Deepcell-spots

🧰 Maintenance

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<summary>Change model output to dictionary elaubsch (22)</summary>
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<summary>Update PyPI version elaubsch (23)</summary>
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<summary>Remove postcode import from setup.py elaubsch (21)</summary>


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🚀 Features

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<summary>Update example notebook for singleplex app elaubsch (18)</summary>


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<summary>Add Mesmer segmentation to Polaris app elaubsch (17)</summary>

Add Mesmer to options of segmentation applications for Polaris
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<summary>Singleplex Polaris app elaubsch (15)</summary>

Adding the singleplex application, which will now be referred to as the Polaris application. The previous iteration of the Polaris application (without cell segmentation) has been refactored to the SpotDetection application.
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🧰 Maintenance

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<summary>Remove PoSTcode import elaubsch (20)</summary>

PoSTcode [repo](https://github.com/gerstung-lab/postcode) is no longer cloned as a requirement for this repository, necessary functions have been copied to local scripts
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<summary>Update copyright to 2022 elaubsch (14)</summary>

Update copyright year to 2022 and some minor dependency fixes
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🚀 Features

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<summary>Rename SpotDetection application to Polaris elaubsch (13)</summary>


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<summary>Repo management elaubsch (8)</summary>

Added Dataset objects to load data needed to run example notebooks
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<summary>Model dev elaubsch (6)</summary>

Adding singleplex code and notebook
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<summary>Model dev elaubsch (3)</summary>


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<summary>Update Dockerfile elaubsch (2)</summary>


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🐛 Bug Fixes

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<summary>Update Dockerfile, fix imports, and lint docstrings. willgraf (9)</summary>

- Update Dockerfile to use published `deepcell-tf` images.
- Change `opencv-python` to `opencv-python-headless` for a smaller, lighter installation (Fixes 4)
- Lint a bunch of docstrings
- Fix import ordering with `isort`
- Ignore `training.py` from coverage reports.
- Add `.idea` directory to `.gitignore` and remove it from the project.

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Existing issues:
- `rn_classification_head` uses imports that don't exist
- `gene_counts_DBSCAN`: `DBSCAN` is never imported

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🧰 Maintenance

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<summary>Update README badges and other minor touchups for first release. willgraf (12)</summary>

- update link for coverage badge
- add license badge
- updates `.gitattributes` to ignore the Jupyter notebooks from code statistics.
- replace space with `-` in package name
- fix python_requires definition in setup.py
- publish docker images on release.
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<summary>Remove unused code and files elaubsch (11)</summary>

Fixes 10 and removes unnecessary data directory.
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<summary>Repo management elaubsch (7)</summary>


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📚️ Documentation

<details>
<summary>Update Dockerfile, fix imports, and lint docstrings. willgraf (9)</summary>

- Update Dockerfile to use published `deepcell-tf` images.
- Change `opencv-python` to `opencv-python-headless` for a smaller, lighter installation (Fixes 4)
- Lint a bunch of docstrings
- Fix import ordering with `isort`
- Ignore `training.py` from coverage reports.
- Add `.idea` directory to `.gitignore` and remove it from the project.

---

Existing issues:
- `rn_classification_head` uses imports that don't exist
- `gene_counts_DBSCAN`: `DBSCAN` is never imported

</details>