Introduction

MERMAKE processes MERFISH and smFISH imaging data by detecting local intensity maxima (puncta) in 3D image stacks. In multiplexed experiments (MERFISH), these puncta are decoded using a user-supplied codebook, while in smFISH mode, the puncta are simply called and reported as-is.

To install MERMAKE,

python3 -m pip install mermake

⚠️ GPU Requirements & CUDA Toolkit

MERMAKE relies on CuPy for GPU-accelerated image processing. To run MERMAKE successfully, you must have:

1. An NVIDIA GPU with CUDA support
2. The CUDA Toolkit installed (Refer to the official CuPy installation guide)

MERMAKE Usage

To run MERMAKE, you'll need to provide a configuration TOML file with a few key settings describing your experiment.

mermake my_settings.toml

If mermake is run without providing a toml file, it will warn about the usage and print out the toml file format. Most users only need to edit the [paths] section.

TOML Section	Variable Name	Description
[paths]	codebook	Path to the CSV codebook for decoding barcodes (for MERFISH data only)
[paths]	psf_file	Path to the PSF file used for deconvolution (e.g., .npy or .pkl)
[paths]	flat_field_tag	Prefix path for flat field correction files (e.g., "Scope3_")
[paths]	hyb_range	Range of hybridization rounds to process (e.g., 'H1_*_set1:H1_*_set3')
[paths]	hyb_folders	List of folders containing raw imaging data
[paths]	output_folder	Path to the folder where MERMAKE should save results

All other sections ([hybs], [dapi], etc.) are preconfigured for most use cases and usually do not need to be changed. Though to use multi-psfs you will want to set the tilesize to the size of the samping grid (ie 300).

---

Example Config (config.toml)

[paths]
codebook = "codebook.csv"
psf_file = "psfs/psf_scope3.npy"
flat_field_tag = "flat_field/Scope3_"
hyb_range = "H1_*_set1:H16_*_set3"
hyb_folders = ["experiment_folder"]
output_folder = "output"

#---------------------------------------------------------------------------------------#
#---------------------------------------------------------------------------------------#
#           you probably dont have to change any of the settings below                  #
#---------------------------------------------------------------------------------------#
#---------------------------------------------------------------------------------------#

hyb_save =  '{fov}--{tag}--col{icol}__Xhfits.npz'
dapi_save = '{fov}--{tag}--dapiFeatures.npz'
regex = '''([A-z]+)(\d+)_([^_]+)_set(\d+)(.*)''' #use triple quotes to avoid double escape

[hybs]
tile_size = 500
overlap = 89
beta = 0.0001
threshold = 3600
blur_radius = 30
delta = 1
delta_fit = 3
sigmaZ = 1
sigmaXY = 1.5

[dapi]
tile_size = 500
overlap = 89
beta = 0.01
threshold = 3.0
blur_radius = 50
delta = 5
delta_fit = 5
sigmaZ = 1
sigmaXY = 1.5