4. Python examples

These examples are all shipped with the owl python package. To find them, navigate to the owl directory of your installation and look for them in the examples directory.

The examples are located inside:

/home/ramona/falcongui/lib/python3.10/site-packages/owl/examples

Synchronous acquisition

"""This script shows you how to acquire an image and save it to a folder
using the built in transmission illumination board for illumination.

Ramona Optics, Inc.
Copyright 2018-2024
"""
from owl import mcam_data
from owl.instruments import MCAM
from owl.util import sys_info as owl_sys_info
# Import the required packages
from owl.visualize import quickview

print(owl_sys_info())

# Open the mcam
mcam = MCAM(serial_number='Kestrel0101R')

# 100 ms is the default exposure
mcam.exposure = 0.1
mcam.set_illumination_brightness(.5)

dataset = mcam.acquire_full_field_of_view()
# Save the data
raw_data_file = mcam_data.save(dataset, 'demo')

# %% View the acquired data
quickview(dataset)

# Close after the data has been viewed, and saved
mcam.close()

Controlling Fluorescence Units Programmatically

"""
This script shows how to control the fluorescence illumination controlled
digitally in a script.
It requires owl version 0.9.30 or greater

Copyright Ramona Optics Inc, 2019-2024. All rights reserved.
"""
from owl.instruments import MCAM

mcam = MCAM(serial_number='Kestrel0053R')
fluorescence = mcam.fluorescence_illumination

# Enable the first LED (or the only LED if only one is connected)
fluorescence.led_selected = 0

# Set to 25 percent power
fluorescence.led_power_percentage = 25

# Set to 60 percent power
fluorescence.led_power_percentage = 60

# Set to 0 percent power
# This makes the LEDs appear off.
# Power below 10 percent may also manifest itself as being off
fluorescence.led_power_percentage = 0

# Turn off and deselect the LEDs (safer, more proper way of turning off LEDs)
fluorescence.clear()

# Read the temperature recorded by all the temperature sensors in the system
temperatures = fluorescence.temperatures

Z Stack acquisition with Web API

"""Z stack acquisition with the Ramona Optics MCAM using the web API.

This example demonstrates how to acquire a Z stack acquisition using the MCAM web API.

The Z stack assay allows for the acquisition of a series of images at different focal planes.
The assay is configured using json with the following parameters.

The `save_location` parameter specifies the location where the data will be saved on the
MCAM computer or NAS (Network Attached Storage).

The `metadata` parameter is a dictionary that can be used to store any additional information
you would like to associate with the assay.

The `parameters` parameter is a dictionary that contains the parameters for the assay.
A full list of parameters can be found in the MCAM documentation.
https://docs.ramonaoptics.com/models.html#z-stack-assay

The `configuration` parameter is a string that specifies the file path to a configuration file
generated by the MCAM software.
This file contains the parameters for the assay and is generally stored on the MCAM computer
or on a NAS.

Ramona Optics, Inc. Copyright 2023-2024
"""
import requests

# Change the serial number to the one provided to you by Ramona Optics
serial_number = "Kestrel0001"
url = "http://localhost:8800"

# Connect to the MCAM device using the webAPI endpoint
requests.post(f"{url}/v1/mcam/{serial_number}", timeout=10)

# Set the MCAM device to sample loading state, which will extend the plate nest
requests.post(
    f"{url}/v1/mcam/{serial_number}/state",
    json={"state": "sample_loading"},
    timeout=10,
)

# Set the MCAM device to the acquisition state, which will insert the plate nest
requests.post(
    f"{url}/v1/mcam/{serial_number}/state",
    json={"state": "acquisition"},
    timeout=10,
)

assay_parameters = {
    "save_location": "/MCAM_data/my_z_stack_acquisition/",
    "metadata": {
        "operator": "Mike Roscopy"
    },
    "parameters": {
        "save_mode": "export",
        "z_positions": [1E-3, 2E-3, 3E-3]
    }
}
# Start the Z stack plate scan acquisition
response = requests.post(
    f"{url}/v1/mcam/{serial_number}/assay/z_stack",
    json=assay_parameters,
    # This assay can take more than 10 seconds if saving to slow storage
    timeout=30,
)

# Set the MCAM device to sample loading state, which will extend the plate nest
requests.post(
    f"{url}/v1/mcam/{serial_number}/state",
    json={"state": "sample_loading"},
    timeout=10
)

# Disconnect from the MCAM device
requests.delete(
    f"{url}/v1/mcam/{serial_number}",
    timeout=10
)

Advanced Usage: Volumetric Scan with the MCAM Falcon