Unify pipelines #3
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If magnification differs from the default, re-scale tile_size and parameters for segmenting traps.
Removed OMERO_channels and spatial_positions from pipeline.py
Works for legacy log files only; no examples yet of new log file.
time_settings/ntimepoints should be int not List[int].
Necessary to calculate the noise for the mother and bud.
channels can can be specified in the general dict, overriding OMERO
Many improvements needed for CellProfiler features compatibility - functools used to load functions dynamically - support selecting channels numerically - remove custom functions (these were never used) - support metrics that return multiple results as a dictionary
Missing brackets were giving non-monotonic time values.
Fixed signal to work on old legacy h5 files, where channels are stored differently.
refactor: replace bottleneck with numpy (bn->np)
[refactor]: Refactored segmenter and tracker dispatch functions to improve compatibility with Baby and Cellpose models, and added monkey patching for segmentation class to return masks only.
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Closed in favour of #1 |
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This PR enables the usage of the same pipeline for yeast and arbitrary experiments. The additional features added to aliby are: