Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

Unreleased

[3.4.1] - 2021-11-14

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.

[3.0.4] - 2018-07-02

Added

Version info to package dependencies in setup.py.
More flexible adaptive threshold behavior in tools.binarize.
Option to use dilated mask only for dots assignment, and not for distance calculation, as gpseq_fromfish --dots-assignment-only.
(Un)Compression log to tiffcu.

Changed

Now depending on scikit-image v0.14.0 (upgraded package).
Output directory now optional in nd2_to_tiff.
gpseq_fromfish now not crashing when a tiff file is corrupted, only an error message is showed.
Better error message during initialization if a series does not have either DNA or Signal channel(s).

Fixed

Minor bugs in binarizer that crashed the script with certain parameter combinations.
Local threshold behavior.
Order of output table columns in gpseq_fromfish.
nd2_to_tiff now compatible with single-channel nd2 files.
nd2_to_tiff now exporting tiff files with proper axes order.
Mask import in gpseq_anim.

[3.0.3] - 2018-06-29

Fixed

Typo in gpseq_fromfish that rendered the --dilate-Z flag useless.

[3.0.2] - 2018-06-22

Fixed

Bug that crashed gpseq_anim when option -m is not used.

[3.0.1] - 2018-06-21

Fixed

tiff_auto3dseg minor bug due to unbound staticmethod.

[3.0.0] - 2018-06-12

Added

Enzyme diffusion simulation.
gpseq_fromfish
- Settings export.
- Debug mode.
gpseq_anim
- --do-all/-y option.
- -M, -m, --labeled and --compressed to export/import masks.

Changed

Moved distance functions to separate tools sub-module.
Now using ggc to confirm settings in gpseq_anim.

Fixed

return bug crashing the pipeline when a condition has no nuclei.

[2.1.8] - 2018-06-07

Fixed

datetime import in gpseq_anim.

Added

Volume density merge through gpseq_fromfish_merge.

[2.1.7] - 2018-06-01

Added

Nuclear density merge through gpseq_fromfish_merge.
Volume profile to gpseq_fromfish.

Fixed

Center as percentile option is now used also for the nuclear density calculation in gpseq_fromfish.

[2.1.6] - 2018-05-31

Fixed

Bug in gpseq_fromfish due to wrong column labeling.
Bug in gpseq_fromfish_merge.

Added

Python version, command line and timestamp to gpseq_anim exported settings file.

[2.1.5] - 2018-05-07

Added

Option --min-radius/-R to gpseq_anim to change the XY size filter of segmented objects.

[2.1.4] - 2018-05-03

Added

Intensity sum on sum Z-projection for each nucleus as flat_sumI.
Density profile for each nucleus to gpseq_anim and gpseq_fromfish.
Settings confirmation to gpseq_fromfish

[2.1.3] - 2018-04-24

Added

Plotting option to tiff_findoof script.
Option to skip hole filling in segmented masks (--no-hole-filling) in gpseq_anim.
Option to define nucleus center as top percentile (--center-as-percentile).
Settings to file in gpseq_anim.

Fixed

Axes order in nd2_to_tiff.
Lamin distance calculation in 3D.

[2.1.2] - 2018-04-10

Fixed

Fixed dataset aggregated view file names.
Extension now present in nd2_to_tiff output.

[2.1.1] - 2018-03-28

Changed

Z dilation is now turned off by default.

Fixed

Compartment assignment.
Fixed colors in aggregated visualization.

[2.1.0] - 2018-03-28

Added

Aggregated visualization per field of view and for the whole dataset, per channel and for all channels.
Dilation can be enforced to XY dimensions only (--no-Z-dilation).

Changed

In 3-ortho-view plot nuclei are now occupying as much space as possible.
In 3-ortho-view plot are now colored based on the channel.

Fixed

Now rotating only on XY plane for nuclear compartmentalization.

Removed

Option --annotate-compart is now the default behaviour.

[2.0.1]

Fixed

Fixed sub packages import.
Now possible to install not in development status.

[2.0.1]

Added

tiff_split from tiff-tools-gg.
--skip-channels option to gpseq_fromfish.
nd2_to_tiff conversion script.
Progress bar to tiff_findoof.

Fixed

Fixed gpseq_fromfish missing istruct passing.
Input directory list issue in gpseq_fromfish_merge.
Allowed for only partial information in gpseq_fromfish_merge input.
TIFF mask import/export in gpseq_fromfish.

[2.0.0]

Changed

Cleaned up const.py.
wraps module renamed anim, will contain all wrappers for GPSeq standard image dataset analysis.
main library moved to anim module.
Cleaned up and re-structure comment style in all libraries and modules.

Added

License text in bin/gpseq_anim.
TIFF automatic 3D segmentation script from tiff-tools-gg.
TIFF (un)compress script from tiff-tools-gg.
Out Of Focus detection/plot scripts from tiff-tools-gg.
FISH lamin distance calculation script from dotter2gpseq.
gpseq_fromfish output merge from dotter2gpseq.

[1.1.0] - 2018-03-13

Added

Capturing TIFF read issues.
Voxel aspect unit of measure.
Max profile.

Fixed

Now borders are properly cleared when analyzing in 3D.
Nuclear threshold plot size.
Report format.
Plot titles.

Changed

Cleaned package structure.
Renamed pygpseq-run.py to gpseq_anim and allowed for easy installation.
VERSION constant now source only from setup.py.
Setup base for unit testing with nosetests.
Sigma used for smoothing and density curve production are now separate.

[1.0.0]

Changed

Now normalizing lamin distance over its sum with central distance.

Added

Sigma option to pygpseq-run.py.

[0.1.2]

Changed

CSV output files in separate folder.
X-axis intercepts of profiles and profiles 1st/2nd derivatives are reported.
Profile areas are reported.
Single-nucleus data summaries are exported in CSV format.
Background levels are now reported as barplots.

Added

Automatic stop if no conditions are found.
Automatic stop if no series are found in a condition.

[0.1.1]

Changed

Better documentation is now available.
DocStrings are now in Napoleon format.
Improved report.
Nuclear selection can now be skipped.
Nuclear selection can now be perform with up to 3 features.
Moved image binarization in a separate class.
Generalized channel reading function.

Added

Distribution comparison using Wilcoxon-Mann-Whitney U test.
Implemented different middle-section definitions.

[0.1.0] - 2017-07-26

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Changelog

Unreleased

[3.4.1] - 2021-11-14

Changed

Fixed

[3.3.5] - 2019-02-13

Added

Changed

Fixed

[3.3.4] - 2018-09-21

Added

Changed

[3.3.3] - 2018-09-11

Added

[3.3.2] - 2018-08-28

Fixed

Added

[3.3.1] - 2018-08-23

Fixed

[3.3.0] - 2018-08-22

Added

Changed

Fixed

Removed

[3.2.1] - 2018-08-20

Fixed

Changed

[3.2.0] - 2018-08-16

Added

Fixed

[3.1.0] - 2018-07-16

Added

Changed

[3.0.4] - 2018-07-02

Added

Changed

Fixed

[3.0.3] - 2018-06-29

Fixed

[3.0.2] - 2018-06-22

Fixed

[3.0.1] - 2018-06-21

Fixed

[3.0.0] - 2018-06-12

Added

Changed

Fixed

[2.1.8] - 2018-06-07

Fixed

Added

[2.1.7] - 2018-06-01

Added

Fixed

[2.1.6] - 2018-05-31

Fixed

Added

[2.1.5] - 2018-05-07

Added

[2.1.4] - 2018-05-03

Added

[2.1.3] - 2018-04-24

Added

Fixed

[2.1.2] - 2018-04-10

Fixed

[2.1.1] - 2018-03-28

Changed

Fixed

[2.1.0] - 2018-03-28

Added

Changed

Fixed

Removed

[2.0.1]