1.6.0

• scikit-image minimum version is now 0.23.2
• The code has been refactored into a proper package. Run pip install /path/to/source to install directly, or python -m build /path/to/source to build a .whl file and pip install that .whl. Then, run mcquant or python -m mcquant.cli instead of the previous python CommandSingleCellExtraction.py.
• The --version argument has been implemented, which prints the version of the tool.

Added intensity_sum

New --intensity_props intensity_sum for spot counting.

Added imagecodecs

Added imagecodecs to handle LZW-compressed images

Proper handling of filenames with dots in them

The new version correctly removes the filename extension from the input images to determine the output filename.

Fixed HDF5 support; early check for number of channels

-Fixed support of images in HDF5 format
-The module now verifies whether the number of channels matches between the images and markers.csv. The check is done early and an informative error is displayed in case of a mismatch.

Custom intensity and mask properties

Two new flags --mask_props and --intensity_props allow users to request any properties from region_props() to be calculated on masks and intensity values, respectively.

Mask suffixes moved to filenames

• Suffixes of the form _nucleiMask have been moved from column names to file names. Column names now directly match markers.csv
• Fixed a bug, where marker expression and morphological features were mismatched when multiple masks were being quantified.

1.3.2

Added .btf comparability: labsyspharm/mcmicro#234
Minor changes to documentation as well.

Thank you @clarenceyapp

1.3.1

This release enables the use of multiple masks: labsyspharm/mcmicro#121

WARNING: The naming in the CSV file changed.

1.3.0

WARNING:
This release changes naming for X and Y coordinates of cellular centroid position and adds column and row representation according to #18