Hardware Triggering and Sequencing

Hardware triggering and sequencing are crucial for achieving fast, precisely synchronized image acquisition by minimizing computer-hardware communication. This approach can significantly reduce latency between image frames.

How It Works

In hardware-triggered setups:

  1. Hardware components are pre-loaded with sequences of instructions (e.g., stage positions or digital outputs to control lasers).

  2. The sequence is executed independently of the computer.

  3. TTL (Transistor-Transistor Logic) pulses are routed between devices for synchronization.

  4. Images are read from the camera as quickly as possible.

Automatic Hardware Sequencing

The Acquisition class automatically applies hardware sequencing when:

  1. No delays are requested between successive images.

  2. All hardware position changes support instruction sequencing.

  3. All events are submitted to acq.acquire() in a single call.

Synchronization Strategies

Pycro-Manager supports two general synchronization strategies:

  1. Camera as Leader (Default): - The camera runs at maximum speed. - Other devices update based on TTL pulses from the camera.

  2. External Device as Leader: - An external device timing device controls synchronization. - The camera is set to wait for external triggers. - Use a post_camera_hook_fn to signal the external leader device to start:

    def hook_fn(event):
    # Start external leader device here
    return event

with Acquisition(directory='/path/to/saving/dir', name='acquisition_name',
                 post_camera_hook_fn=hook_fn) as acq:
    # Acquisition code here

Using Acquisition Hooks with Hardware Sequencing

When hardware sequencing is engaged: - The event passed to hooks will be a list of dict objects (a sequence of events). - Hooks are called once for the whole sequence, not for each event.

Disabling Hardware Sequencing

To disable hardware sequencing, submit events one at a time:

with Acquisition(directory='/path/to/saving/dir', name='acquisition_name') as acq:
    events = multi_d_acquisition_events(num_time_points=10)
    for event in events:
        acq.acquire(event)

Practical Example: Light-Sheet Microscopy

This notebook shows an example of how to setup Pycro-Manager to run a microscope that utilizes an external controller as the leader device. Specifically, this tutorial controls a light-sheet microscope where a sample with fluorescent labels is scanned at a constant speed through an oblique light sheet. The stage controller provides the TTL signals that ensure the camera is synchronized to the scanning stage. This approach makes use of post_hardware and post_camera hook functions built into Pycro-Manager. Using these hook functions, it is possible to rapidly build and acquire a multiple terabyte acquisition consisting of millions of images.