NPMCV

A Python script for segmenting cells in microscope images and calculating the coefficient of variation (CV).

Installation

Download the latest .whl package from the release page and install with pip

$ pip install npmcv-2.1.3.whl

Alternatively you can build the package yourself from the source with python -m build

How to Use

usage: npmcv [-h] [-D] [-n [NAME]] [-V] <path>

positional arguments:
  <path>                directory containing lif images

optional arguments:
  -h, --help            show this help message and exit
  -D, --no_imgs         Don't save overlays and individual cell images
  -n [NAME], --name [NAME]
                        Set basename for the output files
  -V, --version         show program's version number and exit

The script generates several output files

   NAME.csv:     cleaned output file
   NAME_RAW.csv: output data without outliners removed  
   NAME_OUT.csv: the outliners removed from data

By default the output files will be named after the input folder. Columns in RAW output corresponds to the CV values calculated for each segmented cell in an individual image. Columns in standard output file are grouped by .lif file

Additional Image Outputs:

By default the program will save processed cell images to verify segmentation.

<directory>/dapi_seg/<img>_seg.png:

Generates an image overlaying the cell segmentation on the original image to validate the segmentation.

<directory>/inv_cells/<img>_cell<n>.png:

The actual cells where CV was calculated, <n> corresponds to the row number in the csv files.