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

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
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
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

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
103polaroplast Annotation ID: AN-31004 Ground Truth	SegmentationMask	Hybrid	Dataset: Cryo-ET datasets (1 and 2) of dormant microporidian spores from Encephalitozoon intestinalis Run: tomo_0003
102plasma membrane Annotation ID: AN-31003 Ground Truth	SegmentationMask	Hybrid	Dataset: Cryo-ET datasets (1 and 2) of dormant microporidian spores from Encephalitozoon intestinalis Run: tomo_0003
101microsporidian-type endospore Annotation ID: AN-31002 Ground Truth	SegmentationMask	Hybrid	Dataset: Cryo-ET datasets (1 and 2) of dormant microporidian spores from Encephalitozoon intestinalis Run: tomo_0003
100microsporidian-type exospore Annotation ID: AN-31001 Ground Truth	SegmentationMask	Hybrid	Dataset: Cryo-ET datasets (1 and 2) of dormant microporidian spores from Encephalitozoon intestinalis Run: tomo_0003
107spore wall Annotation ID: AN-31000 Ground Truth	SegmentationMask	Hybrid	Dataset: Cryo-ET datasets (1 and 2) of dormant microporidian spores from Encephalitozoon intestinalis Run: tomo_0001
106polar tube Annotation ID: AN-30999 Ground Truth	SegmentationMask	Hybrid	Dataset: Cryo-ET datasets (1 and 2) of dormant microporidian spores from Encephalitozoon intestinalis Run: tomo_0001
105polar tube Annotation ID: AN-30998 Ground Truth	SegmentationMask	Hybrid	Dataset: Cryo-ET datasets (1 and 2) of dormant microporidian spores from Encephalitozoon intestinalis Run: tomo_0001
104nuclear lumen Annotation ID: AN-30997 Ground Truth	SegmentationMask	Hybrid	Dataset: Cryo-ET datasets (1 and 2) of dormant microporidian spores from Encephalitozoon intestinalis Run: tomo_0001
103nuclear envelope Annotation ID: AN-30996 Ground Truth	SegmentationMask	Hybrid	Dataset: Cryo-ET datasets (1 and 2) of dormant microporidian spores from Encephalitozoon intestinalis Run: tomo_0001
102plasma membrane Annotation ID: AN-30995 Ground Truth	SegmentationMask	Hybrid	Dataset: Cryo-ET datasets (1 and 2) of dormant microporidian spores from Encephalitozoon intestinalis Run: tomo_0001
101microsporidian-type endospore Annotation ID: AN-30994 Ground Truth	SegmentationMask	Hybrid	Dataset: Cryo-ET datasets (1 and 2) of dormant microporidian spores from Encephalitozoon intestinalis Run: tomo_0001
100microsporidian-type exospore Annotation ID: AN-30993 Ground Truth	SegmentationMask	Hybrid	Dataset: Cryo-ET datasets (1 and 2) of dormant microporidian spores from Encephalitozoon intestinalis Run: tomo_0001
107polar tube Annotation ID: AN-30992 Ground Truth	SegmentationMask	Hybrid	Dataset: Cryo-ET dataset of dormant microporidian spores from Encephalitozoon hellem Run: tomo_0112
106polar tube Annotation ID: AN-30991 Ground Truth	SegmentationMask	Hybrid	Dataset: Cryo-ET dataset of dormant microporidian spores from Encephalitozoon hellem Run: tomo_0112
105polar tube Annotation ID: AN-30990 Ground Truth	SegmentationMask	Hybrid	Dataset: Cryo-ET dataset of dormant microporidian spores from Encephalitozoon hellem Run: tomo_0112
104polar tube Annotation ID: AN-30989 Ground Truth	SegmentationMask	Hybrid	Dataset: Cryo-ET dataset of dormant microporidian spores from Encephalitozoon hellem Run: tomo_0112
103polaroplast Annotation ID: AN-30988 Ground Truth	SegmentationMask	Hybrid	Dataset: Cryo-ET dataset of dormant microporidian spores from Encephalitozoon hellem Run: tomo_0112
102plasma membrane Annotation ID: AN-30987 Ground Truth	SegmentationMask	Hybrid	Dataset: Cryo-ET dataset of dormant microporidian spores from Encephalitozoon hellem Run: tomo_0112
101microsporidian-type endospore Annotation ID: AN-30986 Ground Truth	SegmentationMask	Hybrid	Dataset: Cryo-ET dataset of dormant microporidian spores from Encephalitozoon hellem Run: tomo_0112
100microsporidian-type exospore Annotation ID: AN-30985 Ground Truth	SegmentationMask	Hybrid	Dataset: Cryo-ET dataset of dormant microporidian spores from Encephalitozoon hellem Run: tomo_0112