Deposition

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

Deposition ID:CZCDP-10331

Release Date: 2026-03-09

Last Modified: 2026-03-09

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

Deposition Data

Annotations:4,916

Tomograms:0

Publications

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Methods Summary

Annotations	Method Type	Method Details	Method Links
2237	Automated	Prediction using SABER	Source Code:SABER +1 more
1936	Automated	Prediction using SABER + Threshold at 0.5	Source Code:SABER +1 more

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4,916 of 4,916 Annotations

Annotation Name	Object Shape Type	Method Type	Deposited In
108inclusion body Annotation ID: AN-16146 Ground Truth	SegmentationMask	Hybrid	Dataset: L. pneumophila JV1181 Run: dga2017-02-02-31
107inclusion body Annotation ID: AN-16145 Ground Truth	SegmentationMask	Hybrid	Dataset: L. pneumophila JV1181 Run: dga2017-02-02-31
105intracellular anatomical structure Annotation ID: AN-16143 Ground Truth	InstanceSegmentationMask	Hybrid	Dataset: L. pneumophila JV1181 Run: dga2017-02-02-31
104intracellular anatomical structure Annotation ID: AN-16142 Ground Truth	SegmentationMask	Hybrid	Dataset: L. pneumophila JV1181 Run: dga2017-02-02-31
108inclusion body Annotation ID: AN-16009 Ground Truth	SegmentationMask	Hybrid	Dataset: L. pneumophila JV1181 Run: dga2017-02-02-29
107inclusion body Annotation ID: AN-16007 Ground Truth	SegmentationMask	Hybrid	Dataset: L. pneumophila JV1181 Run: dga2017-02-02-29
105intracellular anatomical structure Annotation ID: AN-16003 Ground Truth	InstanceSegmentationMask	Hybrid	Dataset: L. pneumophila JV1181 Run: dga2017-02-02-29
104intracellular anatomical structure Annotation ID: AN-16002 Ground Truth	SegmentationMask	Hybrid	Dataset: L. pneumophila JV1181 Run: dga2017-02-02-29
106inclusion body Annotation ID: AN-15859 Ground Truth	SegmentationMask	Hybrid	Dataset: L. pneumophila JV1181 Run: dga2017-02-02-27
105inclusion body Annotation ID: AN-15858 Ground Truth	SegmentationMask	Hybrid	Dataset: L. pneumophila JV1181 Run: dga2017-02-02-27
104intracellular anatomical structure Annotation ID: AN-15857 Ground Truth	InstanceSegmentationMask	Hybrid	Dataset: L. pneumophila JV1181 Run: dga2017-02-02-27
103intracellular anatomical structure Annotation ID: AN-15856 Ground Truth	SegmentationMask	Hybrid	Dataset: L. pneumophila JV1181 Run: dga2017-02-02-27
108inclusion body Annotation ID: AN-15748 Ground Truth	SegmentationMask	Hybrid	Dataset: L. pneumophila JV1181 Run: dga2017-02-02-26
107inclusion body Annotation ID: AN-15747 Ground Truth	SegmentationMask	Hybrid	Dataset: L. pneumophila JV1181 Run: dga2017-02-02-26
105intracellular anatomical structure Annotation ID: AN-15745 Ground Truth	InstanceSegmentationMask	Hybrid	Dataset: L. pneumophila JV1181 Run: dga2017-02-02-26
104intracellular anatomical structure Annotation ID: AN-15744 Ground Truth	SegmentationMask	Hybrid	Dataset: L. pneumophila JV1181 Run: dga2017-02-02-26
108inclusion body Annotation ID: AN-15611 Ground Truth	SegmentationMask	Hybrid	Dataset: L. pneumophila JV1181 Run: dga2017-02-02-25
107inclusion body Annotation ID: AN-15610 Ground Truth	SegmentationMask	Hybrid	Dataset: L. pneumophila JV1181 Run: dga2017-02-02-25
105intracellular anatomical structure Annotation ID: AN-15608 Ground Truth	InstanceSegmentationMask	Hybrid	Dataset: L. pneumophila JV1181 Run: dga2017-02-02-25
104intracellular anatomical structure Annotation ID: AN-15607 Ground Truth	SegmentationMask	Hybrid	Dataset: L. pneumophila JV1181 Run: dga2017-02-02-25