Deposition

CZII 2-protein phantom (version 1.0)

Deposition ID:CZCDP-10341

Release Date: 2026-01-09

Last Modified: 2026-01-09

key visualization for CZII 2-protein phantom (version 1.0)

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

Deposition Overview

This deposition has two datasets, one acquired with the Volta phase plate at low defocus and one acquired without at higher defocus. The datasets are comprised of movie stacks, tiltseries, alignments, tomograms and hand-curated ground truth annotations of PP7 virus like particles. The data was acquired on a Krios G4 using a Falcon 4i detector and SelctrisX energy filter. Tomograms were aligned using AreTomo3 2.2.2. Each run provides denoised and CTF-corrected tomograms.

Authors

Deposition Data

Annotations:1,516

Tomograms:624

Publications

Not Submitted

Related Databases

Not Submitted

Methods Summary

Annotations	Method Type	Method Details	Method Links
505	Hybrid	octopi prediction + slabpick + py2rely 2D classification + manual class selection + py2rely 3D refinement	Source Code:slabpick +4 more
304	Hybrid	octopi prediction + slabpick + py2rely 2D classification + manual class selection	Source Code:slabpick +4 more
312	Automated	Prediction using membrain-seg without rescaling and weights MemBrain_seg_v10_alpha.ckpt	Source Code:membrain-seg +1 more
380	Automated	octopi prediction	Source Code:Octopi +1 more
15	Manual	manual particle selection	Source Code:chimerax-copick +1 more

Deposited Data

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Data Contents

Tilt SeriesAvailable

FramesAvailable

CTFAvailable

AlignmentAvailable

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1,516 of 1,516 Annotations

Annotation Name	Object Shape Type	Method Type	Deposited In
101virus-like capsid Annotation ID: AN-128216 Ground Truth	Point	Manual	Dataset: CZII 2-protein phantom (version 1.0) with defocus-based imaging Run: 25jul02a_Position_13_3
101virus-like capsid Annotation ID: AN-128194 Ground Truth	Point	Manual	Dataset: CZII 2-protein phantom (version 1.0) with defocus-based imaging Run: 25jul02a_Position_12_3
101virus-like capsid Annotation ID: AN-128187 Ground Truth	Point	Manual	Dataset: CZII 2-protein phantom (version 1.0) with defocus-based imaging Run: 25jul02a_Position_12_2
101virus-like capsid Annotation ID: AN-128180 Ground Truth	Point	Manual	Dataset: CZII 2-protein phantom (version 1.0) with defocus-based imaging Run: 25jul02a_Position_12
101virus-like capsid Annotation ID: AN-128174 Ground Truth	Point	Manual	Dataset: CZII 2-protein phantom (version 1.0) with defocus-based imaging Run: 25jul02a_Position_11_6
101virus-like capsid Annotation ID: AN-128167 Ground Truth	Point	Manual	Dataset: CZII 2-protein phantom (version 1.0) with defocus-based imaging Run: 25jul02a_Position_11_5
105cytosolic ribosome Annotation ID: AN-128163 Ground Truth	Point	Manual	Dataset: CZII 2-protein phantom (version 1.0) with defocus-based imaging Run: 25jul02a_Position_11_4
101virus-like capsid Annotation ID: AN-128159 Ground Truth	Point	Manual	Dataset: CZII 2-protein phantom (version 1.0) with defocus-based imaging Run: 25jul02a_Position_11_4
101virus-like capsid Annotation ID: AN-128152 Ground Truth	Point	Manual	Dataset: CZII 2-protein phantom (version 1.0) with defocus-based imaging Run: 25jul02a_Position_11_3
101virus-like capsid Annotation ID: AN-128141 Ground Truth	Point	Manual	Dataset: CZII 2-protein phantom (version 1.0) with defocus-based imaging Run: 25jul02a_Position_11
101virus-like capsid Annotation ID: AN-128136 Ground Truth	Point	Manual	Dataset: CZII 2-protein phantom (version 1.0) with defocus-based imaging Run: 25jul02a_Position_10_7
101virus-like capsid Annotation ID: AN-128120 Ground Truth	Point	Manual	Dataset: CZII 2-protein phantom (version 1.0) with defocus-based imaging Run: 25jul02a_Position_10_4
101virus-like capsid Annotation ID: AN-128114 Ground Truth	Point	Manual	Dataset: CZII 2-protein phantom (version 1.0) with defocus-based imaging Run: 25jul02a_Position_10_3
101virus-like capsid Annotation ID: AN-128108 Ground Truth	Point	Manual	Dataset: CZII 2-protein phantom (version 1.0) with defocus-based imaging Run: 25jul02a_Position_10_2
101virus-like capsid Annotation ID: AN-128102 Ground Truth	Point	Manual	Dataset: CZII 2-protein phantom (version 1.0) with defocus-based imaging Run: 25jul02a_Position_10
105cytosolic ribosome Annotation ID: AN-129614	OrientedPoint	Hybrid	Dataset: CZII 2-protein phantom (version 1.0) with the Volta Phase Plate Run: 25jul16a_Position_99
104cytosolic ribosome Annotation ID: AN-129613	Point	Hybrid	Dataset: CZII 2-protein phantom (version 1.0) with the Volta Phase Plate Run: 25jul16a_Position_99
103virus-like capsid Annotation ID: AN-129612	OrientedPoint	Hybrid	Dataset: CZII 2-protein phantom (version 1.0) with the Volta Phase Plate Run: 25jul16a_Position_99
102virus-like capsid Annotation ID: AN-129611	Point	Hybrid	Dataset: CZII 2-protein phantom (version 1.0) with the Volta Phase Plate Run: 25jul16a_Position_99
101virus-like capsid Annotation ID: AN-129610	Point	Automated	Dataset: CZII 2-protein phantom (version 1.0) with the Volta Phase Plate Run: 25jul16a_Position_99