lilferrit/larvae-counter

Larvae Counter

Welcome to the Larvae Counter repo! This web-app utilizes several computer vision techniques to automate mosquito larvae and pupae counting tasks in a lab setting. To get started visit the web-app here.

About

The Larvae Counter web-app is implemented purely in python. Most image processing is done using the OpenCV library and the web-ui is written using Plotly's Dash library. The web-app is currently hosted on Huggingface here.

Running Locally

To run the larvae counter app locally first clone the repo. Next, navigate to the repo folder using:

cd larvaecount

or your system's equivalent. Next, install the project dependencies (you may choose to so in a virtual environment):

pip install -r requirements.txt

Then install the larvaecount package itself:

pip install .

to run the web app run

python3 -m larvaecount.app --debug=<True/False> --port="<port>" --host="<host-addr>"

Note: The debug, port, and host arguments are optional and default to False, 8080 and 127.0.0.1 respectively.

Using the CLI

All of the counting methods are also available via the command line. To run the CLI run the command:

python3 -m larvaecount.cli <counting_method> <args>

The command line arguments are passed directly to the functions in larvaecount/cli.py using the python-fire library. See larvaecount/cli.py for usage instructions.

License

This project uses the MIT license, see license.txt