Deposition

AreTomo3 reprocessing of isolated synaptic vesicle tomograms (EMPIAR-12794)

Deposition ID:CZCDP-10359

Release Date: 2026-06-30

Last Modified: 2026-06-30

key visualization for AreTomo3 reprocessing of isolated synaptic vesicle tomograms (EMPIAR-12794)

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

Deposition Overview

Reprocessing of the isolated synaptic vesicle dataset from mouse brain (EMPIAR-12794), performed from the raw movie frames. This deposition provides AreTomo3-based tilt-series alignments with CTF estimation, weighted-back-projection tomograms at 10 A, IsoNet2-denoised tomograms, and automated membrane segmentations produced with MemBrain-seg, complementing the existing tomograms of dataset 10453.

Authors

Deposition Data

Annotations:95

Tomograms:190

Publications

DOI:10.1073/pnas.2407375121

Related Databases

EMPIAR ID:EMPIAR-12794

Methods Summary

Annotations	Method Type	Method Details	Method Links
95	Automated	Automated membrane segmentation with MemBrain-seg (v10 model) applied to the IsoNet-denoised tomograms at 10 A.	Source Code:MemBrain-seg

Deposited Data

Group by

Data Contents

Tilt SeriesAvailable

FramesAvailable

CTFAvailable

AlignmentAvailable

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95 of 95 Annotations

Annotation Name	Object Shape Type	Method Type	Deposited In
100membrane Annotation ID: AN-183329	SegmentationMask	Automated	Dataset: CryoET of isolated synaptic vesicles from mouse brain Run: tomogram_111
100membrane Annotation ID: AN-183328	SegmentationMask	Automated	Dataset: CryoET of isolated synaptic vesicles from mouse brain Run: tomogram_110
100membrane Annotation ID: AN-183327	SegmentationMask	Automated	Dataset: CryoET of isolated synaptic vesicles from mouse brain Run: tomogram_109
100membrane Annotation ID: AN-183326	SegmentationMask	Automated	Dataset: CryoET of isolated synaptic vesicles from mouse brain Run: tomogram_108
100membrane Annotation ID: AN-183325	SegmentationMask	Automated	Dataset: CryoET of isolated synaptic vesicles from mouse brain Run: tomogram_107
100membrane Annotation ID: AN-183324	SegmentationMask	Automated	Dataset: CryoET of isolated synaptic vesicles from mouse brain Run: tomogram_106
100membrane Annotation ID: AN-183323	SegmentationMask	Automated	Dataset: CryoET of isolated synaptic vesicles from mouse brain Run: tomogram_105
100membrane Annotation ID: AN-183322	SegmentationMask	Automated	Dataset: CryoET of isolated synaptic vesicles from mouse brain Run: tomogram_104
100membrane Annotation ID: AN-183321	SegmentationMask	Automated	Dataset: CryoET of isolated synaptic vesicles from mouse brain Run: tomogram_103
100membrane Annotation ID: AN-183320	SegmentationMask	Automated	Dataset: CryoET of isolated synaptic vesicles from mouse brain Run: tomogram_102
100membrane Annotation ID: AN-183319	SegmentationMask	Automated	Dataset: CryoET of isolated synaptic vesicles from mouse brain Run: tomogram_101
100membrane Annotation ID: AN-183318	SegmentationMask	Automated	Dataset: CryoET of isolated synaptic vesicles from mouse brain Run: tomogram_100
100membrane Annotation ID: AN-183317	SegmentationMask	Automated	Dataset: CryoET of isolated synaptic vesicles from mouse brain Run: tomogram_099
100membrane Annotation ID: AN-183316	SegmentationMask	Automated	Dataset: CryoET of isolated synaptic vesicles from mouse brain Run: tomogram_098
100membrane Annotation ID: AN-183315	SegmentationMask	Automated	Dataset: CryoET of isolated synaptic vesicles from mouse brain Run: tomogram_097
100membrane Annotation ID: AN-183314	SegmentationMask	Automated	Dataset: CryoET of isolated synaptic vesicles from mouse brain Run: tomogram_096
100membrane Annotation ID: AN-183313	SegmentationMask	Automated	Dataset: CryoET of isolated synaptic vesicles from mouse brain Run: tomogram_095
100membrane Annotation ID: AN-183312	SegmentationMask	Automated	Dataset: CryoET of isolated synaptic vesicles from mouse brain Run: tomogram_094
100membrane Annotation ID: AN-183311	SegmentationMask	Automated	Dataset: CryoET of isolated synaptic vesicles from mouse brain Run: tomogram_093
100membrane Annotation ID: AN-183310	SegmentationMask	Automated	Dataset: CryoET of isolated synaptic vesicles from mouse brain Run: tomogram_092