/MERFISH_simulator

A simulator for generating MERFISH data

Primary LanguagePythonMIT LicenseMIT

MERFISH_simulator

A simulator for generating MERFISH data.

Warning: Alpha version, may change rapidly and unpredictably.

Dependencies

Usage

This requires an existing MERlin merfish-parameters directory. Sample simulation parameter and position files are in the examples directory.

  1. Create a sub-directory in merfish-parameters called simulation and put the your simulation parameters json file in this directory.

  2. Place a csv file containing positions in the merfish-parameters/positions directory.

  3. Run simulator as follows:

mersim \
   -a simulation_parameters.json \
   -m microscope_parameters.json \
   -o data_organization.csv \
   -c codebook.csv \
   -p positions.csv \
   simulate

This will create a directory called simulate in your MERlin data directory containing the simulated images.