spot2cell

Spot2cell is a tool that assigns spots to labeled masks with minimum instalation requirements.
It aims to provide a simple, easy-to-use way for assigning spots to cell masks.

Installation

spot2cell is available on PyPI and Conda-Forge and can be installed using pip or conda.

Install using pip:

pip install spot2cell

Install using conda:

conda install -c conda-forge spot2cell

Docker

Build Docker image from Dockerfile

docker build -t spot2cell .

CLI

spot2cell --help

usage: spots2cells.py [-h] [-s SPOTS] [-m MASK] [-x X_COL] [-y Y_COL] [-o OUTPUT] [--verbose] [--version]

This scripts assigns a list of spots to the objects in an instance mask.

options:
  -h, --help           show this help message and exit
  -s, --spots SPOTS    Path to the spot table file.
  -m, --mask MASK      Path to the isntance mask file.
  -x, --x-col X_COL    Column index of the x coordinate in the spots table [default: 0].
  -y, --y-col Y_COL    Column index of the y coordinate in the spots table [default: 1].
  -o, --output OUTPUT  Path to the output csv file.
  --verbose            Verbose logging.
  --version            show programs version number and exit

Expected Inputs

Spot2cell expects two inputs:

• spots: A comma-separated .csv table of spots with x and y coordinates.
• mask: An instance mask .tif file. In which each object is labeled with a unique positive number and each pixel belongs to exactly one object.