feat: Update SABER deposition to include authors, more data, instance segmentation masks. #614
feat: Update SABER deposition to include authors, more data, instance segmentation masks. #614
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| annotation_object: | ||
| id: GO:0016234 | ||
| name: inclusion body | ||
| annotation_software: SABER |
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annotation software should be nnInteractive? i.e. annotation_software: nnInteractive
| annotation_object: | ||
| id: GO:0016234 | ||
| name: inclusion body | ||
| annotation_software: SABER |
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same as the comment above - annotation software should be nnInteractive? i.e. annotation_software: nnInteractive
| method_type: hybrid | ||
| version: 1.0 | ||
| sources: | ||
| - SemanticSegmentationMask: |
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Should this be InstanceSegmentationMask? Above is also SemanticSegmentationMask with the same glob_string
| an expert-in-the-loop approach to refine segmentations based on the embedding | ||
| space of SAM2. Segmentations are provided as semantic masks, with a point at | ||
| the center of mask indicating object instances. Authors are redacted pending | ||
| peer review process. |
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Authors are redacted pending peer review process.
Should this be removed?
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And in general, update the deposition description to add the new annotations, mention nnInteractive, and change the "center of mask indicating object instances" to instance segmentation masks?
For example:
deposition_description: This deposition contains segmentations of whole cells,
inclusion bodies, virus-like particles, and components of bacterial cells and
microsporidia. The segmentations were generated using the SABER package,
which is a SAM2-based segmentation framework that uses an
expert-in-the-loop approach to refine segmentations based on the embedding
space of SAM2, and with nnInteractive for semi-manual annotation.
Segmentations are provided as semantic masks and instance segmentation
masks.
| # parent_filters: | ||
| # include: | ||
| # dataset: | ||
| # - '10442' |
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Is this still a work in progress? Or should these comments be removed?
| file_format: zarr | ||
| glob_string: '{dataset_name}/overlay/ExperimentRuns/{run_name}/Segmentations/10.000_SABER_1_minicell-multilabel.zarr' | ||
| glob_string: '{dataset_name}/overlay/ExperimentRuns/{run_name}/Segmentations/*_saber_1_virus-multilabel.zarr' | ||
| is_visualization_default: true |
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Should this be false (following a similar pattern as the other semantic seg + instance seg pairs)?
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Updating SABER-depostion to: