All Depositions

Deposition

CZII CryoET Object Identification Challenge - 9th place solution - Avengers

  • Deposition ID:CZCDP-10327

Release Date: 2025-02-25

Last Modified: 2025-02-25

key visualization for CZII CryoET Object Identification Challenge - 9th place solution - Avengers

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

Deposition Overview

For the 9th place solution, a 3D ConvNeXt-like segmentation model is employed with modifications to the encoder including smaller 2x2 stem and 3x3 kernel size in convolution blocks to better detect small particles. Binary cross-entropy loss is used for training with basic rot90 augmentations, and the final submission ensembles multiple models with DBSCAN clustering applied to refine particle centroids. A key distinction of this approach is the custom adjustment of ground truth mask sizes for different particle types with factors of 0.5 for smaller particles and 0.33 for larger ones, which significantly improved performance from 0.62 to 0.70-0.77 on the public leaderboard.

Authors

  • Koki Wada

Deposition Data

Annotations:2,385

Publications

Not Submitted

Related Databases

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Methods Summary

Annotations
Method Type
Method Details
Method Links
2385
Automated
3D ConvNeXt segmentation with reduced kernel sizes and adjusted masks.
Source Code:Inference code
+4 more

Deposited Data

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Data Contents

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FramesAvailable
CTFAvailable
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2,385 of 2,385 Annotations

Annotation Name
Object Shape Type
Method Type
Deposited In

151virus-like capsid

Annotation ID: AN-97156

Point
Automated

150Thyroglobulin

Annotation ID: AN-97155

Point
Automated

149cytosolic ribosome

Annotation ID: AN-97154

Point
Automated

148Beta-galactosidase

Annotation ID: AN-97153

Point
Automated

147ferritin complex

Annotation ID: AN-97152

Point
Automated

157virus-like capsid

Annotation ID: AN-97104

Point
Automated

150Thyroglobulin

Annotation ID: AN-97097

Point
Automated

149cytosolic ribosome

Annotation ID: AN-97096

Point
Automated

148Beta-galactosidase

Annotation ID: AN-97095

Point
Automated

147ferritin complex

Annotation ID: AN-97094

Point
Automated

148virus-like capsid

Annotation ID: AN-97040

Point
Automated

147Thyroglobulin

Annotation ID: AN-97039

Point
Automated

146cytosolic ribosome

Annotation ID: AN-97038

Point
Automated

145Beta-galactosidase

Annotation ID: AN-97037

Point
Automated

144ferritin complex

Annotation ID: AN-97036

Point
Automated

150virus-like capsid

Annotation ID: AN-96985

Point
Automated

149Thyroglobulin

Annotation ID: AN-96984

Point
Automated

148cytosolic ribosome

Annotation ID: AN-96983

Point
Automated

147Beta-galactosidase

Annotation ID: AN-96982

Point
Automated

146ferritin complex

Annotation ID: AN-96981

Point
Automated
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