Question 1

How do I set up PAQUO with a custom QuPath installation?

Accepted Answer

Use the `paquo get_qupath` command to download a specific version to a desired path, then configure it via environment variables or a .paquo.toml file as described in the README. This allows precise control over the QuPath version used with PAQUO.

Question 2

Can PAQUO export annotations to common formats like GeoJSON or CSV?

Accepted Answer

PAQUO supports adding, modifying, and exporting annotations, but specific export formats depend on QuPath's underlying capabilities. Check the documentation for details on how to programmatically handle annotations and leverage QuPath's export features.

Question 3

PAQUO vs writing QuPath scripts in Groovy: which is better for automation?

Accepted Answer

PAQUO is ideal for Python-centric workflows, offering better integration with libraries like scikit-learn or TensorFlow. Groovy scripts are native to QuPath and might be simpler for basic tasks, but PAQUO provides a more pythonic and maintainable approach for complex, data-heavy pipelines.

Question 4

How to handle large whole slide images efficiently with PAQUO?

Accepted Answer

PAQUO leverages QuPath's backend for image handling, so performance is similar to using QuPath directly. For efficiency, use batch processing methods and optimize annotation retrieval as documented, but be mindful of memory usage with very large datasets.

Question 5

Is PAQUO suitable for real-time analysis in clinical settings?

Accepted Answer

PAQUO is designed for programmatic access and batch processing, not real-time interaction. For clinical use, ensure stable, offline setups and test workflows thoroughly, as latency might be a concern in automated analyses.

Question 6

How to contribute to PAQUO development?

Accepted Answer

Follow the contributing guidelines in the README: use pep-8 with 120-character lines, adopt numpy docstrings, and submit pull requests via GitHub. Set up the development environment using conda and the provided configuration files.

PAQUO

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