[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.