feat: Add support/config for InstanceSegmentationMask #5

aranega · 2025-09-04T14:25:50Z

Relates to

Description

InstanceSegmentationMask

seankmartin

left a few markers for potential questions

ingestion_tools/dataset_configs/template.yaml

schema/core/v1.1.0/metadata.yaml

schema/core/v2.0.0/metadata.yaml

…ackend into feature/CC-429

v2

…ackend into feature/CC-429

this was causing all data to be one singular label

seankmartin

Again just leaving some notes for us :)

ingestion_tools/dataset_configs/template.yaml

ingestion_tools/scripts/importers/annotation.py

ingestion_tools/scripts/importers/visualization_config.py

seankmartin

just a small question, looks good overall, thanks!

ingestion_tools/scripts/importers/annotation.py

ingestion_tools/scripts/common/image.py

…ackend into feature/CC-429

masks

seankmartin

looking great thanks! Left a few comments

ingestion_tools/poetry.lock

ingestion_tools/scripts/common/image.py

schema/ingestion_config/v1.0.0/codegen/ingestion_config_models.py

apiv2/schema/schema.yaml

apiv2/database/migrations/versions/20250819_111511_autogenerated.py

ingestion_tools/scripts/common/image.py

schema/ingestion_config/v1.0.0/ingestion_config_models.yaml

schema/core/v1.1.0/metadata.yaml

…or v1.1.0

…ackend into feature/CC-429

aranega added 4 commits August 15, 2025 10:52

feat: Add support/config for InstanceSegmentationMask

cbb334f

chore: Add new generated code from the new config for

c4aa044

InstanceSegmentationMask

feat: add instance segmentation mask class and instance creation

c4527da

chore: remove debug/test code in configuration 10441.yaml

2bb7506

aranega requested a review from seankmartin September 4, 2025 14:25

seankmartin reviewed Sep 4, 2025

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ingestion_tools/dataset_configs/template.yaml Show resolved Hide resolved

schema/core/v1.1.0/metadata.yaml Outdated Show resolved Hide resolved

schema/core/v1.1.0/metadata.yaml Outdated Show resolved Hide resolved

schema/core/v2.0.0/metadata.yaml Outdated Show resolved Hide resolved

aranega and others added 8 commits September 12, 2025 06:58

Merge branch 'main' of github.com:chanzuckerberg/cryoet-data-portal-b…

4a3d320

…ackend into feature/CC-429

feat: remove the instancesegmentation mask from v1, and enhance it for

bdf0085

v2

Merge branch 'main' of github.com:chanzuckerberg/cryoet-data-portal-b…

5d4bb52

…ackend into feature/CC-429

feat: add first steps for the InstanceSegmentationMask ingestion

598e594

fix: remove bad guard and simplify it

00a379d

feat: add dedicated shape for the InstanceSegmentationMask

6dec931

fix: remove labels param to convert function of instance seg masks

5d6ac85

this was causing all data to be one singular label

feat: allow passing seg list into gen and v1 of instance seg mask config

6101bb2

seankmartin reviewed Oct 2, 2025

View reviewed changes

aranega added 2 commits October 7, 2025 05:35

feat: Add configuration generation for InstanceSegmentationMask

129fde5

feat: Remove mask_label for InstanceSegmentationMask

0cf3ffe

seankmartin reviewed Oct 7, 2025

View reviewed changes

ingestion_tools/scripts/importers/annotation.py Outdated Show resolved Hide resolved

aranega force-pushed the feature/CC-429 branch from 4d29377 to 3f80993 Compare October 8, 2025 12:48

feat: add label computation and storing before configuration generation

7eccd55

aranega force-pushed the feature/CC-429 branch from 3f80993 to 7eccd55 Compare October 8, 2025 12:50

seankmartin reviewed Oct 13, 2025

View reviewed changes

ingestion_tools/scripts/common/image.py Outdated Show resolved Hide resolved

aranega added 8 commits October 17, 2025 07:22

Merge branch 'main' of github.com:chanzuckerberg/cryoet-data-portal-b…

0968ac4

…ackend into feature/CC-429

feat: clean schema attribute for the InstanceSegmentationMask

a438369

feat: add tests for the instance segmentation mask

ac1f46e

chore: Updating schema to add InstanceSegmentationMask

0af2440

fix: change is_a property of InstanceSegmentationMask in metadata.yaml

23cd1c5

chore: update portal-neuroglancer to v1.7.0

2233c94

feat: change metadata storing for labels in image-label

6f024df

feat: add tests for instance segmentation mask db ingestion

8ec69d7

feat: add a different method for downscaling multi-label segmentation

6f48941

masks

seankmartin reviewed Oct 28, 2025

View reviewed changes

apiv2/database/migrations/versions/20250819_111511_autogenerated.py Show resolved Hide resolved

aranega added 4 commits October 28, 2025 08:23

chore: Add back missing migration script

6702b85

chore: Update schema to add InstanceSegmentationMask shape

37005bb

chore: Fix comment and poetry version

6bc118c

feat: change the container for the image-label metadata

72a0379

seankmartin reviewed Oct 29, 2025

View reviewed changes

apiv2/database/migrations/versions/20250819_111511_autogenerated.py Show resolved Hide resolved

ingestion_tools/scripts/common/image.py Show resolved Hide resolved

chore: apply old formatter for the migration

9ce3ceb

seankmartin reviewed Oct 29, 2025

View reviewed changes

schema/ingestion_config/v1.0.0/ingestion_config_models.yaml Outdated Show resolved Hide resolved

aranega added 2 commits October 29, 2025 11:24

chore: remove InstanceSegmentationMask from v1 schema

4ac545e

chore: remove lefovers for v1 for InstanceSegmenationMask

bf96a29

seankmartin reviewed Oct 30, 2025

View reviewed changes

schema/core/v1.1.0/metadata.yaml Show resolved Hide resolved

aranega added 2 commits October 31, 2025 05:30

chore: add back AnnotationInstanceSegmentationFile in metadata.yaml f…

a15f3e6

…or v1.1.0

Merge branch 'main' of github.com:chanzuckerberg/cryoet-data-portal-b…

b31d94c

…ackend into feature/CC-429

feat: Add support/config for InstanceSegmentationMask #5

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aranega commented Sep 4, 2025

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