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Add is_curator_recommended and is_visualization_default to 10000 …
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…- 10010

Reimports required:
- 10000: Annotation metadata
- 10001: Annotation metadata
- 10002: Annotation metadata
- 10003: Annotation metadata
- 10004: Annotation metadata
- 10005: Annotation metadata
- 10006: Annotation metadata
- 10007: Annotation metadata
- 10008: Annotation metadata
- 10009: Annotation metadata
- 10010: Annotation metadata
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@uermel
uermel committed Feb 9, 2024
1 parent 36584b2 commit 166ec26
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Showing 11 changed files with 100 additions and 1 deletion.
30 changes: 30 additions & 0 deletions ingestion_tools/dataset_configs/10000.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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:
Expand All @@ -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:
Expand All @@ -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:
Expand All @@ -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:
Expand All @@ -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:
Expand All @@ -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:
Expand All @@ -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:
Expand All @@ -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:
Expand All @@ -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:
Expand All @@ -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:
Expand All @@ -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:
Expand All @@ -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:
Expand All @@ -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:
Expand All @@ -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: []
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