You may download the latest release with:
shell
git clone -b v0.6.4 https://github.com/angelolab/ark-analysis.git
What's new in Ark Analysis?
Python Compatibility
**The minimum supported Python is now version 3.9.**
We have an Anaconda `environment.yml` file so users do not need to use the Docker Image if they wish. This will create a Python 3.11 environment. Here is how to use it.
shell
cd ark-analysis
conda env create -f environment.yml
conda activate ark_env
Pixie Improvements
Pixie now features improved fallback protection during the clustering step, preventing duplicate cluster names and the ability to save cluster masks as colored images.
K-Means Improvements
K-means now has improved plots, default parameters, and has received minor improvements.
Cell Neighbors Analysis
We have a new analysis pipeline containing two independent features: analyzing the homogeneity/diversity of the neighbors surrounding each of the cells and analyzing the proximity/distance between cell phenotypes in samples.
Fiber Segmentation
Fiber segmentation acquires more properties and has received optimizations regarding extracting distinct fiber objects.
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🚀 Features
- Add progress bars in Cell Neighbors Analysis notebook camisowers ([1022](https://github.com/angelolab/ark-analysis/pull/1022))
- Drop 3rd dimension in segmentation masks camisowers ([1018](https://github.com/angelolab/ark-analysis/pull/1018))
- Mixing score default thresholds camisowers ([1015](https://github.com/angelolab/ark-analysis/pull/1015))
- Include all fiber properties in stats generation camisowers ([1014](https://github.com/angelolab/ark-analysis/pull/1014))
- Save Colored Pixie Masks srivarra ([1007](https://github.com/angelolab/ark-analysis/pull/1007))
- Initial commit of phenotype by neighbour analysis khoulahan ([988](https://github.com/angelolab/ark-analysis/pull/988))
- Cell neighborhood diversity camisowers ([989](https://github.com/angelolab/ark-analysis/pull/989))
- Downstream fiber analysis updates camisowers ([974](https://github.com/angelolab/ark-analysis/pull/974))
🐛 Bug Fixes
- Maximize Available GitHub Storage Space srivarra ([1025](https://github.com/angelolab/ark-analysis/pull/1025))
- Allow FOVs to contain various maximum clusters srivarra ([1021](https://github.com/angelolab/ark-analysis/pull/1021))
- Pixie percentile saving camisowers ([1020](https://github.com/angelolab/ark-analysis/pull/1020))
- Fix error from zero fibers in an image camisowers ([1011](https://github.com/angelolab/ark-analysis/pull/1011))
- Fix segmentation rescale\_factor camisowers ([1008](https://github.com/angelolab/ark-analysis/pull/1008))
- Add fallback protection to Pixie cell clustering alex-l-kong ([999](https://github.com/angelolab/ark-analysis/pull/999))
- Prevent duplicate renamed metaclusters in Pixie remapping alex-l-kong ([993](https://github.com/angelolab/ark-analysis/pull/993))
- Pixel Clustering - Run without segmentaiton files srivarra ([998](https://github.com/angelolab/ark-analysis/pull/998))
- Mantis Directory with no segmentation files srivarra ([994](https://github.com/angelolab/ark-analysis/pull/994))
- Extended Attributes on macOS srivarra ([973](https://github.com/angelolab/ark-analysis/pull/973))
- Mutiple tiled stitching tweaks camisowers ([981](https://github.com/angelolab/ark-analysis/pull/981))
- Fix pixel and cell cluster mask generation index for rectangular images alex-l-kong ([983](https://github.com/angelolab/ark-analysis/pull/983))
- Kmeans plotting cell border fix camisowers ([978](https://github.com/angelolab/ark-analysis/pull/978))
- Set Kmeans parameter to prior default camisowers ([977](https://github.com/angelolab/ark-analysis/pull/977))
- Kmeans notebook minor fixes camisowers ([966](https://github.com/angelolab/ark-analysis/pull/966))
- Stitching Large Images srivarra ([939](https://github.com/angelolab/ark-analysis/pull/939))
🧰 Maintenance
- GitHub Actions, Python 3.9+ Support, Jupyterlab Extensions srivarra ([991](https://github.com/angelolab/ark-analysis/pull/991))
- Added Conda environment file srivarra ([1006](https://github.com/angelolab/ark-analysis/pull/1006))
- Skip spatial LDA visualization tests due to Numpy error alex-l-kong ([984](https://github.com/angelolab/ark-analysis/pull/984))
alex-l-kong, camisowers, khoulahan and srivarra