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.
-
Create a sub-directory in
merfish-parameters
calledsimulation
and put the your simulation parameters json file in this directory. -
Place a csv file containing positions in the
merfish-parameters/positions
directory. -
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.