""" Inscoper API Example Script: Z-Stack Acquisition ================================================ This script performs a Z-stack acquisition using a list of Status states. Configuration Prerequisites: --------------------------- 1. Environment Variable: Ensure 'InscoperConfigsPath' is defined in your environment and points to your Inscoper configurations folder. 2. Configuration Name: This script assumes a hardware configuration named "camera_and_microscope_and_fluo_source". Change it below if your configuration is named differently. 3. Device/Channel Names: Customize device and focus sub-device names below. """ import os from typing import Dict from dataclasses import dataclass import numpy as np import matplotlib.pyplot as plt import inscoper_api @dataclass class SubDevice: name: str = None # a descriptive string for the sub-device tag: int = None # a unique identifier within the device for this sub-device inscoper_type: int = None # a "purpose" type for the sub-device (what it does, e.g., CUBE, OBJECTIVE, SHUTTER...) @dataclass class Device: name: str # the name given to the device during the configuration step hardware_id: int # an identifier for this device model sub_device_map: Dict[int, SubDevice] # the collection of chosen sub-devices for this particular device instance class CustomImageListener(inscoper_api.ImageListener): def __init__(self): super().__init__() self._received_images = [] self._image_counter = 0 def handleNewImage(self, image): print(f"Image {self._image_counter} received!") self._image_counter += 1 self._received_images.append(image) def getReceivedImages(self): return self._received_images # Macro to all Inscoper configurations CONFIG_PATH = os.environ['InscoperConfigsPath'] my_bridge = inscoper_api.Bridge() my_listener = CustomImageListener() my_bridge.addImageListener(my_listener) config = my_bridge.readConfigFile(os.sep.join([CONFIG_PATH, "camera_and_microscope_and_fluo_source"])) my_bridge.loadConfigFile(os.sep.join([CONFIG_PATH, "camera_and_microscope_and_fluo_source"])) my_bridge.initDevices() # Dictionary to store the mapping of hardware IDs to our Device objects. device_map = {} # Step 0: Iterate over the "Device List" from the configuration. # This tells us what specific devices have been added to this system's configuration. for device in config.getDeviceList(): driver_config = device.getDriverConfig() # In this example, we only keep devices controlled by the Inscoper Device Controller. if isinstance(driver_config, inscoper_api.InscoperBoxDriverConfig): device_name = device.getId() # e.g., "My Microscope" or "My Stage" device_id = driver_config.getHardwareId() # The internal hardware identifier sub_device_map = {} # Iterate over all sub-devices configured for this device. for sub_device_config in device.getSubDeviceConfigList(): sub_device_tag = sub_device_config.getTag() # The unique tag will allow us to connect config and description sub_device_id = sub_device_config.getId() # Descriptive name of the sub-device # Create our SubDevice instance and map it by its tag. sub_device_map[sub_device_tag] = SubDevice(name=sub_device_id, tag=sub_device_tag) # Store the complete Device object (with its sub-devices) in our global map. device_map[device_id] = Device(name=device_name, hardware_id=device_id, sub_device_map=sub_device_map) # At this point, device_map contains our devices, but we are missing the "purpose" of each sub-device. print(device_map) # Step 0: Iterate over the "Device Description List". # This information acts as the "class definitions" (descriptions.xml) for all possible hardware supported by Inscoper, # providing metadata like the generic type (purpose) of the sub-devices. for device_desc in my_bridge.getDeviceDescriptionList(): driver_desc = device_desc.getDriverDescription() # Again, we only keep devices controlled by the Inscoper Device Controller. if isinstance(driver_desc, inscoper_api.InscoperBoxDriverDescription): device_id = driver_desc.getHardwareId() # If this hardware_id matches one of the devices we found in our configuration... if device_id in device_map: current_device = device_map[device_id] sub_device_map = current_device.sub_device_map # Look at all possible sub-devices described for this hardware model. for sub_device_desc in device_desc.getSubDeviceDescriptionList(): sub_device_tag = sub_device_desc.getTag() sub_device_type = sub_device_desc.getType() # The general purpose of the sub-device (e.g., CUBE, SHUTTER, etc.) # If this configured device actually uses this specific sub-device... if sub_device_tag in sub_device_map: current_sub_device = sub_device_map[sub_device_tag] # Store the human-readable string of the sub-device type current_sub_device.inscoper_type = inscoper_api.Utils.subDeviceTypeToString(sub_device_type) objective_turret_sub_device_id = None # Turret that selects the objective cube_turret_sub_device_id = None # Filter-cube turret tl_power_sub_device_id = None # Power controller for the transmitted light tl_shutter_sub_device_id = None # Shutter inside the microscope for the transmitted light epi_shutter_sub_device_id = None # Shutter inside the microscope for the epi-fluorescence led_blue_power_sub_device_id = None # Power controller for the blue (440nm) LED led_blue_shutter_sub_device_id = None # Shutter inside the light source for the blue (440nm) LED for device_id, device in device_map.items(): for sub_device_tag, sub_device in device.sub_device_map.items(): if sub_device.inscoper_type == "SHUTTER" and "TL" in sub_device.name: # Transmitted-light shutter: type is SHUTTER and the name contains "TL" tl_shutter_sub_device_id = inscoper_api.SubDeviceId(device.name, sub_device.name) elif sub_device.inscoper_type == "SHUTTER" and "IL" in sub_device.name and "Down" in sub_device.name: # Epi-fluorescence (incident-light) shutter: type is SHUTTER, path is "IL Down" epi_shutter_sub_device_id = inscoper_api.SubDeviceId(device.name, sub_device.name) elif sub_device.inscoper_type == "OBJECTIVE": # Objective turret: uniquely identified by the "OBJECTIVE" type objective_turret_sub_device_id = inscoper_api.SubDeviceId(device.name, sub_device.name) elif sub_device.inscoper_type == "CUBE" and "Down" in sub_device.name: # Filter-cube turret in the epi (downward) light path cube_turret_sub_device_id = inscoper_api.SubDeviceId(device.name, sub_device.name) elif ("Intensity" in sub_device.name or "Power" in sub_device.name) and "TL" in sub_device.name: # Transmitted-light intensity: name contains "Intensity" or "Power" AND "TL" tl_power_sub_device_id = inscoper_api.SubDeviceId(device.name, sub_device.name) elif ("Intensity" in sub_device.name or "Power" in sub_device.name) and "440" in sub_device.name: # 440 nm LED power: name contains "Intensity" or "Power" AND the wavelength "440" led_blue_power_sub_device_id = inscoper_api.SubDeviceId(device.name, sub_device.name) elif sub_device.inscoper_type == "SHUTTER" and "440" in sub_device.name: # 440 nm LED shutter: type is SHUTTER and the wavelength "440" appears in the name led_blue_shutter_sub_device_id = inscoper_api.SubDeviceId(device.name, sub_device.name) blue_channel_description = {objective_turret_sub_device_id: 1, cube_turret_sub_device_id: 2, tl_power_sub_device_id: 0, tl_shutter_sub_device_id: 0, epi_shutter_sub_device_id: 1, led_blue_power_sub_device_id: 100, led_blue_shutter_sub_device_id: 1} blue_status = inscoper_api.Status() for sub_device_id, value in blue_channel_description.items(): blue_status.addParam(sub_device_id, value) # --8<-- [start:main_logic] # ── Step 1: Resolve the sub-device IDs for the focus focus_sub_device_id = None # Focus controller for device_id, device in device_map.items(): for sub_device_tag, sub_device in device.sub_device_map.items(): if sub_device.inscoper_type == "FOCUS": # Focus controller: uniquely identified by the "FOCUS" type focus_sub_device_id = inscoper_api.SubDeviceId(device.name, sub_device.name) # ── Step 2: Start the camera in the correct mode start_cam_status = inscoper_api.Status() start_cam_status.addTag("MyCamera") start_cam_status.addTag("SOFTWARE_TRIGGER") my_bridge.loadSequence(0, "StartCamera", [start_cam_status]) my_bridge.runSequence(0, False) # ── Step 3: Set the blue channel my_bridge.loadSequence(1, "DeviceUpdate", [blue_status]) my_bridge.runSequence(1, False) # ── Step 4: Wait for the user to adjust the focus on the microscope input("Please manually adjust the focus on the microscope. Once done, press Enter to continue...") # ── Step 5: Get current Z position and define the Zstack current_z = my_bridge.getLongValue(focus_sub_device_id) print(f"Current Z position: {current_z} nm") zstack_status = [] step = 10000 # 10 micron in nanometers (Inscoper Z focus unit) volume = 100000 # 100 microns in nanometers half_volume = volume // 2 for z in range(current_z - half_volume, current_z + half_volume + 1, step): slice_status = inscoper_api.Status() for sub_device_id, value in blue_channel_description.items(): slice_status.addParam(sub_device_id, value) slice_status.addParam(focus_sub_device_id, z) slice_status.addTag("MyCamera") slice_status.addTag("SOFTWARE_TRIGGER") zstack_status.append(slice_status) # ── Step 6: Load and run the acquisition my_bridge.loadSequence(2, "Acquisition", zstack_status) my_bridge.runSequence(2, False) # ── Step 7: Retrieve and display the images received_images = my_listener.getReceivedImages() if received_images: N = len(received_images) cols = int(np.ceil(np.sqrt(N))) rows = int(np.ceil(N / cols)) fig, axes = plt.subplots(rows, cols, figsize=(cols * 3, rows * 3)) if N == 1: axes = np.array([axes]) else: axes = axes.flatten() for idx, image in enumerate(received_images): image_data = image.getImageData() image_width = image.getWidth() image_height = image.getHeight() pixel_size_bytes = image.getPixelSize() bit_depth = image.getBitDepth() bytes_per_value = bit_depth // 8 values_per_pixel = pixel_size_bytes // bytes_per_value img = np.reshape(image_data, (image_height, image_width, values_per_pixel)) ax = axes[idx] ax.imshow(img[:, :, 0], cmap="gray") ax.set_title(f"Slice {idx}") ax.axis("off") # Hide any unused subplots in the grid for idx in range(N, len(axes)): axes[idx].axis("off") plt.tight_layout() plt.show() else: print("No images received to plot.") # --8<-- [end:main_logic] my_bridge.close()