FISHsim (Multiplexed Spots Simulator)

This is a simulation software that generates photorealistic images of flourescent probes.

Installation

We recommend using conda to set up a virtual environment.

conda env create -f environments.yml

Configuring the Program Parameters

Update src/config.yml to set the parameters for the simulator.

Some parameters can also be set using the Command Line Interface. This overrides the settings defined in the config.yml file for those specific parameters

Program Usage

Running as an installed package

If you have installed fishsim as a package, then

1. Update the parameters in resources\configs\config.yml

2. Run in command line to simulate images. For dataset-name, no need to include 'merfish_' in the beginning

fishsim run_merfish --config-file .\resources\config_serval_experiment_default.yml --output-dir-name serval_experiment_default

3. If you wish to subdivide. For dataset-name, no need to include 'merfish_' in the beginning

fishsim subdivide --dataset-name '' --total-fov 10

Note: If the distribution column is provided in the specified codebook, the number_emitter specified in the CLI or the config file is overridden.

Running the Unit Tests

Run pytest in the src directory the run the unit tests associated with the program