All Depositions

Deposition

Refined organelle segmentations of axonal varicosity tomograms

  • Deposition ID:CZCDP-10366

Release Date: 2026-08-28

Last Modified: 2026-08-28

key visualization for Refined organelle segmentations of axonal varicosity tomograms

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

Related Databases

Not Submitted

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

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Data Contents

Tilt SeriesAvailable
FramesAvailable
CTFNA
AlignmentNA

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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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