21. Release notes¶

21.1. Developer version¶

21.2. Version 2.3.12¶

fusion.py: correction for hierarchical fusion. There was an error in the choice of the reference image for the final resampling
enrich documentation

21.3. Version 2.3.11¶

mars.py: correction for images with more than 32767 labels/cells

21.4. Version 2.3.10¶

ioproperties.py: adjust verboseness level
diagnosis.py: enrich and adjust diagnosis outputs; adjust verboseness level

21.5. Version 2.3.9¶

ioproperties.py: update some property/morphonet file names

21.6. Version 2.3.8¶

manualcorrection.py: bug corrections in change file reading (case of time interval)

21.7. Version 2.3.7¶

Update documentation
Update morphonet related property names issued from naming propagation (ascidian package)
- naming_agreement:
- naming_score:
- naming_unequal_division_flag:
- renaming_flag:
Correct _erode_cell() in astec.py. scipy.ndimage.find_objects() no more accepts ndarray of booleans (issued from binary_erosion()) as input

21.8. Version 2.3.6¶

update documentation

21.9. Version 2.3.5¶

allows backward segmentation propagation with delta_time_point = -1. It assumes propagation_strategy ='seeds_from_previous_segmentation'. In other words, cell division are not identified, and cell fusion are not done. Last, it may cause cells to appear in the lineage (if a cell disappear in the backward propagation).

21.10. Version 2.3.4¶

refactoring properties mangement; better management of IO properties
correct numpy induced behavior (np.frombuffer yields a non-writable/mutable numpy array)

21.11. Version 2.3.3¶

remove calls to numpy.fromstring, deprecated from numpy 1.14, yields error from numpy 2.3.0 (see Numpy 2.3.0 release notes).
remove python 3.9 from build (see status of Python versions).

21.12. Version 2.3.2¶

add python 3.12 to build

21.13. Version 2.3.1¶

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

21.14. 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

21.15. 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

21.16. Version 2.2.12¶

update CI files (remove python 3.7)

21.17. Version 2.2.11¶

fixes yaml files

21.18. 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

21.19. Version 2.2.9¶

fusion: change default weighting scheme
enrich morphonet outputs

21.20. Version 2.2.8¶

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

21.21. 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.

21.22. 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

21.23. Version 2.2.5¶

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

21.24. Version 2.2.4¶

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

21.25. Version 2.2.3¶

Enrich drift computation: score upper threshold; early stop at first iteration
Correct I/O of tissue map fate
Enrich documentation

21.26. Version 2.2.2¶

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

21.27. Version 2.2.1¶

add a missing __init__.py

21.28. 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

21.29. 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

21.30. 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

21.31. Version 2.1.9¶

manualcorrection: corrects the correction files; allows for restarting
enrich morphonet file writing: enables more properties to be written out

21.32. 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.
Note from 16 June 2026, after reinstalling the 2.1.8 version.
```
conda create -n astec-tmp
conda activate astec-tmp
conda install astec=2.1.8 -c morpheme -c conda-forge
```
Because of the evolution of underlying C codes (default parameters of mc-extractMIPembryo), image cropping will yield an error (test with version 1.7.7 of vt, I do not conduct investigations to identify an error-free version of vt), thus desactivating cropping is mandatory.
```
raw_crop = False
fusion_cropping = False
```

21.33. Version 2.1.7¶

manual correction: correct the propagation of newly created divisions

21.34. Version 2.1.6¶

correct inrimage IO

21.35. 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)

21.36. Version 2.1.4¶

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

21.37. 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

21.38. Version 2.1.2¶

improve name comparison behavior
correct bad behavior of astec_astec when restarting the computation

21.39. Version 2.1.1¶

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

21.40. Version 2.1.0¶

documentation updating
pursued code splitting into astec/ascidian repositories
documentation splitting into astec/ascidian

21.41. 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)

21.42. 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

21.43. Version 1.7.1¶

Write embryo as a graph
Computation of symmetric cells
Allows to extract any XZ-section(s) at the fusion stage.

21.44. 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.

21.45. Version 1.6.2¶

Release notes not available