useq-schema 0.6.0

Schema for multi-dimensional microscopy experiments

useq-schema

An open, implementation-agnostic schema for describing multi-dimensional microscopy experiments.

Documentation: https://pymmcore-plus.github.io/useq-schema/

Rationale

The useq-schema library defines a structured schema to represent a sequence of microscope acquisition events. By adopting this schema, various microscopy software tools can facilitate interoperability, allowing end users to potentially switch between different control backends with ease. The goal is to encourage a shared standard, making it straightforward for developers to adopt useq-schema and enhance compatibility across tools.

[!IMPORTANT]

Hey developers! :wave: Not convinced? Don't leave yet!

We are particularly interested in feedback from developers of microscopy-control software.

If you are considering supporting useq-schema in your software, but don't see all the fields in MDAEvent that you would need to support your complex use case, please open an issue or pull request to discuss additional features.

:carrot: The carrot for you?

Anyone who is already using useq-schema to describe a sequence of events in some other software (that supports it) can easily try out your solution, with (hopefully) minimal changes to their code.

useq.MDAEvent

The primary "event" object is useq.MDAEvent. This represents a single event that a microscope should perform, including preparation of the hardware, and execution of the event (such as an image acquisition).

from useq import MDAEvent

event = MDAEvent(
    channel="DAPI",
    exposure=100,
    x_pos=100.0,
    y_pos=100.0,
    z_pos=30.0,
    min_start_time=10.0,
    ... # multiple other fields
)

Downstream libraries that aim to support useq-schema should support driving hardware based on an Iterable[MDAEvent]. See useq.MDAEvent documentation for more details.

Similar objects in existing software packages

• For micro-manager, this object is most similar (though not that similar) to the events generated by generate-acq-sequence in the clojure acquisition engine.
• For pycro-manager, this object is similar to an individual acquisition event dict generated by multi_d_acquisition_events, (and, useq provides a to_pycromanager() method that converts an MDAEvent into a single pycro-manager event dict)
• your object here?...

useq.MDASequence

useq.MDASequence is a declarative representation of an multi-dimensional experiment. It represents a sequence of events: as might be generated by the multidimensional acquisition GUI in most microscope software. It is composed of "plans" for each axis in the experiment (such as a Time Plan, a Z Plan, a list of channels and positions, etc.). A useq.MDASequence object is itself iterable, and yields MDAEvent objects.

See useq.MDASequence documentation for more details.

Similar objects in existing software packages

• For micro-manager, this object is most similar to org.micromanager.acquisition.SequenceSettings, (generated by clicking the "Acquire!" button in the Multi-D Acquisition GUI)
• For pycro-manager, this object is similar to the multi_d_acquisition_events convenience function, (and useq provides a to_pycromanager()method that converts an MDASequence to a list of pycro-manager events)
• your object here?...

Example usage

from useq import MDASequence

mda_seq = MDASequence(
    stage_positions=[(100, 100, 30), (200, 150, 35)],
    channels=["DAPI", "FITC"],
    time_plan={'interval': 1, 'loops': 20},
    z_plan={"range": 4, "step": 0.5},
    axis_order='tpcz',
)

The MDASequence object is iterable, yielding MDAEvent objects in the order specified by the axis_order attribute.

>>> events = list(mda_seq)

>>> print(len(events))
720 

>>> print(events[:3])
[MDAEvent(
    channel=Channel(config='DAPI'),
    index=mappingproxy({'t': 0, 'p': 0, 'c': 0, 'z': 0}),
    min_start_time=0.0,
    x_pos=100.0,
    y_pos=100.0,
    z_pos=28.0,
 ),
 MDAEvent(
    channel=Channel(config='DAPI'),
    index=mappingproxy({'t': 0, 'p': 0, 'c': 0, 'z': 1}),
    min_start_time=0.0,
    x_pos=100.0,
    y_pos=100.0,
    z_pos=28.5,
 ),
 MDAEvent(
    channel=Channel(config='DAPI'),
    index=mappingproxy({'t': 0, 'p': 0, 'c': 0, 'z': 2}),
    min_start_time=0.0,
    x_pos=100.0,
    y_pos=100.0,
    z_pos=29.0,
 )]

Both MDAEvent and MDASequence objects are pydantic models, so they can be easily serialized to and from json or yaml.

print(mda_seq.yaml())

axis_order: tpcz
channels:
- config: DAPI
- config: FITC
stage_positions:
- x: 100.0
  y: 100.0
  z: 30.0
- x: 200.0
  y: 150.0
  z: 35.0
time_plan:
  interval: 0:00:01
  loops: 20
z_plan:
  range: 4.0
  step: 0.5

Installation

pip install useq-schema

or, with conda:

conda install -c conda-forge useq-schema

Executing useq-schema experiments with pymmcore-plus

pymmcore-plus implements an acquisition engine that can execute an iterable of MDAEvents using micro-manager in a pure python environment (no Java required).

from pymmcore_plus import CMMCorePlus

core = CMMCorePlus()
core.loadSystemConfiguration()  # loads demo by default

core.mda.run(mda_seq)  # run the experiment

# or, construct a sequence of MDAEvents anyway you like
events = [MDAEvent(...), MDAEvent(...), ...]
core.mda.run(events)

This can be considered a "reference implementation" of an engine that supports useq-schema.

See pymmcore-plus documentation for details.