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Deposition

Cryo-electron tomography of centrosomes in C. elegans embryonic cells

  • Deposition ID:CZCDP-10345

Release Date: 2026-03-26

Last Modified: 2026-03-26

key visualization for Cryo-electron tomography of centrosomes in C. elegans embryonic cells

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

Deposition Overview

Cryo-electron tomography data of centrosomes in dissociated C. elegans embryonic cells across the cell cycle. The deposition includes raw frames, tilt series stacks, alignment transforms, reconstructed tomograms, and semantic segmentation annotations of centrioles, microtubules, ribosomes, membranes, and pericentriolar material. 12 tomograms from cells at different cell cycle stages (interphase, prophase, metaphase, anaphase, telophase) were collected on a 300 kV Titan Krios with K2 Summit detector and Volta phase plate.

Deposition Data

Annotations:53

Tomograms:12

Related Databases

Methods Summary

Annotations
Method Type
Method Details
Method Links
12
Hybrid
Segmentation of microtubules was carried out using a cylinder correlation function in Amira 2021.1 on Gaussian-filtered 4x binned tomograms. Results were manually examined and erroneous results removed. For one tomogram, binary masks from the other 11 were used to train a DeePiCt model, and the trained model was used for prediction with manual cleanup.
Source Code:DeePiCt
+1 more
12
Hybrid
Ribosomes were segmented using DeePiCt with the model ribo_model2_IF4_D2_0. Results were inspected in Amira 2021.1 to remove false positives.
Source Code:DeePiCt
+1 more
12
Hybrid
Membranes were segmented using DeePiCt with the model full_vpp_memb_model_IF4_D2_BN. Results were inspected in Amira 2021.1 to remove false positives.
Source Code:DeePiCt
+1 more
7
Hybrid
Denoised tomograms were used for matrix segmentation. Centrioles, microtubules, ribosomes and membranes were masked in the tomogram volumes. Two models were generated following manual annotation using Ilastik 1.3.3: one utilized 3D Pixel Classification, while the other used 2D Autocontext trained on the central 50 XY slices. The Autocontext model outputs were combined and binarized in MATLAB 2019a to obtain the final matrix model.
Website:
Ilastik
+1 more
10
Manual
Centriole microtubules were manually traced in Amira 2021.1.

Deposited Data

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Data Contents

Tilt SeriesAvailable
FramesAvailable
CTFNA
AlignmentAvailable

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53 of 53 Annotations

Annotation Name
Object Shape Type
Method Type
Deposited In

102membrane

Annotation ID: AN-141283

Ground Truth
SegmentationMask
Hybrid

101cytosolic ribosome

Annotation ID: AN-141282

Ground Truth
SegmentationMask
Hybrid

100microtubule

Annotation ID: AN-141281

Ground Truth
SegmentationMask
Hybrid

104pericentriolar material

Annotation ID: AN-141280

Ground Truth
SegmentationMask
Hybrid

103membrane

Annotation ID: AN-141279

Ground Truth
SegmentationMask
Hybrid

102cytosolic ribosome

Annotation ID: AN-141278

Ground Truth
SegmentationMask
Hybrid

101microtubule

Annotation ID: AN-141277

Ground Truth
SegmentationMask
Hybrid

100centriole

Annotation ID: AN-141276

Ground Truth
SegmentationMask
Manual

103pericentriolar material

Annotation ID: AN-141275

Ground Truth
SegmentationMask
Hybrid

102membrane

Annotation ID: AN-141274

Ground Truth
SegmentationMask
Hybrid

101cytosolic ribosome

Annotation ID: AN-141273

Ground Truth
SegmentationMask
Hybrid

100microtubule

Annotation ID: AN-141272

Ground Truth
SegmentationMask
Hybrid

104pericentriolar material

Annotation ID: AN-141271

Ground Truth
SegmentationMask
Hybrid

103membrane

Annotation ID: AN-141270

Ground Truth
SegmentationMask
Hybrid

102cytosolic ribosome

Annotation ID: AN-141269

Ground Truth
SegmentationMask
Hybrid

101microtubule

Annotation ID: AN-141268

Ground Truth
SegmentationMask
Hybrid

100centriole

Annotation ID: AN-141267

Ground Truth
SegmentationMask
Manual

104pericentriolar material

Annotation ID: AN-141266

Ground Truth
SegmentationMask
Hybrid

103membrane

Annotation ID: AN-141265

Ground Truth
SegmentationMask
Hybrid

102cytosolic ribosome

Annotation ID: AN-141264

Ground Truth
SegmentationMask
Hybrid
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