Skip to content

Release Notes: v0.7.0 - 12/06/23
Compare
Choose a tag to compare
@github-actions github-actions released this 06 Dec 22:50
· 25 commits to refs/heads/main since this release
v0.7.0
11de0b0
This commit was created on GitHub.com and signed with GitHub’s verified signature. The key has expired.
GPG key ID: 4AEE18F83AFDEB23
Expired
Learn about vigilant mode.

You may download the latest release with:

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

🐛 Bug Fixes

  • Make sure overwrite functionality for pixel clustering propagates into helper functions @alex-l-kong (#1058)
  • Adjustments to Mass Plotting Workflow @srivarra (#1067)

🧰 Maintenance

Contributors

srivarra, alex-l-kong, and camisowers
Assets 2
Loading