API reference¶
All the models used to define a simulation can be imported from
microsim.schema, which is usually imported as ms:
Every model is a pydantic model. Fields are validated when the object is created and when they are assigned, and every field that takes a model also accepts a dictionary with the same keys. Unknown fields raise an error.
The pages in this section are generated from the source code, one per public
module, so they always match the installed version. Each object is documented
once, in the module or subpackage that defines it; most are also importable
from microsim.schema, as above. The main objects, by topic:
Simulation¶
| Object | Description |
|---|---|
Simulation |
the top-level model |
Simulation.run |
run every stage and return the digital image |
Simulation.run_batch |
run once per sample, reusing PSFs and emission rates |
Track |
channels acquired at the same time (guide) |
ground_truth, filtered_emission_rates, optical_image, digital_image |
the stages, run one at a time (guide) |
Spaces¶
| Object | Description |
|---|---|
ShapeScaleSpace, ExtentScaleSpace, ShapeExtentSpace |
a space given by two of shape, extent, and scale |
DownscaledSpace, UpscaledSpace |
a space derived from another one (guide) |
Sample¶
| Object | Description |
|---|---|
Sample, FluorophoreDistribution |
the labels in the sample, and where each one is |
Fluorophore |
spectra, extinction coefficient, quantum yield, lifetime |
MatsLines, CosemLabel |
built-in distributions (guide) |
cosem, allen |
OpenOrganelle (COSEM) datasets, Allen Institute neuron reconstructions |
Optics¶
| Object | Description |
|---|---|
ObjectiveLens |
numerical aperture, immersion and specimen refractive index |
Widefield, Confocal, Identity |
imaging modalities (guide) |
psf |
functions to compute widefield and confocal PSFs directly |
Channels¶
| Object | Description |
|---|---|
OpticalConfig |
a channel: light sources, filters, and optionally its own exposure (and detector QE) (guide) |
LightSource |
an excitation spectrum and its relative power |
Bandpass, Longpass, Shortpass, SpectrumFilter |
filters |
Spectrum |
a sampled spectrum |
optical_config.lib |
built-in filter sets and laser lines |
Detectors¶
| Object | Description |
|---|---|
CameraCCD, CameraCMOS, CameraEMCCD |
cameras (guide) |
PMT, HyD |
point detectors |
detectors.lib |
built-in detectors |
Settings and utilities¶
| Object | Description |
|---|---|
Settings |
array backend, precision, random seed, caching (guide) |
util |
plotting (ortho_plot, ndview, animate) and cache helpers |