feat: update core schema v2 for alignments and mesh

ingestion_tools/dataset_configs/10000.yaml

@@ -62,7 +62,7 @@ annotations:
       columns: xyz
       file_format: csv
       glob_string: particle_lists/{run_name}_fas.csv
-      is_portal_standard: false
+
       is_visualization_default: false
 - metadata:
     annotation_method: Cumulative template-matching trained 2D CNN predictions + visual
@@ -85,7 +85,7 @@ annotations:
       columns: xyz
       file_format: csv
       glob_string: particle_lists/{run_name}_cyto_ribosomes.csv
-      is_portal_standard: false
+
       is_visualization_default: true
 - metadata:
     annotation_method: spectrum equalization filter + 2D CNN prediction + manual correction
@@ -106,7 +106,7 @@ annotations:
   - SemanticSegmentationMask:
       file_format: mrc
       glob_string: labels/180426_{mapped_segmask_name}.labels.mrc
-      is_portal_standard: false
+
       is_visualization_default: false
       mask_label: 1
 - metadata:
@@ -128,7 +128,7 @@ annotations:
   - SemanticSegmentationMask:
       file_format: mrc
       glob_string: labels/180426_{mapped_segmask_name}.labels.mrc
-      is_portal_standard: false
+
       is_visualization_default: true
       mask_label: 2
 - metadata:
@@ -150,7 +150,7 @@ annotations:
   - SemanticSegmentationMask:
       file_format: mrc
       glob_string: labels/180426_{mapped_segmask_name}.labels.mrc
-      is_portal_standard: false
+
       is_visualization_default: false
       mask_label: 3
 - metadata:
@@ -172,7 +172,7 @@ annotations:
   - SemanticSegmentationMask:
       file_format: mrc
       glob_string: labels/180426_{mapped_segmask_name}.labels.mrc
-      is_portal_standard: false
+
       is_visualization_default: true
       mask_label: 4
 - metadata:
@@ -194,7 +194,7 @@ annotations:
   - SemanticSegmentationMask:
       file_format: mrc
       glob_string: labels/180426_{mapped_segmask_name}.labels.mrc
-      is_portal_standard: false
+
       is_visualization_default: true
       mask_label: 5
 - metadata:
@@ -216,7 +216,7 @@ annotations:
   - SemanticSegmentationMask:
       file_format: mrc
       glob_string: labels/180426_{mapped_segmask_name}.labels.mrc
-      is_portal_standard: false
+
       is_visualization_default: true
       mask_label: 6
 - metadata:
@@ -238,7 +238,7 @@ annotations:
   - SemanticSegmentationMask:
       file_format: mrc
       glob_string: labels/180426_{mapped_segmask_name}.labels.mrc
-      is_portal_standard: false
+
       is_visualization_default: false
       mask_label: 7
 - metadata:
@@ -260,7 +260,7 @@ annotations:
   - SemanticSegmentationMask:
       file_format: mrc
       glob_string: labels/180426_{mapped_segmask_name}.labels.mrc
-      is_portal_standard: false
+
       is_visualization_default: false
       mask_label: 8
 - metadata:
@@ -282,7 +282,7 @@ annotations:
   - SemanticSegmentationMask:
       file_format: mrc
       glob_string: labels/180426_{mapped_segmask_name}.labels.mrc
-      is_portal_standard: false
+
       is_visualization_default: false
       mask_label: 9
 - metadata:
@@ -304,7 +304,7 @@ annotations:
   - SemanticSegmentationMask:
       file_format: mrc
       glob_string: labels/180426_{mapped_segmask_name}.labels.mrc
-      is_portal_standard: false
+
       is_visualization_default: true
       mask_label: 10
 - metadata:
@@ -326,7 +326,7 @@ annotations:
   - SemanticSegmentationMask:
       file_format: mrc
       glob_string: labels/180426_{mapped_segmask_name}.labels.mrc
-      is_portal_standard: false
+
       is_visualization_default: false
       mask_label: 11
 - metadata:
@@ -348,7 +348,7 @@ annotations:
   - SemanticSegmentationMask:
       file_format: mrc
       glob_string: labels/180426_{mapped_segmask_name}.labels.mrc
-      is_portal_standard: false
+
       is_visualization_default: false
       mask_label: 13
 - metadata:
@@ -370,7 +370,7 @@ annotations:
   - SemanticSegmentationMask:
       file_format: mrc
       glob_string: labels/{run_name}_membranes.mrc
-      is_portal_standard: false
+
       is_visualization_default: false
       mask_label: 1
 collection_metadata:

ingestion_tools/dataset_configs/10001.yaml

@@ -62,7 +62,7 @@ annotations:
       columns: xyz
       file_format: csv
       glob_string: particle_lists/{run_name}_fas.csv
-      is_portal_standard: false
+
       is_visualization_default: false
 - metadata:
     annotation_method: Cumulative template-matching trained 2D CNN predictions + visual
@@ -85,7 +85,7 @@ annotations:
       columns: xyz
       file_format: csv
       glob_string: particle_lists/{run_name}_cyto_ribosomes.csv
-      is_portal_standard: false
+
       is_visualization_default: true
 - metadata:
     annotation_method: manual segmentation
@@ -105,7 +105,7 @@ annotations:
   - SemanticSegmentationMask:
       file_format: mrc
       glob_string: labels/{run_name}_organelles.mrc
-      is_portal_standard: false
+
       is_visualization_default: false
       mask_label: 1
 - metadata:
@@ -126,7 +126,7 @@ annotations:
   - SemanticSegmentationMask:
       file_format: mrc
       glob_string: labels/{run_name}_organelles.mrc
-      is_portal_standard: false
+
       is_visualization_default: true
       mask_label: 2
 - metadata:
@@ -147,7 +147,7 @@ annotations:
   - SemanticSegmentationMask:
       file_format: mrc
       glob_string: labels/{run_name}_organelles.mrc
-      is_portal_standard: false
+
       is_visualization_default: false
       mask_label: 3
 - metadata:
@@ -168,7 +168,7 @@ annotations:
   - SemanticSegmentationMask:
       file_format: mrc
       glob_string: labels/{run_name}_organelles.mrc
-      is_portal_standard: false
+
       is_visualization_default: true
       mask_label: 4
 - metadata:
@@ -189,7 +189,7 @@ annotations:
   - SemanticSegmentationMask:
       file_format: mrc
       glob_string: labels/{run_name}_organelles.mrc
-      is_portal_standard: false
+
       is_visualization_default: true
       mask_label: 5
 - metadata:
@@ -210,7 +210,7 @@ annotations:
   - SemanticSegmentationMask:
       file_format: mrc
       glob_string: labels/{run_name}_organelles.mrc
-      is_portal_standard: false
+
       is_visualization_default: true
       mask_label: 6
 - metadata:
@@ -231,7 +231,7 @@ annotations:
   - SemanticSegmentationMask:
       file_format: mrc
       glob_string: labels/{run_name}_organelles.mrc
-      is_portal_standard: false
+
       is_visualization_default: false
       mask_label: 7
 - metadata:
@@ -252,7 +252,7 @@ annotations:
   - SemanticSegmentationMask:
       file_format: mrc
       glob_string: labels/{run_name}_organelles.mrc
-      is_portal_standard: false
+
       is_visualization_default: false
       mask_label: 8
 - metadata:
@@ -273,7 +273,7 @@ annotations:
   - SemanticSegmentationMask:
       file_format: mrc
       glob_string: labels/{run_name}_organelles.mrc
-      is_portal_standard: false
+
       is_visualization_default: false
       mask_label: 9
 - metadata:
@@ -294,7 +294,7 @@ annotations:
   - SemanticSegmentationMask:
       file_format: mrc
       glob_string: labels/{run_name}_organelles.mrc
-      is_portal_standard: false
+
       is_visualization_default: true
       mask_label: 10
 - metadata:
@@ -315,7 +315,7 @@ annotations:
   - SemanticSegmentationMask:
       file_format: mrc
       glob_string: labels/{run_name}_organelles.mrc
-      is_portal_standard: false
+
       is_visualization_default: false
       mask_label: 11
 - metadata:
@@ -336,7 +336,7 @@ annotations:
   - SemanticSegmentationMask:
       file_format: mrc
       glob_string: labels/{run_name}_organelles.mrc
-      is_portal_standard: false
+
       is_visualization_default: false
       mask_label: 13
 - metadata:
@@ -358,7 +358,7 @@ annotations:
   - SemanticSegmentationMask:
       file_format: mrc
       glob_string: labels/{run_name}_membranes.mrc
-      is_portal_standard: false
+
       is_visualization_default: false
       mask_label: 1
 collection_metadata:

ingestion_tools/dataset_configs/10002.yaml

@@ -75,7 +75,7 @@ annotations:
   - SemanticSegmentationMask:
       file_format: mrc
       glob_string: labels/{run_name}_actin_ground_truth.mrc
-      is_portal_standard: false
+
       is_visualization_default: true
 - metadata:
     annotation_method: 2D CNN + 3D CNN hyperparameter tuning
@@ -99,7 +99,7 @@ annotations:
   - SemanticSegmentationMask:
       file_format: mrc
       glob_string: prediction/{run_name}_*.mrc
-      is_portal_standard: false
+
       is_visualization_default: false
 collection_metadata:
 - sources:

ingestion_tools/dataset_configs/10003.yaml

@@ -35,7 +35,7 @@ annotations:
       file_format: relion3_star
       filter_value: '{mapped_tomo_name}.tomostar'
       glob_string: run_ct17_it034_data.star
-      is_portal_standard: false
+
       is_visualization_default: true
       order: xyz
 dataset_keyphotos:

ingestion_tools/dataset_configs/10004.yaml

@@ -69,7 +69,7 @@ annotations:
       columns: xyz
       file_format: csv_with_header
       glob_string: '{run_name}/annoRibosome_bin4.txt'
-      is_portal_standard: false
+
       is_visualization_default: true
 collection_metadata:
 - sources:

ingestion_tools/dataset_configs/10005.yaml

@@ -30,7 +30,7 @@ annotations:
       delimiter: ' '
       file_format: csv
       glob_string: coorinates_dmt48/s{run_name}_dmt48_coordinates_bin2.txt
-      is_portal_standard: false
+
       is_visualization_default: true
 - metadata:
     annotation_method: Template matching + manual filtering + 3D classification filtering
@@ -51,7 +51,7 @@ annotations:
       delimiter: ' '
       file_format: csv
       glob_string: coordinates_dmt96/s{run_name}_dmt96_coordinates_bin2.txt
-      is_portal_standard: false
+
       is_visualization_default: true
 dataset_keyphotos:
 - sources:

ingestion_tools/dataset_configs/10006.yaml

@@ -56,7 +56,7 @@ annotations:
       file_format: relion4_star
       filter_value: '{run_name}'
       glob_string: motl_star/czii-remapped-points.star
-      is_portal_standard: false
+
       is_visualization_default: true
       order: xyz
 dataset_keyphotos:

ingestion_tools/dataset_configs/10007.yaml

@@ -44,7 +44,7 @@ annotations:
       binning: 4
       file_format: tomoman_relion_star
       glob_string: '{run_name}/metadata/particles/*.star'
-      is_portal_standard: false
+
       is_visualization_default: true
       order: xyz
 collection_metadata:

ingestion_tools/dataset_configs/10008.yaml

@@ -54,7 +54,7 @@ annotations:
       file_format: stopgap_star
       filter_value: '{run_name}'
       glob_string: subtomo/hdcr/hdcr_tm_bin2_motl_12.star
-      is_portal_standard: false
+
       is_visualization_default: true
       order: xyz
 - metadata:
@@ -76,7 +76,7 @@ annotations:
       file_format: stopgap_star
       filter_value: '{run_name}'
       glob_string: subtomo/ribo/ribo_tm_bin1_motl_12.star
-      is_portal_standard: false
+
       is_visualization_default: true
       order: xyz
 collection_metadata: