Overview of potential improvements, goals, issues and other thoughts worth keeping in the repository repositor y
Overview of potential improvements, goals, issues and other thoughts worth keeping in the repository. In general, it is things that the original developer would have liked to implement had there been enough time.
* General goals
- Simplify code base
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@@ -11,18 +11,19 @@ Overview of potential improvements, goals, issues and other thoughts worth keepi
- (Relevant to BABY): Migrate aliby-baby to Pytorch from Keras. Immediately after upgrade h5py to the latest version (we are stuck in 2.10.0 due to Keras).
* Long-term tasks
- Split segmentation, tracking and lineage into independent Steps
- Implement the pipeline as an acyclic graph
- Isolate lineage and tracking into a section of aliby or an independent package
- Abstract cells into "ROIs" or "Outlines"
- Abstract lineage into "Outline relationships" (this may help study cell-to-cell interactions in the future)
- Support external segmentation/tracking/lineage/processing tools
- Make live cell processing great again!
- Add support to next generation microscopy formats.
* Potential features
- Flat field correction
- Flat field correction (requires research on what is the best way to do it)
- Support for monotiles (e.g., agarose pads)
- Support the user providing location of tiles (could be a GUI)
- Support the user providing location of tiles (could be a GUI in which the user selects a region)
- Support multiple neural networks (e.g., vacuole/nucleus in adition to cell segmentation)
* Potential CLI(+matplotlib) interfaces
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@@ -71,6 +72,7 @@ Pipeline is in dire need of refactoring, as it coordinates too many things. The
- Pandas -> Polars: Reconsider after pandas 2.0; they will become interoperable
- awkward arrays: Better way to represent
- h5py -> zarr: OME-ZARR format is out now, it is possible that the field will move in that direction. This would also make us being stuck in h5py 2.10.0 less egregious.
- Use CellACDC's work on producing a common interface to access a multitude of segmentation algorithms.
* Secrets in the code
- As aliby is adapted to future Python versions, keep up with the "FUTURE" statements that enunciate how code can be improved in new python version
