microsim

Microscope simulation library for generating realistic microscope images.

Installation

For now, please install from github. This library is in early development, expect rapid changes and breakages.

pip install git+https://github.com/tlambert03/microsim

Usage

Construct and run a microsim.Simulation object.

using objectsusing dicts

from microsim import schema as ms
from microsim.util import ortho_plot

sim = ms.Simulation(
    truth_space=ms.ShapeScaleSpace(shape=(128, 512, 512), scale=(0.02, 0.01, 0.01)),
    output_space={'downscale': 8},
    sample=ms.Sample(
        labels=[ms.MatsLines(density=0.5, length=30, azimuth=5, max_r=1)]
    ),
    modality=ms.Confocal(pinhole_au=0.2),
)
result = sim.run()
ortho_plot(result)

If you don't like importing all the names, you can also use dictionaries, and pydantic will convert them to the correct objects.

from microsim import Simulation
from microsim.util import ortho_plot

sim = Simulation(
    truth_space={'shape': (128, 512, 512), 'scale': (0.02, 0.01, 0.01)},
    output_space={'downscale': 8},
    sample=dict(
        labels=[
            {   
                'type': 'matslines',
                'density': 0.5,
                'length': 30,
                'azimuth': 5,
                'max_r': 1,
            }
        ]
    ),
    modality={'type': 'confocal', 'pinhole_au': 0.2}
)
result = sim.run()
ortho_plot(result)

Note that you can also construct a simulation from a JSON object. This is particularly useful with the output parameter, to dump the result of the simulation to a file.

confocal.json

{
    "truth_space": {
        "shape": [128, 512, 512],
        "scale": [0.02, 0.01, 0.01]
    },
    "output_space": {
        "downscale": 8
    },
    "sample": {
        "labels": [
        {
            "type": "matslines",
            "density": 0.5,
            "length": 30,
            "azimuth": 5,
            "max_r": 1
        }
        ]
    },
    "modality": {
        "type": "confocal",
        "pinhole_au": 0.2
    },
    "output": "au02.tiff"
}

... and then load a Simulation from that file and run().

from microsim import Simulation
from pathlib import Path

spec = Path('confocal.json').read_text()
sim = Simulation.model_validate_json(spec)
sim.run()