_configs/10010.yaml @@ -114,11 +114,13 @@ annotations: precision: ~ recall: ~ ground_truth_used: ~ + is_curator_recommended: true sources: - file_format: mrc shape: SemanticSegmentationMask glob_string: &segmentation_glob 'Voxel_Segmentations/{run_name}_labels.rec.mrc' mask_label: 1 + is_visualization_default: true - metadata: annotation_object: id: GO:0005743 @@ -134,11 +136,13 @@ annotations: annotation_software: TomoSegMemTV+AMIRA version: "1.0" confidence: *annotation_confidence + is_curator_recommended: true sources: - file_format: mrc shape: SemanticSegmentationMask glob_string: *segmentation_glob mask_label: 2 + is_visualization_default: true - metadata: annotation_object: id: GO:0005789 @@ -154,11 +158,13 @@ annotations: annotation_software: TomoSegMemTV+AMIRA version: "1.0" confidence: *annotation_confidence + is_curator_recommended: true sources: - file_format: mrc shape: SemanticSegmentationMask glob_string: *segmentation_glob mask_label: 3 + is_visualization_default: true standardization_config: destination_prefix: '10010' source_prefix: Grotjahn