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Description:

microsim 0.0.6

microsim

Light microscopy simulation in python.
The goal of this library is to generate highly realistic simulated data such as the following:

(this data was generated using segmentations from
cell jrc_hela-3 at OpenOrganelle as the ground truth)
Installation
from PyPI
pip install microsim

from github
To get the bleeding edge version, which will change rapidly, you can install from github.
pip install git+https://github.com/tlambert03/microsim

If available, microsim can use either Jax or Cupy to accelerate computations.
These are not installed by default, see the
jax
or cupy installation instructions,
paying attention to your GPU requirements. Support for torch is planned.
Usage
Construct and run a
microsim.Simulation
object.
from microsim import schema as ms
from microsim.util import ortho_plot

# define the parameters of the simulation
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),
output_path="au02.tiff",
)

# run it
result = sim.run()

# optionally plot the result
ortho_plot(result)

Documentation
See the API Reference (https://tlambert03.github.io/microsim/api/) for details
on the Simulation object and options for all of the fields.