[3.4.1] - 2021-10-18

!DISCLAIMER!

1. This package is not currently maintained. A new package that will include all pygpseq features is being implemented at radiantkit.
2. This package has been developed and tested ONLY for Python3.6, which will reach its end of life On December 23rd, 2021.
3. Versions 3.4.* of this package only change package dependencies to fix an issue due to incorrect dependency declaration.

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This release fixes dependency conflicts that were caused by an improper dependency setup.
As such, no functionality is changed. The same can be said for the way a user interacts with the package.
The main change is related to the new dependency manager: Poetry.

We would still recommend using our new radiantkit package instead.
Use pygpseq==3.3.6 only if strictly necessary and at your own risk, as this package is not currently maintained.

Changed

• Now supporting specifically only Python 3.6.
• Moved scripts to sub-module and updated entry points.
• Switched to Poetry for dependency management.
• Using black for format consistency.

Fixed

• Analysis of 2D images now works properly.
• Dependency conflicts.

[3.3.5] - 2019-02-13

Added

• czi_to_tiff
  • Support for 2D conversion.
• nd2_to_tiff
  • Support for 2D conversion.
• tiff_findoof
  • Parallelization.

Changed

• Now using ggc functions to export settings in: gpseq_anim, gpseq_fromfish and tiff_auto3dseg.
• czi_to_tiff
  • Refactored for easier development.
• Now using seaborn for color palettes.

Fixed

• Missing dependencies in setup.py.
  • Installation through pypi.org.
• tiff_auto3dseg
  • --neighbour now works properly.
  • Provided better error message when 2D mask folder not found.
• nd2_to_tiff: case of single-channel stacks.
• gpseq_anim: fixed skipping of boxplot step (previously broke skipping)

[3.3.4] - 2018-09-21

Added

• czi_to_tiff: to convert CZI files to TIFF.
• gpseq_fromfish_merge
  • Option for no-date prefix to output.
  • Support for date in dataset name.
• tiff_findoof
  • Silent mode with -s.

Changed

• gpseq_anim
  • Now using ggc.check_threads().
• tiff_auto3dseg
  • Now using ggc.check_threads().
• Fixed --compressed option label (now compatible with ImageJ).
• tools.plot.save_tif
  • Added support to retain voxel resolution in TIFF metadata (ImageJ compatible).
• nd2_to_tiff
  • Now saves Resolution (XYZ) metadata when exporting.

[3.3.3] - 2018-09-11

Added

• tiff_split v1.1.0
  • Allowed for splitting into non-square/cubic images.
  • Option to change splitting orientation.

[3.3.2] - 2018-08-28

Fixed

• gpseq_fromfish
  • Incompatibility with newer version of tiff_auto3dseg (v3.1.0+) script caused by unexpected channel axis in input mask.

Added

• gpseq_fromfish
  • Enforcing re-slicing to 3 axes of the input masks, to match the input images.
  • Readable error message in case of inconsistent shape between input mask and image, reverting to binarization in that case.

[3.3.1] - 2018-08-23

Fixed

• gpseq_fromfish
  • Bug in nuclear semi-axes length calculation.

[3.3.0] - 2018-08-22

Added

• Clearer documentation for homologue copy pairs to gpseq_fromfish and gpseq_fromfish_merge.
• gpseq_fromfish
  • Additional help page with -H.
  • Option for 0-indexed input.
  • New columns to output nuclear table:
    • Using slice, row and col for coordinates, instead of z, y and x.
    • box_start_slice, box_start_row, box_start_col: nuclear box starting point 1-indexed coordinates (integer).
    • box_end_slice, box_end_row, box_end_col: nuclear box ending point 1-indexed coordinates (integer).
    • com_slice, com_row, com_col: nuclear mask center of mass 0-indexed coordinates (float).
  • New columns to output compartment table:
    • *_slice_component, *_row_component, *_col_component: with the components of the three major nuclear axes over the image dimensions.

Changed

• Clarified warning when input image axes do not match with metadata.
• gpseq_fromfish
  • Split script help page in -h for attributes and standard help, and -H for more descriptive and readable text.
  • FISH coordinates can now be floating point (integer is not enforced anymore). Lamina/Center distances are interpolated on the regulard grid.
  • Silenced low contrast warnings when saving stacks in debugging mode.
  • Changed extension of output tables to .tsv, for consistency with actual formatting.
  • Output compartment table renamed to nuclear_compartment.out.dilate*.*.
• gpseq_fromfish_merge
  • Clarified no copy pairs found warning message.
  • --aspect default changed to 300. 130. 130. (ZYX).
  • Now compatible with both new and old nuclear compartment table naming.
• tiff_findoof
  • Gradient magnitude mode now default, switch to intensity sum mode with -S or --intensity-sum.

Fixed

• gpseq_anim
  • Crash when 2D mask folder is not provided.
  • Wrong variable name in anim.series.Series.

Removed

• gpseq_fromfish
  • Removed com (center of mass) column from the output dot table. Now the same information is available in the nuclei table (although the CoM coordinates are box-wise, and not image-wise).
  • Exporting dot table before Allele (homologue copy pair) labeling.

[3.2.1] - 2018-08-20

Fixed

• Now writing tiff files with proper axes metadata.

Changed

• gpseq_fromfish
  • Removed double-negation in plot settings confirmation.

[3.2.0] - 2018-08-16

Added

• tiff_auto3dseg
  • Added option to discard objects touching the Z borders during segmentation.
  • -F option for dilate-fill-erode operation (10 as default).
• tiff_findoof
  • -G option for gradient magnitude mode.
  • -R rename option.

Fixed

• gpseq_fromfish
  • Allowed for missing labels.
  • Removing NaN and Inf when plotting aggregated visualization.
  • Bug due to high imprecision when calculating angles.
• tiff_auto3dseg
  • Combination with 2D mask now moved before border clearing.

[3.1.0] - 2018-07-16

Added

• tiff_auto3dseg
  • Added option to combine 2D mask with 3D ones.
  • Allowed for labeled input (2D masks).
• gpseq_fromfish & gpseq_anim
  • Added option for 2D-to-3D mask combination (also labeled input).

Changed

• tiff_auto3dseg
  • Removed superfluous nargs argument in add_argument.