Ark-analysis

🚀 Features

- Kmeans notebook cleanup camisowers ([946](https://github.com/angelolab/ark-analysis/pull/946))

🐛 Bug Fixes

- For `docker.yml` checkout the tag used in `pypi_publish` srivarra ([948](https://github.com/angelolab/ark-analysis/pull/948))
- Fix zero pixels cliu72 ([956](https://github.com/angelolab/ark-analysis/pull/956))

🧰 Maintenance

- Pinned `ipywidgets` srivarra ([953](https://github.com/angelolab/ark-analysis/pull/953))

📚️ Documentation

- Next Release - v0.6.2 srivarra ([959](https://github.com/angelolab/ark-analysis/pull/959))
camisowers, cliu72 and srivarra

- Change os.rename to shutil.move cliu72 ([951](https://github.com/angelolab/ark-analysis/pull/951))
- Deprecate use of cluster, metacluster, and mc\_name outside of remapping alex-l-kong ([950](https://github.com/angelolab/ark-analysis/pull/950))
alex-l-kong and cliu72

This latest release contains the revised Pixie pixel and cell clustering algorithm.


Pixie Paper Implementation
- Next Release - v0.6.0 alex-l-kong ([945](https://github.com/angelolab/ark-analysis/pull/945))
- Temporarily remove pixel preprocessing normalization for Candace's paper alex-l-kong ([913](https://github.com/angelolab/ark-analysis/pull/913))
- Pixie notebook text changes cliu72 ([942](https://github.com/angelolab/ark-analysis/pull/942))

🚀 Features

- Refactor Pixie modules alex-l-kong ([940](https://github.com/angelolab/ark-analysis/pull/940))
- Split spatial analysis module camisowers ([938](https://github.com/angelolab/ark-analysis/pull/938))
- Ark Refactor srivarra ([935](https://github.com/angelolab/ark-analysis/pull/935))
- Github Actions - Merge Queue srivarra ([932](https://github.com/angelolab/ark-analysis/pull/932))
- Sunset Pairwise Distance Notebook srivarra ([929](https://github.com/angelolab/ark-analysis/pull/929))
- Mixing score camisowers ([836](https://github.com/angelolab/ark-analysis/pull/836))
- Integrate existing Pixie cell clustering process with generic cell clustering process alex-l-kong ([885](https://github.com/angelolab/ark-analysis/pull/885))

🐛 Bug Fixes

- Add a hidden parameter to overwrite certain portions of the pipeline alex-l-kong ([914](https://github.com/angelolab/ark-analysis/pull/914))

🧰 Maintenance

- :arrow\_up: Bump release-drafter/release-drafter from 5.20.1 to 5.22.0 dependabot ([916](https://github.com/angelolab/ark-analysis/pull/916))

📚️ Documentation

- Make sure `data_types.md` displays newlines alex-l-kong ([930](https://github.com/angelolab/ark-analysis/pull/930))
alex-l-kong, camisowers, cliu72, dependabot, dependabot[bot] and srivarra

The latest version of ark-analysis include many improvements to the Pixie pipeline such as allowing the ability to rerun SOM training, and allowing users to skip many of the `regionprops` fields which are computationally expensive to generate.

🚀 Features

- Remove deterministic argument from `som` function in `pyFlowSOM` alex-l-kong ([893](https://github.com/angelolab/ark-analysis/pull/893))
- GitHub Actions srivarra ([895](https://github.com/angelolab/ark-analysis/pull/895))
- Ensure `cluster_helpers.PixelSOMCluster` receives the `fovs` argument alex-l-kong ([905](https://github.com/angelolab/ark-analysis/pull/905))
- Allow user to set an explicit skip flag for custom regionprops and marker extraction functionality in notebook 1 alex-l-kong ([897](https://github.com/angelolab/ark-analysis/pull/897))

🐛 Bug Fixes

- Turn off minor ticks for pixel and cell cluster overlay colorbar alex-l-kong ([912](https://github.com/angelolab/ark-analysis/pull/912))
- Remove zero column pixel cluster columns from cell clustering pipeline alex-l-kong ([884](https://github.com/angelolab/ark-analysis/pull/884))
- Ensure z-score slider adjusts colorbar range when changed alex-l-kong ([904](https://github.com/angelolab/ark-analysis/pull/904))
- Ensure pixel SOM training reruns if new markers specified alex-l-kong ([903](https://github.com/angelolab/ark-analysis/pull/903))
- Correct 99.9% normalization to 100% normalization for "many-zero" columns alex-l-kong ([894](https://github.com/angelolab/ark-analysis/pull/894))

🧰 Maintenance

- Bump ipython from 8.4.0 to 8.10.0 in /docs dependabot ([908](https://github.com/angelolab/ark-analysis/pull/908))
alex-l-kong, dependabot, and srivarra

This latest version of Ark Analysis includes moving shared utility functions across [angelolab/ark-analysis](https://github.com/angelolab/ark-analysis), [angelolab/toffy](https://github.com/angelolab/toffy), and [angelolab/mibi-bin-tools](https://github.com/angelolab/mibi-bin-tools) to their new home in [angelolab/tmi](https://github.com/angelolab/tmi). In addition some other updates include the ability to convert to and from OME-TIFFs and adding `inverse` as a custom method to allow for more recent versions of `matplotlib`. In addition a majority of the requirements were adjusted to be less strict.

🚀 Features

- Added `nuc_seg_suffix` for `filter_with_nuclear_mask` srivarra ([879](https://github.com/angelolab/ark-analysis/pull/879))
- Add `inverse` method to `ZScoreNorm` to integrate with current `matplotlib` alex-l-kong ([871](https://github.com/angelolab/ark-analysis/pull/871))
- OME-TIFF Read / Write srivarra ([819](https://github.com/angelolab/ark-analysis/pull/819))
- Load Utils - Expanding Acceptable File Types srivarra ([878](https://github.com/angelolab/ark-analysis/pull/878))

🧰 Maintenance

- Next Release v0.5.1 srivarra ([889](https://github.com/angelolab/ark-analysis/pull/889))
- Adding TMI srivarra ([825](https://github.com/angelolab/ark-analysis/pull/825))
alex-l-kong and srivarra