Basic Tutorial for Users New to Surface Morphometrics

[quental96]

For users with limited prior knowledge of surface morphometrics, using the surface-morphometrics-gui with a cryo-ET reconstruction and segmentation is not straightforward.

To make the tool more accessible, I’d like to request a basic tutorial that assumes little to no prior knowledge of surface morphometrics. Ideally, this tutorial would include:

• A step-by-step guide to setting up and running the pipeline with example sample data.
• Clear explanations of key concepts (e.g., what surface morphometrics entails, how segmentations are processed, and what the output files mean).
• Guidance on preparing input files (e.g., cryo-ET reconstructions and segmentations) and configuring the config.yml file.
• Troubleshooting tips for common issues.

Thanks, I’m happy to provide more details about my specific challenges if needed!

[bbarad]

Thanks Quentin! This is on the roadmap currently and I've assigned both myself and hemanth to it. For point 2, we have relatively extensive descriptions of files on the surface morphometrics git - which will continue to be the primary home for future morphometrics development. Are you finding that documentation insufficient? Or are you hoping to get it duplicated here?

[hemanthkapa]

@quental96 When you have a chance, could you please go through the tutorial at GUI Documentation, run the full pipeline on the example data, and let us know if you encounter any issues at any step?
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All quantification-related details are documented here: https://github.com/GrotjahnLab/surface_morphometrics/blob/main/quantifications_documentation.md.