Deposition

Expert-in-the-loop guided automatic segmentations of cells and cellular structures using SABER

Deposition ID:CZCDP-10331

Release Date: 2025-05-22

Last Modified: 2025-05-22

key visualization for Expert-in-the-loop guided automatic segmentations of cells and cellular structures using SABER

Photo Caption: Central slab of 4 representative tomograms with selected sets of annotations.

Deposition Overview

This deposition contains segmentations of whole cells, lysosomes and components of bacterial cells. 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. Segmentations are provided as semantic masks, with a point at the center of mask indicating object instances. Authors are redacted pending peer review process.

Authors

Anonymous Author

Deposition Data

Annotations:1,314

Tomograms:0

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Methods Summary

Annotations	Method Type	Method Details	Method Links
657	Automated	Prediction using SABER	Not Submitted

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1,314 of 1,314 Annotations

Annotation Name	Object Shape Type	Method Type	Deposited In
102intracellular anatomical structure Annotation ID: AN-98497	SegmentationMask	Automated	Dataset: CryoET of near-minimal cells Mycoplasma mycoides JCVI-Syn3A for the development of subtomogram averaging pipelines Run: 24jul24a_Position_9_3
102intracellular anatomical structure Annotation ID: AN-98497	InstanceSegmentation	Automated	Dataset: CryoET of near-minimal cells Mycoplasma mycoides JCVI-Syn3A for the development of subtomogram averaging pipelines Run: 24jul24a_Position_9_3
102intracellular anatomical structure Annotation ID: AN-98496	InstanceSegmentation	Automated	Dataset: CryoET of near-minimal cells Mycoplasma mycoides JCVI-Syn3A for the development of subtomogram averaging pipelines Run: 24jul24a_Position_9
102intracellular anatomical structure Annotation ID: AN-98496	SegmentationMask	Automated	Dataset: CryoET of near-minimal cells Mycoplasma mycoides JCVI-Syn3A for the development of subtomogram averaging pipelines Run: 24jul24a_Position_9
102intracellular anatomical structure Annotation ID: AN-98495	InstanceSegmentation	Automated	Dataset: CryoET of near-minimal cells Mycoplasma mycoides JCVI-Syn3A for the development of subtomogram averaging pipelines Run: 24jul24a_Position_7
102intracellular anatomical structure Annotation ID: AN-98495	SegmentationMask	Automated	Dataset: CryoET of near-minimal cells Mycoplasma mycoides JCVI-Syn3A for the development of subtomogram averaging pipelines Run: 24jul24a_Position_7
102intracellular anatomical structure Annotation ID: AN-98494	SegmentationMask	Automated	Dataset: CryoET of near-minimal cells Mycoplasma mycoides JCVI-Syn3A for the development of subtomogram averaging pipelines Run: 24jul24a_Position_6_2
102intracellular anatomical structure Annotation ID: AN-98494	InstanceSegmentation	Automated	Dataset: CryoET of near-minimal cells Mycoplasma mycoides JCVI-Syn3A for the development of subtomogram averaging pipelines Run: 24jul24a_Position_6_2
102intracellular anatomical structure Annotation ID: AN-98493	SegmentationMask	Automated	Dataset: CryoET of near-minimal cells Mycoplasma mycoides JCVI-Syn3A for the development of subtomogram averaging pipelines Run: 24jul24a_Position_6
102intracellular anatomical structure Annotation ID: AN-98493	InstanceSegmentation	Automated	Dataset: CryoET of near-minimal cells Mycoplasma mycoides JCVI-Syn3A for the development of subtomogram averaging pipelines Run: 24jul24a_Position_6
102intracellular anatomical structure Annotation ID: AN-98492	SegmentationMask	Automated	Dataset: CryoET of near-minimal cells Mycoplasma mycoides JCVI-Syn3A for the development of subtomogram averaging pipelines Run: 24jul24a_Position_5_4
102intracellular anatomical structure Annotation ID: AN-98492	InstanceSegmentation	Automated	Dataset: CryoET of near-minimal cells Mycoplasma mycoides JCVI-Syn3A for the development of subtomogram averaging pipelines Run: 24jul24a_Position_5_4
102intracellular anatomical structure Annotation ID: AN-98491	SegmentationMask	Automated	Dataset: CryoET of near-minimal cells Mycoplasma mycoides JCVI-Syn3A for the development of subtomogram averaging pipelines Run: 24jul24a_Position_5_2
102intracellular anatomical structure Annotation ID: AN-98491	InstanceSegmentation	Automated	Dataset: CryoET of near-minimal cells Mycoplasma mycoides JCVI-Syn3A for the development of subtomogram averaging pipelines Run: 24jul24a_Position_5_2
102intracellular anatomical structure Annotation ID: AN-98490	InstanceSegmentation	Automated	Dataset: CryoET of near-minimal cells Mycoplasma mycoides JCVI-Syn3A for the development of subtomogram averaging pipelines Run: 24jul24a_Position_5
102intracellular anatomical structure Annotation ID: AN-98490	SegmentationMask	Automated	Dataset: CryoET of near-minimal cells Mycoplasma mycoides JCVI-Syn3A for the development of subtomogram averaging pipelines Run: 24jul24a_Position_5
102intracellular anatomical structure Annotation ID: AN-98489	InstanceSegmentation	Automated	Dataset: CryoET of near-minimal cells Mycoplasma mycoides JCVI-Syn3A for the development of subtomogram averaging pipelines Run: 24jul24a_Position_4_2
102intracellular anatomical structure Annotation ID: AN-98489	SegmentationMask	Automated	Dataset: CryoET of near-minimal cells Mycoplasma mycoides JCVI-Syn3A for the development of subtomogram averaging pipelines Run: 24jul24a_Position_4_2
102intracellular anatomical structure Annotation ID: AN-98488	SegmentationMask	Automated	Dataset: CryoET of near-minimal cells Mycoplasma mycoides JCVI-Syn3A for the development of subtomogram averaging pipelines Run: 24jul24a_Position_49_4
102intracellular anatomical structure Annotation ID: AN-98488	InstanceSegmentation	Automated	Dataset: CryoET of near-minimal cells Mycoplasma mycoides JCVI-Syn3A for the development of subtomogram averaging pipelines Run: 24jul24a_Position_49_4