Optimization backend — napari_easytrack.analysis.optim_backend

Backend for preparing napari Labels layers for btrack optimization.

This module handles: - Converting napari Labels layers to CTC format - Creating temporary directory structures - Preparing ground truth data (filling gaps, no divisions) - Creating dataset objects for optimization

napari_easytrack.analysis.optim_backend._fill_gaps_in_segmentation(segmentation)

Fill temporal gaps in segmentation with placeholder pixels.

For each label with gaps, place a single placeholder pixel at the centroid of its last known position. This maintains track continuity for CTC format without requiring the full mask.

Parameters:

segmentation – 3D array (T, Y, X) with integer labels

Returns:

3D array with gaps filled