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
1936	Automated	Prediction using SABER + Threshold at 0.5	Source Code:SABER +1 more
2237	Automated	Prediction using SABER	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-131424 Ground Truth	SegmentationMask	Hybrid	Dataset: L. pneumophila JV1181 Run: dga2017-02-02-31
107inclusion body Annotation ID: AN-131423 Ground Truth	SegmentationMask	Hybrid	Dataset: L. pneumophila JV1181 Run: dga2017-02-02-31
105intracellular anatomical structure Annotation ID: AN-131421 Ground Truth	InstanceSegmentationMask	Hybrid	Dataset: L. pneumophila JV1181 Run: dga2017-02-02-31
104intracellular anatomical structure Annotation ID: AN-131420 Ground Truth	SegmentationMask	Hybrid	Dataset: L. pneumophila JV1181 Run: dga2017-02-02-31
108inclusion body Annotation ID: AN-131376 Ground Truth	SegmentationMask	Hybrid	Dataset: L. pneumophila JV1181 Run: dga2017-02-02-29
107inclusion body Annotation ID: AN-131375 Ground Truth	SegmentationMask	Hybrid	Dataset: L. pneumophila JV1181 Run: dga2017-02-02-29
105intracellular anatomical structure Annotation ID: AN-131373 Ground Truth	InstanceSegmentationMask	Hybrid	Dataset: L. pneumophila JV1181 Run: dga2017-02-02-29
104intracellular anatomical structure Annotation ID: AN-131372 Ground Truth	SegmentationMask	Hybrid	Dataset: L. pneumophila JV1181 Run: dga2017-02-02-29
109inclusion body Annotation ID: AN-131341 Ground Truth	SegmentationMask	Hybrid	Dataset: L. pneumophila JV7058 Run: dga2016-03-31-45
108inclusion body Annotation ID: AN-131340 Ground Truth	SegmentationMask	Hybrid	Dataset: L. pneumophila JV7058 Run: dga2016-03-31-45
106intracellular anatomical structure Annotation ID: AN-131338 Ground Truth	InstanceSegmentationMask	Hybrid	Dataset: L. pneumophila JV7058 Run: dga2016-03-31-45
105intracellular anatomical structure Annotation ID: AN-131337 Ground Truth	SegmentationMask	Hybrid	Dataset: L. pneumophila JV7058 Run: dga2016-03-31-45
106inclusion body Annotation ID: AN-131330 Ground Truth	SegmentationMask	Hybrid	Dataset: L. pneumophila JV1181 Run: dga2017-02-02-27
105inclusion body Annotation ID: AN-131328 Ground Truth	SegmentationMask	Hybrid	Dataset: L. pneumophila JV1181 Run: dga2017-02-02-27
104intracellular anatomical structure Annotation ID: AN-131326 Ground Truth	InstanceSegmentationMask	Hybrid	Dataset: L. pneumophila JV1181 Run: dga2017-02-02-27
103intracellular anatomical structure Annotation ID: AN-131324 Ground Truth	SegmentationMask	Hybrid	Dataset: L. pneumophila JV1181 Run: dga2017-02-02-27
108inclusion body Annotation ID: AN-131288 Ground Truth	SegmentationMask	Hybrid	Dataset: L. pneumophila JV1181 Run: dga2017-02-02-26
107inclusion body Annotation ID: AN-131287 Ground Truth	SegmentationMask	Hybrid	Dataset: L. pneumophila JV1181 Run: dga2017-02-02-26
105intracellular anatomical structure Annotation ID: AN-131285 Ground Truth	InstanceSegmentationMask	Hybrid	Dataset: L. pneumophila JV1181 Run: dga2017-02-02-26
104intracellular anatomical structure Annotation ID: AN-131284 Ground Truth	SegmentationMask	Hybrid	Dataset: L. pneumophila JV1181 Run: dga2017-02-02-26