Deposition

Automated Synaptic Vesicle Segmentation in Synaptosomes

Deposition ID:CZCDP-10330

Release Date: 2025-02-19

Last Modified: 2025-02-19

key visualization for Automated Synaptic Vesicle Segmentation in Synaptosomes

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

Deposition Overview

This deposition contains segmentations of synaptic vesicles in cryo ET data of synaptosomes. The segmentations were produced with SynapseNet by re-training its vesicle segmentation network on ca. 50 synaptosome tomograms via unsupervised domain adaptation. TThe vesicles are segmented as instances: each vesicle is assigned a unique id per tomogram by SynapseNet (however, represented as binary masks on the cryoET data portal), each vesicle is also assigned its centroid calculated using the SynapseNet instances. For more details on SynapseNet check out the GitHub repository and the preprint linked below.

Authors

Deposition Data

Annotations:70

Publications

DOI:10.1101/2024.12.02.626387

Related Databases

Not Submitted

Methods Summary

Annotations	Method Type	Method Details	Method Links
70	Automated	Prediction using SynapseNet after unsupervised domain adaptation	Source Code:SynapseNet

Deposited Data

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Data Contents

Tilt SeriesAvailable

FramesAvailable

CTFNA

AlignmentAvailable

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140 of 140 Annotations

Annotation Name	Object Shape Type	Method Type	Deposited In
101synaptic vesicle Annotation ID: AN-68929	SegmentationMask	Automated	Dataset: Synaptosomes from rat hippocampi (200 mg, no centrifugation, Cu grid, low tilt range, 1:100)Run: 24sep24a_Position_99
101synaptic vesicle Annotation ID: AN-68929	InstanceSegmentation	Automated	Dataset: Synaptosomes from rat hippocampi (200 mg, no centrifugation, Cu grid, low tilt range, 1:100)Run: 24sep24a_Position_99
101synaptic vesicle Annotation ID: AN-68928	InstanceSegmentation	Automated	Dataset: Synaptosomes from rat hippocampi (200 mg, no centrifugation, Cu grid, low tilt range, 1:100)Run: 24sep24a_Position_98_2
101synaptic vesicle Annotation ID: AN-68928	SegmentationMask	Automated	Dataset: Synaptosomes from rat hippocampi (200 mg, no centrifugation, Cu grid, low tilt range, 1:100)Run: 24sep24a_Position_98_2
101synaptic vesicle Annotation ID: AN-68927	InstanceSegmentation	Automated	Dataset: Synaptosomes from rat hippocampi (200 mg, no centrifugation, Cu grid, low tilt range, 1:100)Run: 24sep24a_Position_97_3
101synaptic vesicle Annotation ID: AN-68927	SegmentationMask	Automated	Dataset: Synaptosomes from rat hippocampi (200 mg, no centrifugation, Cu grid, low tilt range, 1:100)Run: 24sep24a_Position_97_3
101synaptic vesicle Annotation ID: AN-68926	InstanceSegmentation	Automated	Dataset: Synaptosomes from rat hippocampi (200 mg, no centrifugation, Cu grid, low tilt range, 1:100)Run: 24sep24a_Position_94
101synaptic vesicle Annotation ID: AN-68926	SegmentationMask	Automated	Dataset: Synaptosomes from rat hippocampi (200 mg, no centrifugation, Cu grid, low tilt range, 1:100)Run: 24sep24a_Position_94
101synaptic vesicle Annotation ID: AN-68925	InstanceSegmentation	Automated	Dataset: Synaptosomes from rat hippocampi (200 mg, no centrifugation, Cu grid, low tilt range, 1:100)Run: 24sep24a_Position_92
101synaptic vesicle Annotation ID: AN-68925	SegmentationMask	Automated	Dataset: Synaptosomes from rat hippocampi (200 mg, no centrifugation, Cu grid, low tilt range, 1:100)Run: 24sep24a_Position_92
101synaptic vesicle Annotation ID: AN-68924	SegmentationMask	Automated	Dataset: Synaptosomes from rat hippocampi (200 mg, no centrifugation, Cu grid, low tilt range, 1:100)Run: 24sep24a_Position_91_2
101synaptic vesicle Annotation ID: AN-68924	InstanceSegmentation	Automated	Dataset: Synaptosomes from rat hippocampi (200 mg, no centrifugation, Cu grid, low tilt range, 1:100)Run: 24sep24a_Position_91_2
101synaptic vesicle Annotation ID: AN-68923	SegmentationMask	Automated	Dataset: Synaptosomes from rat hippocampi (200 mg, no centrifugation, Cu grid, low tilt range, 1:100)Run: 24sep24a_Position_91
101synaptic vesicle Annotation ID: AN-68923	InstanceSegmentation	Automated	Dataset: Synaptosomes from rat hippocampi (200 mg, no centrifugation, Cu grid, low tilt range, 1:100)Run: 24sep24a_Position_91
101synaptic vesicle Annotation ID: AN-68922	InstanceSegmentation	Automated	Dataset: Synaptosomes from rat hippocampi (200 mg, no centrifugation, Cu grid, low tilt range, 1:100)Run: 24sep24a_Position_8_4
101synaptic vesicle Annotation ID: AN-68922	SegmentationMask	Automated	Dataset: Synaptosomes from rat hippocampi (200 mg, no centrifugation, Cu grid, low tilt range, 1:100)Run: 24sep24a_Position_8_4
101synaptic vesicle Annotation ID: AN-68921	SegmentationMask	Automated	Dataset: Synaptosomes from rat hippocampi (200 mg, no centrifugation, Cu grid, low tilt range, 1:100)Run: 24sep24a_Position_89_2
101synaptic vesicle Annotation ID: AN-68921	InstanceSegmentation	Automated	Dataset: Synaptosomes from rat hippocampi (200 mg, no centrifugation, Cu grid, low tilt range, 1:100)Run: 24sep24a_Position_89_2
101synaptic vesicle Annotation ID: AN-68920	SegmentationMask	Automated	Dataset: Synaptosomes from rat hippocampi (200 mg, no centrifugation, Cu grid, low tilt range, 1:100)Run: 24sep24a_Position_87
101synaptic vesicle Annotation ID: AN-68920	InstanceSegmentation	Automated	Dataset: Synaptosomes from rat hippocampi (200 mg, no centrifugation, Cu grid, low tilt range, 1:100)Run: 24sep24a_Position_87