nuclei-counter 0.1.0

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Nuclei Image Processing Program

This python program processes and counts nuclei in images. The following sections detail how to use the various command-line arguments available in the program.

Setup

On windows-based systems, you may use one of the pre-built executable files provided in releases; this does not require installation of python. However, if you wish to modify the code, you must clone this repository and build or run the program from source.

NOTE: Due to using pyinstaller to package this code as a windows executable, this file may be flagged as a virus or as malware. This is unfortunately common for software built using pyinstaller. If your antivirus blocks the file, you'll need to flag it as safe when downloading it.

Requirements

To build or run this program as a python script, ensure you have python 3.10 or later installed on your system. Then clone this repository by downloading and extracting the zip file or by using git.

Project installation

This library uses a PEP-518 compliant pyproject.toml file to manage project dependencies. To install this library locally, you may use your preferred python package manager (e.g., poetry) or run the following from the repository root:

pip install -e .

This will install all project dependencies and allow you to run the project as a python script from the command line. If you've downloaded the executable file, replace python count_nuclei.py with count_nuclei.exe; all command line options remain the same.

Program usage

To use this program, open a terminal and change your working directory into \nuclei_counter where count_nuclei.py exists. You may run the python program with the command line arguments as described; note that only --img_dir is required; other arguments may be omitted.

1. Image Directory (--img_dir) (REQUIRED)

Specify the directory containing the images you wish to process.

Usage:

python count_nuclei.py --img_dir "path/to/your/image/directory"

2. Output Directory (--output_dir) (OPTIONAL)

Defines where the results files should be saved. If not specified, results will be saved in a folder named results in the current working directory.

Usage:

python count_nuclei.py --img_dir "path/to/your/image/directory" --output_dir "path/to/your/output/directory"

3. Save Transformed Images (--save_images) (OPTIONAL)

Include this flag if you wish to save the transformed images used during the counting process. This flag is optional and excluding it will not save a copy of the transformed images.

Usage:

python count_nuclei.py --img_dir "path/to/your/image/directory" --save_images

4. Output Count Filename (--output_count_filename) (OPTIONAL)

Specify the filename of the resulting CSV that contains the count of nuclei. If not provided, it will default to count_results.csv.

Usage:

python count_nuclei.py --img_dir "path/to/your/image/directory" --output_count_filename "your_desired_filename.csv"

Default: count_results.csv

Full Example:

To use all the arguments in one command:

python count_nuclei.py --img_dir "path/to/images" --output_dir "path/to/output" --save_images --output_count_filename "results.csv"

License

See the LICENSE file for license rights and limitations (MIT).