About periodic execution of snap and image processing

[hiroalchem]

I would like to capture an image periodically (e.g., once every 5 minutes). Is there an easy way to do this? Also, I would like to process the images when they are acquired. How do I connect the image acquisition to the image processing? Thanks for your help!

[fdrgsp]

Hi @hiroalchem, if you want to use napari-micromanager, you can acquire a time-lapse using the Muti-D Acquisition tab (image below).

After loading your Micro-Manager configuration and setting the channels you want to acquire in the Channels table, you can check the Time box and set the time-lapse parameter. You can define how many timepoints you want to acquire in the Timepoints spinbox and the interval between each timepoints (in your example 5 minutes) in the Interval spinbox (you can also select the interval's unit - ms, sec, min - in the drop-down box). When you press on the Run button, the acquisition will start.

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For the image processing, If you want to analyze each timepoints after they are acquired, you can connect your analysis pipeline to the frameReady pymmcore-plus signal that is emitted every time an image is acquired.

This is an example if you want to use napari-micromanager:

import napari
from useq import MDASequence, MDAEvent
from pymmcore_plus import CMMCorePlus
import numpy as np

viewer = napari.Viewer()
dw, main_window = viewer.window.add_plugin_dock_widget("napari-micromanager")

# get the CMMCorePlus running instance
core = CMMCorePlus.instance()

# your analysis
def _on_mda_frame(image: np.ndarray, event: MDAEvent):
    
    # 'image' is the last image that has been acquired (numpy array)
    print(image)

    # 'event' contains all the info about the acquisition event
    print(event)

    # return if the 'frameReady' signal is not triggered by a Muti-D Acquisition
    sequence_metadata = main_window._mda_meta
    if sequence_metadata.mode != "mda":
        return

    # you can call your image processing pipeline here to perform the analysis on 'image'.

# connect your analysis code to the pymmcore-plus 'frameReady' signal.
core.mda.events.frameReady.connect(_on_mda_frame)

# run napari
napari.run()

You can now setup napari-micromanager and run the Muti-D Acquisition as explained above but this time your analysis pipeline is executed every time a frame is received.

I hope this is helping!

[tlambert03]

closing this @hiroalchem ... but feel free to reopen if you have more questions