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Deposition

CZII CryoET Object Identification Challenge - 6th place solution - tomoon33

  • Deposition ID:CZCDP-10324

Release Date: 2025-02-25

Last Modified: 2025-02-25

key visualization for CZII CryoET Object Identification Challenge - 6th place solution - tomoon33

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

Deposition Overview

The 6th place solution employs a combination of 2.5D UNet and 3D UNet architectures with various backbones (including SegResNet and DynUnet) to predict segmentation maps for particle detection in cryoET data. FocalTversky++ loss is utilized during training on 64×128×128 patches, with models being pretrained on custom-simulated data generated using Polnet and accelerated during inference via TensorRT conversion. A key innovation involves designing prediction maps that reflect model confidence rather than binary outputs, enabling effective ensemble averaging across 10 models.

Authors

  • Tomoki Uchiyama

Deposition Data

Annotations:2,390

Publications

Not Submitted

Related Databases

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Methods Summary

Annotations
Method Type
Method Details
Method Links
2390
Automated
Custom-simulated pretraining with FocalTversky++ loss.
Source Code:Inference notebook on Kaggle
+2 more

Deposited Data

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Tilt SeriesAvailable
FramesAvailable
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2,390 of 2,390 Annotations

Annotation Name
Object Shape Type
Method Type
Deposited In

157virus-like capsid

Annotation ID: AN-97188

Point
Automated

156Thyroglobulin

Annotation ID: AN-97187

Point
Automated

155cytosolic ribosome

Annotation ID: AN-97186

Point
Automated

154Beta-galactosidase

Annotation ID: AN-97185

Point
Automated

153ferritin complex

Annotation ID: AN-97184

Point
Automated

136virus-like capsid

Annotation ID: AN-97141

Point
Automated

135Thyroglobulin

Annotation ID: AN-97140

Point
Automated

134cytosolic ribosome

Annotation ID: AN-97139

Point
Automated

133Beta-galactosidase

Annotation ID: AN-97138

Point
Automated

132ferritin complex

Annotation ID: AN-97137

Point
Automated

136virus-like capsid

Annotation ID: AN-97083

Point
Automated

135Thyroglobulin

Annotation ID: AN-97082

Point
Automated

134cytosolic ribosome

Annotation ID: AN-97081

Point
Automated

133Beta-galactosidase

Annotation ID: AN-97080

Point
Automated

132ferritin complex

Annotation ID: AN-97079

Point
Automated

133virus-like capsid

Annotation ID: AN-97025

Point
Automated

132Thyroglobulin

Annotation ID: AN-97024

Point
Automated

131cytosolic ribosome

Annotation ID: AN-97023

Point
Automated

130Beta-galactosidase

Annotation ID: AN-97022

Point
Automated

129ferritin complex

Annotation ID: AN-97021

Point
Automated
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