uermel commited on
Commit ·
6bf025b
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Parent(s): c16b2ba
more polish for readme
Browse files
README.md
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@@ -82,12 +82,12 @@ protocol) so models can be trained and compared under one roof.
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- **Repository:** https://huggingface.co/datasets/uermel/popsicle
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- **Paper:** POPSICLE (NeurIPS 2026 submission).
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- **Underlying datasets:**
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[DS-10440](https://cryoetdataportal.czscience.com/datasets/10440) (Phantom train),
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[DS-10445](https://cryoetdataportal.czscience.com/datasets/10445) (Phantom public test),
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[DS-10446](https://cryoetdataportal.czscience.com/datasets/10446) (Phantom private test),
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[CZCDP-10350](https://cryoetdataportal.czscience.com/depositions/10350) (Bacterial),
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[CZCDP-10351](https://cryoetdataportal.czscience.com/depositions/10351) (Yeast; underlying tomograms in DS-10000/DS-10001),
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[CZCDP-10332](https://cryoetdataportal.czscience.com/depositions/10332)/[CZCDP-10347](https://cryoetdataportal.czscience.com/depositions/10347) (MotorBench train/test).
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- **Data Portal:** https://cryoetdataportal.czscience.com (Ermel et al.,
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*Nature Methods* 21:2200–2202, 2024).
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- **Tooling:** [copick](https://github.com/copick/copick) reads each
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| `test` | DS-10446 | 364 | CZII Kaggle "private test" set |
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Picks are **restricted to the original ground-truth annotations**. Community-derived submissions hosted on the same
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CDP datasets
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excluded so the benchmark scores against the canonical reference labels.
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#### Loading with copick
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@@ -416,11 +416,6 @@ benchmark. The test slice keeps all 843 *V. cholerae* runs (motor and
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no-motor) because negative samples are an explicit part of the held-out
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evaluation per Owens et al. 2025.
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Picks are scoped to deposition_id so the train and test slices stay
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disjoint even where the same host datasets appear in both depositions'
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neighborhoods — this is implemented via the
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`picks_portal_meta={"deposition_id": ...}` filter on each export pass.
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#### Loading with copick
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```python
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by the BYU Kaggle competition contributors (training corpus
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CZCDP-10332, expanded by the first-place team and MIC-DKFZ); the
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held-out test set (CZCDP-10347, V. cholerae) was authored by Owens
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et al. 2025.
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test slices stay disjoint even though the train deposition reuses
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tomograms from many host datasets.
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#### Who are the annotators?
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- **Repository:** https://huggingface.co/datasets/uermel/popsicle
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- **Paper:** POPSICLE (NeurIPS 2026 submission).
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- **Underlying datasets:**
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- [DS-10440](https://cryoetdataportal.czscience.com/datasets/10440) (Phantom train),
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- [DS-10445](https://cryoetdataportal.czscience.com/datasets/10445) (Phantom public test),
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- [DS-10446](https://cryoetdataportal.czscience.com/datasets/10446) (Phantom private test),
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- [CZCDP-10350](https://cryoetdataportal.czscience.com/depositions/10350) (Bacterial),
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- [CZCDP-10351](https://cryoetdataportal.czscience.com/depositions/10351) (Yeast; underlying tomograms in [DS-10000](https://cryoetdataportal.czscience.com/datasets/10000) / [DS-10001](https://cryoetdataportal.czscience.com/datasets/10001)),
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- [CZCDP-10332](https://cryoetdataportal.czscience.com/depositions/10332)/[CZCDP-10347](https://cryoetdataportal.czscience.com/depositions/10347) (MotorBench train/test).
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- **Data Portal:** https://cryoetdataportal.czscience.com (Ermel et al.,
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*Nature Methods* 21:2200–2202, 2024).
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- **Tooling:** [copick](https://github.com/copick/copick) reads each
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| `test` | DS-10446 | 364 | CZII Kaggle "private test" set |
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Picks are **restricted to the original ground-truth annotations**. Community-derived submissions hosted on the same
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CDP datasets, including Kaggle challenge entries, are intentionally
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excluded so the benchmark scores against the canonical reference labels.
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#### Loading with copick
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no-motor) because negative samples are an explicit part of the held-out
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evaluation per Owens et al. 2025.
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#### Loading with copick
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```python
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by the BYU Kaggle competition contributors (training corpus
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CZCDP-10332, expanded by the first-place team and MIC-DKFZ); the
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held-out test set (CZCDP-10347, V. cholerae) was authored by Owens
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et al. 2025.
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#### Who are the annotators?
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