20. Release notes

20.1. Developer version

20.2. Version 2.3.3

20.3. Version 2.3.2

  • add python 3.12 to build

20.4. Version 2.3.1

  • add name_choice_score (score computed when ascidian names are propagated) to embryo properties

20.5. Version 2.3.0

  • change management of auxiliary and transformation directories

  • allows to keep auxiliary directories with parameter keep_temporary_files

  • refactoring of fusion

  • fusion: add ‘border’ cropping method for acquisition with missing slices

  • fusion: initialize translation with object center of mass

  • fusion: enable hierachical fusion for drift compensated fusion

20.6. Version 2.2.13

  • correct incoherencies between diagnosis.py and keydictionary in ioproperties.py.

  • fusion: correction of T_init transformation in _fusion_process(). Crucial when reference image is not the left camera of stack #0, especially when cropping is disabled.

  • migration numpy.tostring() -> numpy.tobytes() for images (metaimage, inrimage) I/O

20.7. Version 2.2.12

  • update CI files (remove python 3.7)

20.8. Version 2.2.11

  • fixes yaml files

20.9. Version 2.2.10

  • enrich properties. Add embryo-related properties as weel as time alignment properties

  • fusion: better management of acquisition file names

  • manualcorrection: enrich tests

20.10. Version 2.2.9

  • fusion: change default weighting scheme

  • enrich morphonet outputs

20.11. Version 2.2.8

  • fusion: correction of guignard’s weight computation wrt numpy2.x releases.

20.12. Version 2.2.7

  • manualcorrection: code refactoring; try to keep the same cell labels when propagating a new/created division; if the creation of a new division is not possible, allow to postpone it for a few time points.

20.13. Version 2.2.6

  • Mars: sort seed labels wrt component size, to handle more efficiently the 3 seeds case in astec

  • Astec: indicate computation time details

  • Post-correction: add tests

20.14. Version 2.2.5

  • I/O for morphonet: cell map was not written properly.

20.15. Version 2.2.4

  • Post-correction: property name uniformisation was not propagated properly.

20.16. Version 2.2.3

  • Enrich drift computation: score upper threshold; early stop at first iteration

  • Correct I/O of tissue map fate

  • Enrich documentation

20.17. Version 2.2.2

  • Correction of extrapolation of weight image for drift-based fusion.

20.18. Version 2.2.1

  • add a missing __init__.py

20.19. Version 2.2.0

  • introduce drift estimation within a fused time series, and between corresponding images of two fused time series

  • fusion: introduce drift-compensated fusion

  • fusion: generalize transformation saving for both drift-compensated fusion and hierarchical fusion

20.20. Version 2.1.11

  • I/O: correct conversion procedures (they did not work properly)

  • I/O: correct tulip file writing (was not compatible with new properties definition)

  • astec_embryoproperties: do not write tulip file anymore

20.21. Version 2.1.10

  • I/O: conversion procedures, to avoir writing numpy types in output files for backward compatibility with older versions of numpy/python. It seems that some “equivalence” with raw python type are now lost (see NEP 40 — Legacy datatype implementation in NumPy and related NEPs)

  • fusion: transformations are saved in a separate directory

  • fusion: corrections to fuse with a subset of views

20.22. Version 2.1.9

  • manualcorrection: corrects the correction files; allows for restarting

  • enrich morphonet file writing: enables more properties to be written out

20.23. Version 2.1.8

  • manual correction: correct potential overflow problem (see NEP 50 — Promotion rules for Python scalars)

    • python 3.9: (np.uint16) * (int) -> (np.int64)

    • python 3.11: (np.uint16) * (int) -> (np.uint16)

    This may cause similar troubles in the future.

20.24. Version 2.1.7

  • manual correction: correct the propagation of newly created divisions

20.25. Version 2.1.6

  • correct inrimage IO

20.26. Version 2.1.5

  • allows to change for the images kept for fusion, while keeping the same point of view fusion (ie from the same camera)

20.27. Version 2.1.4

  • correct bad behavior for direct fusion when the left camera image from stack #0 is not present

20.28. Version 2.1.3

  • allows to have new labels when dividing cell in astec_manualcorrection, and mother cell label is not reused for a daughter cell

  • update documentation

20.29. Version 2.1.2

  • improve name comparison behavior

  • correct bad behavior of astec_astec when restarting the computation

20.30. Version 2.1.1

  • documentation updating

  • correct bad behavior of ReconstructionParameters.is_normalization_equal() when intensity_transformation is None

20.31. Version 2.1.0

  • documentation updating

  • pursued code splitting into astec/ascidian repositories

  • documentation splitting into astec/ascidian

20.32. Version 2.0.0

  • moved ascidian algorithms/binaries to a dedicated git repository

  • replaced pkg_resources by importlib.metadata

  • added test infrastructure

  • refactor setup.py (adding setup.cfg)

20.33. Version 1.7.2

  • Review of conda env files (*.yaml) and build

  • Use builtin which command instead of external process to launch astec binaries

  • Removed obsolete python-3.7 builds, added python-3.10 and python-3.11

20.34. Version 1.7.1

  • Write embryo as a graph

  • Computation of symmetric cells

  • Allows to extract any XZ-section(s) at the fusion stage.

20.35. Version 1.7.0

  • Fusion of one single time point: allows longer suffixes than recognized image extensions.

  • Pre-processed images (see Image preprocessing) are no more stored into .../SEG/SEG_XXX/RECONSTRUCTION/ but in their own directories .../REC-MEMBRANE/REC_XXX/ and/or .../REC-SEED/REC_XXX/ and/or .../REC-MORPHOSNAKE/REC_XXX/. They can be transformed by the motion compensation stage (see astec_intraregistration).

  • User-provided outer contour images (to be stored in .../CONTOUR_/CONTOUR_XXX/) can be used in image pre-processing (see Image preprocessing)

  • Properties computation (see astec_embryoproperties) computes cell lineage when it is not available.

20.36. Version 1.6.2

Release notes not available