Cell Viability Assay

This repository contains the source code for analyzing cell viability assays using high-content screening (HCS) images. The pipeline includes image processing and data mining for quantitative analysis of the number of cells in each image.

Installation

To install via pip, run the following command:

pip install CellViability

To install the developmental version, clone the repository and run:

git clone https://github.com/cnpem/CellViability.git
cd CellViability
make install

Usage

To run the analysis for all cell viability assays (i.e., drug screening), use the following command:

CellViability --config path/to/config.json --npy --instances --basedir results/ --verbose

Optional flags:

• --npy: saves the results in a NumPy binary file
• --instances: saves segmented images.
• --basedir: specifies the directory where results will be saved.
• --verbose: enables detailed, step-by-step logging.

To run a specific cell viability assay, use the following command:

CellViability --config path/to/config.json --index <index> --npy --instances --basedir results/ --verbose

• --index <index>: selects a single condition (0-based index) from the list defined in the --config file.

Authors

• Ana A. S. Iacia
• Jacqueline F. Shimizu
• João V. S. Guerra
• José G. C. Pereira
• Kayllany L. S. Oliveira
• Pablo S. Silva
• Rafael E. Marques
• Thayná M. Avelino

License

This software is licensed under the terms of the GNU General Public License version 3 (GPL3) and is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.