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

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.
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. |
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Deposited Data
Data Contents
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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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