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

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Methods Summary

Annotations	Method Type	Method Details	Method Links
304	Hybrid	octopi prediction + slabpick + py2rely 2D classification + manual class selection	Source Code:slabpick +4 more
505	Hybrid	octopi prediction + slabpick + py2rely 2D classification + manual class selection + py2rely 3D refinement	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

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-37172 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-36723 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-36600 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-36540 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-36483 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-36365 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-36239 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-36235 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-36168 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-35956 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-35900 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-35640 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-35567 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-35520 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-35459 Ground Truth	Point	Manual	Dataset: CZII 2-protein phantom (version 1.0) with defocus-based imaging Run: 25jul02a_Position_10
104cytosolic ribosome Annotation ID: AN-48443	OrientedPoint	Hybrid	Dataset: CZII 2-protein phantom (version 1.0) with defocus-based imaging Run: 25jul02a_Position_8_5
103virus-like capsid Annotation ID: AN-48442	OrientedPoint	Hybrid	Dataset: CZII 2-protein phantom (version 1.0) with defocus-based imaging Run: 25jul02a_Position_8_5
102virus-like capsid Annotation ID: AN-48441	Point	Hybrid	Dataset: CZII 2-protein phantom (version 1.0) with defocus-based imaging Run: 25jul02a_Position_8_5
101virus-like capsid Annotation ID: AN-48440	Point	Automated	Dataset: CZII 2-protein phantom (version 1.0) with defocus-based imaging Run: 25jul02a_Position_8_5
100membrane Annotation ID: AN-48439	SegmentationMask	Automated	Dataset: CZII 2-protein phantom (version 1.0) with defocus-based imaging Run: 25jul02a_Position_8_5