All Depositions

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:803

Publications

Not Submitted

Related Databases

Not Submitted

Annotation Methods Summary

Datasets with Deposition Data

6 of 6 Datasets

Dataset Name
Organism
Runs

With deposition data

Annotations

Deposition only

Annotated Objects

Deposition only

key visualization for L. pneumophila JV2067
L. pneumophila JV2067

Dataset ID: DS-10064

  • Debnath Ghosal,
  • Grant Jensen
Legionella pneumophila
61
95
  • inclusion body
  • intracellular anatomical structure
key visualization for CryoET of near-minimal cells Mycoplasma mycoides JCVI-Syn3A for the development of subtomogram averaging pipelines
CryoET of near-minimal cells Mycoplasma mycoides JCVI-Syn3A for the development of subtomogram averaging pipelines

Dataset ID: DS-10442

  • Mallak Ali,
  • Ariana Peck,
  • Yue Yu,
  • Jonathan Schwartz,
  • ... ,
  • Mohammadreza Paraan
Mycoplasma mycoides subsp. capri str. GM12
231
231
  • intracellular anatomical structure
key visualization for L. pneumophila JV7058
L. pneumophila JV7058

Dataset ID: DS-10077

  • Debnath Ghosal,
  • Grant Jensen
Legionella pneumophila
51
82
  • inclusion body
  • intracellular anatomical structure
key visualization for L. pneumophila JV1181
L. pneumophila JV1181

Dataset ID: DS-10062

  • Debnath Ghosal,
  • Grant Jensen
Legionella pneumophila
75
127
  • inclusion body
  • intracellular anatomical structure
key visualization for L. pneumophila JV9114
L. pneumophila JV9114

Dataset ID: DS-10084

  • Debnath Ghosal,
  • Grant Jensen
Legionella pneumophila
78
122
  • inclusion body
  • intracellular anatomical structure
key visualization for Affinity-Captured Endo-/Lysosomes
Affinity-Captured Endo-/Lysosomes

Dataset ID: DS-10444

  • Hannah Siems,
  • Yue Yu,
  • Ariana Peck,
  • Jonathan Schwartz,
  • Elizabeth Montabana,
  • Mohammadreza Paraan,
  • Daniel Serwas
Homo sapiens
146
146
  • lysosome