Deposition

In situ architecture of the polar tube invasion apparatus from microsporidian parasites

Deposition ID:CZCDP-10307

Release Date: 2024-07-29

Last Modified: 2024-07-24

key visualization for In situ architecture of the polar tube invasion apparatus from microsporidian parasites

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

Deposition Overview

This deposition contains three datasets of dormant microsporidian spores from Encephalitozoon intestinalis and Encephalitozoon hellem. The datasets contain raw frames, tilt series, tomogram reconstructions and segmentations. Samples were prepared using the waffle-method and cryo-FIB milled. A subset of runs contains manual and manually curated annotations of spore organelles.

Authors

Deposition Data

Annotations:78

Tomograms:197

Publications

DOI:10.1101/2024.07.13.603322

Related Databases

EMDB ID:EMD-45674

Methods Summary

Annotations	Method Type	Method Details	Method Links
42	Hybrid	Manually annotate 5 slices of object of interest on 8X binned tomogram+ Train a 2D U net model with DICE Loss in segmentation wizard of dragonfly + Use trained model to predict segmentation for all slices in the tomogram + manually correct any aberrations, then retrain + Overlay predicted segmentations with raw slices and perform any clean up manually + convert to contour meshes and smooth	Not Submitted
24	Hybrid	Each organelle was segmented as a separate region of interest in 8X binned tomogram by tracing + A 3-D reconstruction of each organelle was generated + Reconstructions were converted to contour meshes which were smoothed.	Not Submitted
12	Hybrid	Each organelle was segmented as a separate region of interest in 8X binned tomogram by tracing + A 3-D reconstruction of each organelle was generated + Reconstructions were converted to contour meshes which were smoothed	Not Submitted

Deposited Data

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Data Contents

Tilt SeriesAvailable

FramesAvailable

CTFNA

AlignmentAvailable

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78 of 78 Annotations

Annotation Name	Object Shape Type	Method Type	Deposited In
107polar tube Annotation ID: AN-33687 Ground Truth	SegmentationMask	Hybrid	Dataset: Cryo-ET dataset of dormant microporidian spores from Encephalitozoon hellem Run: tomo_0112
106polar tube Annotation ID: AN-33686 Ground Truth	SegmentationMask	Hybrid	Dataset: Cryo-ET dataset of dormant microporidian spores from Encephalitozoon hellem Run: tomo_0112
105polar tube Annotation ID: AN-33685 Ground Truth	SegmentationMask	Hybrid	Dataset: Cryo-ET dataset of dormant microporidian spores from Encephalitozoon hellem Run: tomo_0112
104polar tube Annotation ID: AN-33684 Ground Truth	SegmentationMask	Hybrid	Dataset: Cryo-ET dataset of dormant microporidian spores from Encephalitozoon hellem Run: tomo_0112
103polaroplast Annotation ID: AN-33683 Ground Truth	SegmentationMask	Hybrid	Dataset: Cryo-ET dataset of dormant microporidian spores from Encephalitozoon hellem Run: tomo_0112
102plasma membrane Annotation ID: AN-33682 Ground Truth	SegmentationMask	Hybrid	Dataset: Cryo-ET dataset of dormant microporidian spores from Encephalitozoon hellem Run: tomo_0112
101microsporidian-type endospore Annotation ID: AN-33681 Ground Truth	SegmentationMask	Hybrid	Dataset: Cryo-ET dataset of dormant microporidian spores from Encephalitozoon hellem Run: tomo_0112
100microsporidian-type exospore Annotation ID: AN-33680 Ground Truth	SegmentationMask	Hybrid	Dataset: Cryo-ET dataset of dormant microporidian spores from Encephalitozoon hellem Run: tomo_0112
107vesicle Annotation ID: AN-33621 Ground Truth	SegmentationMask	Hybrid	Dataset: Cryo-ET dataset of dormant microporidian spores from Encephalitozoon hellem Run: tomo_0110
106polar tube Annotation ID: AN-33620 Ground Truth	SegmentationMask	Hybrid	Dataset: Cryo-ET dataset of dormant microporidian spores from Encephalitozoon hellem Run: tomo_0110
105polar tube Annotation ID: AN-33619 Ground Truth	SegmentationMask	Hybrid	Dataset: Cryo-ET dataset of dormant microporidian spores from Encephalitozoon hellem Run: tomo_0110
104polar tube Annotation ID: AN-33618 Ground Truth	SegmentationMask	Hybrid	Dataset: Cryo-ET dataset of dormant microporidian spores from Encephalitozoon hellem Run: tomo_0110
103polaroplast Annotation ID: AN-33617 Ground Truth	SegmentationMask	Hybrid	Dataset: Cryo-ET dataset of dormant microporidian spores from Encephalitozoon hellem Run: tomo_0110
102plasma membrane Annotation ID: AN-33616 Ground Truth	SegmentationMask	Hybrid	Dataset: Cryo-ET dataset of dormant microporidian spores from Encephalitozoon hellem Run: tomo_0110
101microsporidian-type endospore Annotation ID: AN-33615 Ground Truth	SegmentationMask	Hybrid	Dataset: Cryo-ET dataset of dormant microporidian spores from Encephalitozoon hellem Run: tomo_0110
100microsporidian-type exospore Annotation ID: AN-33614 Ground Truth	SegmentationMask	Hybrid	Dataset: Cryo-ET dataset of dormant microporidian spores from Encephalitozoon hellem Run: tomo_0110
107polar tube Annotation ID: AN-33575 Ground Truth	SegmentationMask	Hybrid	Dataset: Cryo-ET dataset of dormant microporidian spores from Encephalitozoon hellem Run: tomo_0109
106polar tube Annotation ID: AN-33574 Ground Truth	SegmentationMask	Hybrid	Dataset: Cryo-ET dataset of dormant microporidian spores from Encephalitozoon hellem Run: tomo_0109
105polar tube Annotation ID: AN-33573 Ground Truth	SegmentationMask	Hybrid	Dataset: Cryo-ET dataset of dormant microporidian spores from Encephalitozoon hellem Run: tomo_0109
104polar tube Annotation ID: AN-33572 Ground Truth	SegmentationMask	Hybrid	Dataset: Cryo-ET dataset of dormant microporidian spores from Encephalitozoon hellem Run: tomo_0109