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Deposition

CZII CryoET Object Identification Challenge - 10th place solution - Josef Slavicek

  • Deposition ID:CZCDP-10328

Release Date: 2025-02-25

Last Modified: 2025-02-25

key visualization for CZII CryoET Object Identification Challenge - 10th place solution - Josef Slavicek

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

Deposition Overview

The 10th place solution employs an ensemble of nine 3D UNets, pretrained on simulated data and finetuned on competition data, using a combination of Tversky loss and multiclass cross-entropy as the training objective. Predictions are merged by averaging logits equally across models, followed by thresholding to obtain detection regions and a custom KL-divergence based postprocessing approach to separate multiple particles detected within a single region. The solution achieves distinction through its postprocessing method that identifies particle centers by optimally placing theoretical particle probability density functions to minimize KL divergence with predicted density functions, further refined by using circumcenters of randomly selected boundary points to improve centroid predictions.

Authors

  • Josef Slavicek

Deposition Data

Annotations:2,875

Publications

Not Submitted

Related Databases

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Methods Summary

Annotations
Method Type
Method Details
Method Links
2875
Automated
Ensembled 3D UNets with KL-divergence based particle separation postprocessing.

Deposited Data

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2,875 of 2,875 Annotations

Annotation Name
Object Shape Type
Method Type
Deposited In

157virus-like capsid

Annotation ID: AN-97162

Point
Automated

156Thyroglobulin

Annotation ID: AN-97161

Point
Automated

155cytosolic ribosome

Annotation ID: AN-97160

Point
Automated

154Beta-galactosidase

Annotation ID: AN-97159

Point
Automated

153Beta-amylase

Annotation ID: AN-97158

Point
Automated

152ferritin complex

Annotation ID: AN-97157

Point
Automated

156virus-like capsid

Annotation ID: AN-97103

Point
Automated

155Thyroglobulin

Annotation ID: AN-97102

Point
Automated

154cytosolic ribosome

Annotation ID: AN-97101

Point
Automated

153Beta-galactosidase

Annotation ID: AN-97100

Point
Automated

152Beta-amylase

Annotation ID: AN-97099

Point
Automated

151ferritin complex

Annotation ID: AN-97098

Point
Automated

154virus-like capsid

Annotation ID: AN-97046

Point
Automated

153Thyroglobulin

Annotation ID: AN-97045

Point
Automated

152cytosolic ribosome

Annotation ID: AN-97044

Point
Automated

151Beta-galactosidase

Annotation ID: AN-97043

Point
Automated

150Beta-amylase

Annotation ID: AN-97042

Point
Automated

149ferritin complex

Annotation ID: AN-97041

Point
Automated

156virus-like capsid

Annotation ID: AN-96991

Point
Automated

155Thyroglobulin

Annotation ID: AN-96990

Point
Automated
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