crm_gen
Synthetic Microscope Image Generation.
A submodule for cr_mech_coli that provides:
Synthetic microscope image generation pipeline
Image cloning from real microscope images
Parameter optimization to match real images
Usage of the crm_gen script
usage: crm_gen [-h] [--config CONFIG] {run,clone,fit} ...
Synthetic Microscope Image Generation for cr_mech_coli
positional arguments:
{run,clone,fit} Subcommand
run Run the synthetic image generation pipeline
clone Clone a real microscope image to synthetic
fit Optimize parameters to match real microscope images
options:
-h, --help show this help message and exit
--config CONFIG, -c CONFIG
Path to TOML configuration file
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usage: crm_gen run [-h]
Run bacteria growth simulation and generate synthetic microscope images. All parameters come
from the TOML config file.
options:
-h, --help show this help message and exit
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usage: crm_gen clone [-h] [--output OUTPUT] [--n-vertices N_VERTICES] [--seed SEED]
microscope_image segmentation_mask
Create a synthetic version of a real microscope image using cell positions extracted from a
segmentation mask. Imaging parameters come from the TOML config file.
positional arguments:
microscope_image Path to real microscope image (TIF)
segmentation_mask Path to segmentation mask (TIF)
options:
-h, --help show this help message and exit
--output OUTPUT, -o OUTPUT
Output directory (default: ./synthetic_output)
--n-vertices N_VERTICES
Number of vertices per cell (overrides config, default: 8)
--seed SEED Random seed (overrides config)
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usage: crm_gen fit [-h]
Optimize synthetic image generation parameters to match real microscope images using
differential evolution. All parameters come from the TOML config file ([optimization] section).
options:
-h, --help show this help message and exit