You may download the latest release with:
shell
git clone -b v0.7.0 https://github.com/angelolab/ark-analysis.git
What's new?
ezSegmenter support
Starting with `v0.7.0`, support for ezSegmenter masks has been added. The Jupyter notebook for this can be found in `templates/ez_segmenter.ipynb`.
**Please note that this feature may experience frequent updates. Updates may be required for Pixie integration and further downstream analysis.**
Updated mask visualization
`v0.7.0` introduces significant updates to the visualization process of masks. Shared functionality (ex. colormap generation, plotting clusters) has been abstracted away into internal functions and dataclasses. Erosion support has been added to decrease the size of the borders between cells, and `interpolation` has been turned off to prevent interpolation of cell borders.
In the past, users reported problems of incorrectly sorted colors in the cmap file. This has been addressed. Additionally, users may now specify a `dpi` and `fig_size`, as well as multi-compatibility support for saving `matplotlib` figures.
Mantis saving updates
Starting with `v0.7.0`, only a single top-level Mantis directory will be created, and support for subfolders (via the `img_sub_folder` param) has been added.
Pixie updates
During Pixie SOM assignment for pixel clustering, some users reported it taking unusually long. This was caused by the batch size for cluster assignment being too small. With this update, the batch size can now be set by the user to speed the process up, and defaults to a more reasonable value.
Additionally, in some Pixie applications, certain cells won't have any pixel clusters associated with them. These cells now get dropped prior to running the cell clustering portion.
Previously, the `overwrite` flag did not work for certain functions because it wasn't propagated correctly. This has also been addressed by `v0.7.0`.
Versioning Updates
`ark-analysis` now uses `scikit-image==0.19.3` and `alpineer==v0.1.10`.
Licensing
`ark-analysis` has migrated from the Modified Apache 2.0 License to the MIT license. This was made due to the cell segmentation algorithm, Mesmer, having a more restrictive license.
---
🚀 Features
- ezSegmentation srivarra ([958](https://github.com/angelolab/ark-analysis/pull/958))
- Mask Generation Refactoring srivarra ([1030](https://github.com/angelolab/ark-analysis/pull/1030))
- Include `img_sub_folder` as parameter in Mantis calls alex-l-kong ([1050](https://github.com/angelolab/ark-analysis/pull/1050))
- Remove cells that don't have any pixel clusters expressed prior to Pixie alex-l-kong ([1051](https://github.com/angelolab/ark-analysis/pull/1051))
- Single mantis directory camisowers ([1061](https://github.com/angelolab/ark-analysis/pull/1061))
- Allow user to dynamically set batch size of pixel SOM assignments alex-l-kong ([1069](https://github.com/angelolab/ark-analysis/pull/1069))
🐛 Bug Fixes
- Make sure overwrite functionality for pixel clustering propagates into helper functions alex-l-kong ([1058](https://github.com/angelolab/ark-analysis/pull/1058))
- Adjustments to Mass Plotting Workflow srivarra ([1067](https://github.com/angelolab/ark-analysis/pull/1067))
🧰 Maintenance
- Update README from v0.6.5 to v0.6.6 alex-l-kong ([1048](https://github.com/angelolab/ark-analysis/pull/1048))
- Update HuggingFace to main alex-l-kong ([1053](https://github.com/angelolab/ark-analysis/pull/1053))
- Pin to scikit-image to v0.19.3 camisowers ([1060](https://github.com/angelolab/ark-analysis/pull/1060))
- Alpineer v0.1.10 camisowers ([1057](https://github.com/angelolab/ark-analysis/pull/1057))
alex-l-kong, camisowers and srivarra
- MIT license srivarra ([1080](https://github.com/angelolab/ark-analysis/pull/1080))
- Bump to v0.7.0 alex-l-kong ([1093](https://github.com/angelolab/ark-analysis/pull/1093))