HPA_SingleCellClassification_Analysis

Analysis for Kaggle Human Protein Atlas Single Cell Classification challenge

This repo is for analysis of the HPA Single Cell Classification results.

The paper was published in Nature Methods volume 19, pages1221–1229 (2022).

Content

This includes

• Average Precision scores for each class and Jaccard index (IOU) of each submission at per cell level in class_scoring and segmentation_matching. This is scored using Tensorflow Object Detection API under Apache license. Specifically, scoring is done with oid_hpasc_challenge_evaluation.py and oid_hpasc_challenge_evaluation_test.py for testing.
• Analysis scripts as described in the manuscript in analysis
• Winner solution (team1_bestfitting) including model and analysis code provided by Shubin Dai (bestfitting) and modified by Trang Le for analysis and prediction.
• plot contains plotting this competition's metadata obtained from Meta Kaggle.

License

MIT License Apache License 2.0