Deposition
Refined organelle segmentations of axonal varicosity tomograms
- Deposition ID:CZCDP-10366
Release Date: 2026-08-28
Last Modified: 2026-08-28

Photo Caption: Central slab of 4 representative tomograms with selected sets of annotations.
Deposition Overview
Refined organelle segmentations for the subset of axonal varicosity tomograms carried forward into the manuscript. Fifteen tomograms were re-reconstructed at 2x binning (10.8 A/voxel) and IsoNet-denoised, then re-annotated in Amira into the 16-class scheme described in the manuscript, following MemBrain-seg and TARDIS-MT pre-segmentation. Eleven of the fifteen are re-annotations of tomograms already present in the baseline deposition 10362 under its earlier 15-class iteration.
Deposition Data
Annotations:140
Tomograms:0
Publications
Related Databases
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Methods Summary
Annotations | Method Type | Method Details | Method Links |
|---|---|---|---|
| 140 | Hybrid | MemBrain-seg (membranes) and TARDIS-MT (microtubules) pre-segmentation, manually curated in Amira into the manuscript 16-class scheme on 2x-binned, IsoNet-denoised tomograms. | Source Code:IsoNet source code +17 more |
Deposited Data
Data Contents
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140 of 140 Annotations
Annotation Name | Object Shape Type | Method Type | Deposited In |
|---|---|---|---|
115endosomal intralumenal vesicle Annotation ID: AN-182841 | SegmentationMask | Hybrid | |
114endosome Annotation ID: AN-182840 | SegmentationMask | Hybrid | |
113vesicle Annotation ID: AN-182839 | SegmentationMask | Hybrid | |
112phagophore Annotation ID: AN-182838 | SegmentationMask | Hybrid | |
111phagophore Annotation ID: AN-182837 | SegmentationMask | Hybrid | |
110vesicle Annotation ID: AN-182836 | SegmentationMask | Hybrid | |
109lamellar body Annotation ID: AN-182835 | SegmentationMask | Hybrid | |
108cytoplasmic vesicle Annotation ID: AN-182834 | SegmentationMask | Hybrid | |
107multivesicular body, internal vesicle Annotation ID: AN-182833 | SegmentationMask | Hybrid | |
106multivesicular body Annotation ID: AN-182832 | SegmentationMask | Hybrid | |
105vesicle Annotation ID: AN-182831 | SegmentationMask | Hybrid | |
104endoplasmic reticulum Annotation ID: AN-182830 | SegmentationMask | Hybrid | |
103microtubule Annotation ID: AN-182829 | SegmentationMask | Hybrid | |
102plasma membrane Annotation ID: AN-182828 | SegmentationMask | Hybrid | |
101mitochondrial inner membrane Annotation ID: AN-182827 | SegmentationMask | Hybrid | |
100mitochondrial outer membrane Annotation ID: AN-182826 | SegmentationMask | Hybrid | |
111phagophore Annotation ID: AN-182760 | SegmentationMask | Hybrid | |
108cytoplasmic vesicle Annotation ID: AN-182759 | SegmentationMask | Hybrid | |
107multivesicular body, internal vesicle Annotation ID: AN-182758 | SegmentationMask | Hybrid | |
106multivesicular body Annotation ID: AN-182757 | SegmentationMask | Hybrid |
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