Candace Liu

Allow for a subset of FOVs in k-means clustering notebook

1

**Describe the bug** There is no option to choose a subset of FOVs in the k-means neighborhood notebook. Discovered by Avery. Currently, the notebook gets all FOVs in the cell...

Error when starting Docker with update flag

1

*Please refer to our [FAQ](https://ark-analysis.readthedocs.io/en/latest/_rtd/faq.html) and look at our [known issues](https://github.com/angelolab/ark-analysis/issues) before opening a bug report.* **Describe the bug** When I do `start_docker.sh ---update`, I get an error saying that...

Adding cropping utility notebook for Pixie

2

**Is your feature request related to a problem? Please describe.** For very large whole slide images, even loading one image (all the channels) can cause memory errors. Here, the memory...

**Describe the bug** When "population_cell_mask.csv" is created in the Mantis directory, the unassigned cell ID is not included, which results in a cell population confusingly labelled as "Imported Selection #"...