llwiggins

Improved binary masking to retain details from grains

1

Current binary masking in TopoStats causes loss of fine details from the original grain (such as holes or merging of close strands) and this causes downstream issues for detection of...

### Is your feature request related to a problem? The current default configuration file format contains a range of parameters that may not be suitable or relevant for certain samples...

Changes to test files from PR #876

5

This PR isolates the changes to tests made in PR #876 so that they can be reviewed/amended separately to the changes to the main tracing code. Suggestions in the comments...

Following discussion at the TopoStats day, we need to add documentation for the new multiclass functionality. This will include documenting the new structure of all_statistics.csv, which now contains "class_number" and...

[Bug]: "basename" error when image set = 'core' + additional sets

1

### Checklist - [x] Find the offending file in the output. If processing halts, re-run analysis with `topostats --core 1 process`. - [x] Describe the bug. - [x] Include the...