The latest release of Ark Analysis mainly focused on removing `R` dependencies. In order to do so, we have created a small version of FlowSOM over at [angelolab/pyFlowSOM](https://github.com/angelolab/pyFlowSOM).
Other major features include more example datasets, and performance improvements.
Notable bug fixes include removing duplicate FOV loading and making the mantis file extension independent from the segmentation file extension.
Documentation improvements include improved git cloning / installation instructions, and ejecting an imposter Pixie author (āļ).
đ Features
- Load Utils - Expanding Acceptable File Types srivarra ([878](https://github.com/angelolab/ark-analysis/pull/878))
- Example Dataset - Cropped FOV 0 srivarra ([859](https://github.com/angelolab/ark-analysis/pull/859))
- Integrate `pyFlowSOM` with Pixie alex-l-kong ([863](https://github.com/angelolab/ark-analysis/pull/863))
- Clean up Pixie pipeline alex-l-kong ([856](https://github.com/angelolab/ark-analysis/pull/856))
- Make `segmentation_dir` definition more clear for pixel and cell clustering processes alex-l-kong ([855](https://github.com/angelolab/ark-analysis/pull/855))
- Additional Input Validation srivarra ([841](https://github.com/angelolab/ark-analysis/pull/841))
- Add native Python consensus clustering process alex-l-kong ([839](https://github.com/angelolab/ark-analysis/pull/839))
- Subset pixel channel averaging to remove bottleneck alex-l-kong ([823](https://github.com/angelolab/ark-analysis/pull/823))
- Example Dataset - Spatial Datasets srivarra ([832](https://github.com/angelolab/ark-analysis/pull/832))
- Use `random_state` parameter in KMeans clustering for reproducibility alex-l-kong ([834](https://github.com/angelolab/ark-analysis/pull/834))
- Added Parameter for Seg Mask Suffix for Mantis srivarra ([828](https://github.com/angelolab/ark-analysis/pull/828))
- Rename `_feature_0` to `_whole_cell` and `_feature_1` to `_nuclear` alex-l-kong ([786](https://github.com/angelolab/ark-analysis/pull/786))
- Refactor distance matrix saving alex-l-kong ([803](https://github.com/angelolab/ark-analysis/pull/803))
đ Bug Fixes
- Make Mantis mask file extension independent from segmentation file extension alex-l-kong ([870](https://github.com/angelolab/ark-analysis/pull/870))
- `seg_suffix` Requires Explicit File Extension srivarra ([848](https://github.com/angelolab/ark-analysis/pull/848))
- Fix neighborhood matrix indexing due to subsetting alex-l-kong ([824](https://github.com/angelolab/ark-analysis/pull/824))
- Removed duplicate mantis fov loading srivarra ([838](https://github.com/angelolab/ark-analysis/pull/838))
- Don't load the pixel, cell, and neighborhood FOVs in batches for mask generation alex-l-kong ([816](https://github.com/angelolab/ark-analysis/pull/816))
- Ensure neighborhood inertia and silhouette score generation works with varying `min_k` alex-l-kong ([820](https://github.com/angelolab/ark-analysis/pull/820))
- Travis patchelf pypi\_deploy Updates srivarra ([805](https://github.com/angelolab/ark-analysis/pull/805))
𧰠Maintenance
- Next Release v0.5.0 srivarra ([877](https://github.com/angelolab/ark-analysis/pull/877))
đī¸ Documentation
- Tagged Installation Instructions srivarra ([840](https://github.com/angelolab/ark-analysis/pull/840))
- Example Dataset - Adding more info to Overwrite Existing srivarra ([826](https://github.com/angelolab/ark-analysis/pull/826))
- Fix Pixie authorship ngreenwald ([813](https://github.com/angelolab/ark-analysis/pull/813))
- Cell Table Assumptions srivarra ([808](https://github.com/angelolab/ark-analysis/pull/808))
alex-l-kong, ngreenwald and srivarra